1
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Özoğul E, Montaner A, Pol M, Frigola G, Balagué O, Syrykh C, Bousquets-Muñoz P, Royo R, Fontaine J, Traverse-Glehen A, Bühler MM, Giudici L, Roncador M, Zenz T, Carras S, Valmary-Degano S, de Leval L, Bosch-Schips J, Climent F, Salmeron-Villalobos J, Bashiri M, Ruiz-Gaspà S, Costa D, Beà S, Salaverria I, Giné E, Quintanilla-Martinez L, Brousset P, Raffeld M, Jaffe ES, Puente XS, López C, Nadeu F, Campo E. Large B-cell lymphomas with CCND1 rearrangement have different immunoglobulin gene breakpoints and genomic profile than mantle cell lymphoma. Blood Cancer J 2024; 14:166. [PMID: 39313500 PMCID: PMC11420347 DOI: 10.1038/s41408-024-01146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/06/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024] Open
Abstract
Mantle cell lymphoma (MCL) is genetically characterized by the IG::CCND1 translocation mediated by an aberrant V(D)J rearrangement. CCND1 translocations and overexpression have been identified in occasional aggressive B-cell lymphomas with unusual features for MCL. The mechanism generating CCND1 rearrangements in these tumors and their genomic profile are not known. We have reconstructed the IG::CCND1 translocations and the genomic profile of 13 SOX11-negative aggressive B-cell lymphomas using whole genome/exome and target sequencing. The mechanism behind the translocation was an aberrant V(D)J rearrangement in three tumors and by an anomalous IGH class-switch recombination (CSR) or somatic hypermutation (SHM) mechanism in ten. The tumors with a V(D)J-mediated translocation were two blastoid MCL and one high-grade B-cell lymphoma. None of them had a mutational profile suggestive of DLBCL. The ten tumors with CSR/SHM-mediated IGH::CCND1 were mainly large B-cell lymphomas, with mutated genes commonly seen in DLBCL and BCL6 rearrangements in 6. Two cases, which transformed from marginal zone lymphomas, carried mutations in KLF2, TNFAIP3 and KMT2D. These findings expand the spectrum of tumors carrying CCND1 rearrangement that may occur as a secondary event in DLBCL mediated by aberrant CSR/SHM and associated with a mutational profile different from that of MCL.
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Affiliation(s)
- Ece Özoğul
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Pathology Department, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Anna Montaner
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Melina Pol
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Gerard Frigola
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Hospital Clínic de Barcelona, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Olga Balagué
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Hospital Clínic de Barcelona, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Charlotte Syrykh
- Toulouse University Hospital Center, Cancer Institute University of Toulouse-Oncopole, 1 avenue Irène Joliot-Curie, 31059, Toulouse, CEDEX 9, France
- INSERM UMR1037 Cancer Research Center of Toulouse (CRCT), ERL 5294 National Center for Scientific Research (CNRS), University of Toulouse III Paul-Sabatier, Toulouse, France
- Institut Carnot Lymphome CALYM, Laboratoire d'Excellence 'TOUCAN', Toulouse, France
| | - Pablo Bousquets-Muñoz
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Romina Royo
- Barcelona Supercomputer Center, Barcelona, Spain
| | | | | | | | - Luca Giudici
- Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6900, Locarno, Switzerland
| | | | | | - Sylvain Carras
- Grenoble Alpes University, CHU Grenoble Alpes and INSERMN UMR 1209/CNRS 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Severine Valmary-Degano
- Grenoble Alpes University, CHU Grenoble Alpes and INSERMN UMR 1209/CNRS 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Laurence de Leval
- Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Jan Bosch-Schips
- Hospital Universitari de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Fina Climent
- Hospital Universitari de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | | | - Melika Bashiri
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Dolors Costa
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Hospital Clínic de Barcelona, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Itziar Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eva Giné
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Leticia Quintanilla-Martinez
- Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Pierre Brousset
- Toulouse University Hospital Center, Cancer Institute University of Toulouse-Oncopole, 1 avenue Irène Joliot-Curie, 31059, Toulouse, CEDEX 9, France
- INSERM UMR1037 Cancer Research Center of Toulouse (CRCT), ERL 5294 National Center for Scientific Research (CNRS), University of Toulouse III Paul-Sabatier, Toulouse, France
- Institut Carnot Lymphome CALYM, Laboratoire d'Excellence 'TOUCAN', Toulouse, France
| | - Mark Raffeld
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elaine S Jaffe
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Cristina López
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Hospital Clínic de Barcelona, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Hospital Clínic de Barcelona, Barcelona, Spain.
- University of Barcelona, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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2
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Bazarbachi AH, Avet-Loiseau H, Harousseau JL, Bazarbachi A, Mohty M. Precision medicine for multiple myeloma: The case for translocation (11;14). Cancer Treat Rev 2024; 130:102823. [PMID: 39255732 DOI: 10.1016/j.ctrv.2024.102823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 08/11/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024]
Abstract
The t(11;14) translocation is among the most prevalent cytogenetic abnormalities in multiple myeloma (MM), distinguished by its unique features and biology that have been thoroughly explored for decades. What further sets this MM subtype apart is its oscillating prognostic significance, from initially being considered a favorable alteration to intermediate risk and potential future reclassification as favorable risk. Despite not being inherently a high-risk alteration indicative of an aggressive phenotype, it appears that t(11;14)-MM is less responsive to novel agents like proteasome inhibitors and immunomodulatory drugs which have otherwise transformed the disease's treatment landscape, perhaps partially explained by its reduced propensity for immunoglobulin production and oligosecretory nature. However, its distinct reliance on Bcl-2 has heightened its sensitivity to venetoclax. Further subclassification based on morphological and genomic characteristics could enhance our prediction models of treatment responses and enable more tailored therapeutic strategies for patients. This review aims to encapsulate the existing research evidence in this area.
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Affiliation(s)
- Abdul-Hamid Bazarbachi
- Division of Hematology/Oncology, Columbia University Irving Medical Center/New York-Presbyterian Hospital, New York, NY, USA.
| | - Hervé Avet-Loiseau
- Cancer Research Center of Toulouse, INSERM, Myeloma Genomics Laboratory, University Cancer Institute Toulouse Oncopole, Université Paul Sabatier, Toulouse, France
| | - Jean-Luc Harousseau
- Institut de Cancerologie de l'Ouest, Centre René Gauducheau, Nantes-St Herblain, France
| | - Ali Bazarbachi
- Department of Internal Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Mohamad Mohty
- Sorbonne University, Service d'Hematologie Clinique et Thérapie Cellulaire, Hôpital Saint Antoine, and INSERM UMR 938, Paris, France.
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3
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Thomsen H, Chattopadhyay S, Weinhold N, Vodicka P, Vodickova L, Hoffmann P, Nöthen MM, Jöckel KH, Schmidt B, Hajek R, Hallmans G, Pettersson-Kymmer U, Späth F, Goldschmidt H, Hemminki K, Försti A. Haplotype analysis identifies functional elements in monoclonal gammopathy of unknown significance. Blood Cancer J 2024; 14:140. [PMID: 39164264 PMCID: PMC11335940 DOI: 10.1038/s41408-024-01121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024] Open
Abstract
Genome-wide association studies (GWASs) based on common single nucleotide polymorphisms (SNPs) have identified several loci associated with the risk of monoclonal gammopathy of unknown significance (MGUS), a precursor condition for multiple myeloma (MM). We hypothesized that analyzing haplotypes might be more useful than analyzing individual SNPs, as it could identify functional chromosomal units that collectively contribute to MGUS risk. To test this hypothesis, we used data from our previous GWAS on 992 MGUS cases and 2910 controls from three European populations. We identified 23 haplotypes that were associated with the risk of MGUS at the genome-wide significance level (p < 5 × 10-8) and showed consistent results among all three populations. In 10 genomic regions, strong promoter, enhancer and regulatory element-related histone marks and their connections to target genes as well as genome segmentation data supported the importance of these regions in MGUS susceptibility. Several associated haplotypes affected pathways important for MM cell survival such as ubiquitin-proteasome system (RNF186, OTUD3), PI3K/AKT/mTOR (HINT3), innate immunity (SEC14L1, ZBP1), cell death regulation (BID) and NOTCH signaling (RBPJ). These pathways are important current therapeutic targets for MM, which may highlight the advantage of the haplotype approach homing to functional units.
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Affiliation(s)
- Hauke Thomsen
- MSB Medical School Berlin, Hochschule für Gesundheit und Medizin, Berlin, Germany
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Pavel Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Börge Schmidt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Roman Hajek
- Department of Hematooncology, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Umea University, Umea, Sweden
| | - Ulrika Pettersson-Kymmer
- Clinical Pharmacology, Department of Pharmacology and Clinical Neuroscience, Umea University, Umea, Sweden
| | - Florentin Späth
- Department of Diagnostics and Intervention, Cancer Center, Hematology, Umeå University, Umeå, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Centre of Tumor Diseases, Heidelberg, Germany
| | - Kari Hemminki
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Department of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Asta Försti
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
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4
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Went M, Duran-Lozano L, Halldorsson GH, Gunnell A, Ugidos-Damboriena N, Law P, Ekdahl L, Sud A, Thorleifsson G, Thodberg M, Olafsdottir T, Lamarca-Arrizabalaga A, Cafaro C, Niroula A, Ajore R, Lopez de Lapuente Portilla A, Ali Z, Pertesi M, Goldschmidt H, Stefansdottir L, Kristinsson SY, Stacey SN, Love TJ, Rognvaldsson S, Hajek R, Vodicka P, Pettersson-Kymmer U, Späth F, Schinke C, Van Rhee F, Sulem P, Ferkingstad E, Hjorleifsson Eldjarn G, Mellqvist UH, Jonsdottir I, Morgan G, Sonneveld P, Waage A, Weinhold N, Thomsen H, Försti A, Hansson M, Juul-Vangsted A, Thorsteinsdottir U, Hemminki K, Kaiser M, Rafnar T, Stefansson K, Houlston R, Nilsson B. Deciphering the genetics and mechanisms of predisposition to multiple myeloma. Nat Commun 2024; 15:6644. [PMID: 39103364 DOI: 10.1038/s41467-024-50932-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/24/2024] [Indexed: 08/07/2024] Open
Abstract
Multiple myeloma (MM) is an incurable malignancy of plasma cells. Epidemiological studies indicate a substantial heritable component, but the underlying mechanisms remain unclear. Here, in a genome-wide association study totaling 10,906 cases and 366,221 controls, we identify 35 MM risk loci, 12 of which are novel. Through functional fine-mapping and Mendelian randomization, we uncover two causal mechanisms for inherited MM risk: longer telomeres; and elevated levels of B-cell maturation antigen (BCMA) and interleukin-5 receptor alpha (IL5RA) in plasma. The largest increase in BCMA and IL5RA levels is mediated by the risk variant rs34562254-A at TNFRSF13B. While individuals with loss-of-function variants in TNFRSF13B develop B-cell immunodeficiency, rs34562254-A exerts a gain-of-function effect, increasing MM risk through amplified B-cell responses. Our results represent an analysis of genetic MM predisposition, highlighting causal mechanisms contributing to MM development.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Laura Duran-Lozano
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | | | - Andrea Gunnell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Nerea Ugidos-Damboriena
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Philip Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ludvig Ekdahl
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Malte Thodberg
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | | | - Antton Lamarca-Arrizabalaga
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Caterina Cafaro
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Abhishek Niroula
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Ram Ajore
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Aitzkoa Lopez de Lapuente Portilla
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Zain Ali
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Maroulio Pertesi
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Sigurdur Y Kristinsson
- Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Simon N Stacey
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
| | - Thorvardur J Love
- Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Saemundur Rognvaldsson
- Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Roman Hajek
- University Hospital Ostrava and University of Ostrava, Ostrava, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - Florentin Späth
- Department of Radiation Sciences, Umeå University, SE-901 87, Umeå, Sweden
| | - Carolina Schinke
- 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
| | - Patrick Sulem
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
| | | | | | | | | | - Gareth Morgan
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491, Trondheim, Norway
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, 69120, Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
| | | | - Asta Försti
- German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Hopp Children's Cancer Center, Heidelberg, Germany
| | - Markus Hansson
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Section of Hematology, Sahlgrenska University Hospital, Gothenburg, SE-413 45, Sweden
- Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Annette Juul-Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen, Denmark
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Kari Hemminki
- German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Faculty of Medicine in Pilsen, Charles University, 30605, Pilsen, Czech Republic
| | - Martin Kaiser
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Thorunn Rafnar
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
| | - Björn Nilsson
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden.
- Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.
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5
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Kim EE, Jang CS, Kim H, Han B. PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects. BMC Bioinformatics 2024; 25:24. [PMID: 38216869 PMCID: PMC10790263 DOI: 10.1186/s12859-023-05627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Meta-analysis is a statistical method that combines the results of multiple studies to increase statistical power. When multiple studies participating in a meta-analysis utilize the same public dataset as controls, the summary statistics from these studies become correlated. To solve this challenge, Lin and Sullivan proposed a method to provide an optimal test statistic adjusted for the correlation. This method quickly became the standard practice. However, we identified an unexpected power asymmetry phenomenon in this standard framework. This can lead to unbalanced power for detecting protective minor alleles and risk minor alleles. RESULTS We found that the power asymmetry of the current framework is mainly due to the errors in approximating the correlation term. We then developed a meta-analysis method based on an accurate correlation estimator, called PASTRY (A method to avoid Power ASymmeTRY). PASTRY outperformed the standard method on both simulated and real datasets in terms of the power symmetry. CONCLUSIONS Our findings suggest that PASTRY can help to alleviate the power asymmetry problem. PASTRY is available at https://github.com/hanlab-SNU/PASTRY .
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Affiliation(s)
- Emma E Kim
- Department of Chemistry, Seoul National University, Seoul, 03080, Korea
| | - Chloe Soohyun Jang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Hakin Kim
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 03080, Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 03080, Korea.
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6
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Chu E, Wu J, Kang SS, Kang Y. SLAMF7 as a Promising Immunotherapeutic Target in Multiple Myeloma Treatments. Curr Oncol 2023; 30:7891-7903. [PMID: 37754488 PMCID: PMC10529721 DOI: 10.3390/curroncol30090573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023] Open
Abstract
Multiple myeloma (MM) is a common hematological malignancy that has fostered several new therapeutic approaches to combat newly diagnosed or relapsed MM. While the field has advanced over the past 2 decades, the majority of patients will develop resistance to these treatments, causing the need for new therapeutic targets. SLAMF7 is an attractive therapeutic target in multiple myeloma, and a monoclonal antibody that targets SLAMF7 has shown consistent beneficial outcomes in clinical trials to date. In this review, we will focus on the structure and regulation of SLAMF7 and its mechanism of action. The most recent clinical trials will be reviewed to further understand the clinical implications and improve the prognosis of MM. Furthermore, the efficacy of anti-SLAMF7 monoclonal antibodies combined with standard therapies and possible resistance mechanisms will be discussed. This review aimed to provide a detailed summary of the role of SLAMF7 in the pathogenesis of patients with MM and the rationale for further investigation into SLAMF7-mediated molecular pathways associated with MM development.
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Affiliation(s)
- Emily Chu
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (E.C.); (J.W.)
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA
| | - Jian Wu
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (E.C.); (J.W.)
| | - Stacey S. Kang
- College of Arts and Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Yubin Kang
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (E.C.); (J.W.)
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7
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Saleban M, Harris EL, Poulter JA. D-Type Cyclins in Development and Disease. Genes (Basel) 2023; 14:1445. [PMID: 37510349 PMCID: PMC10378862 DOI: 10.3390/genes14071445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
D-type cyclins encode G1/S cell cycle checkpoint proteins, which play a crucial role in defining cell cycle exit and progression. Precise control of cell cycle exit is vital during embryonic development, with defects in the pathways regulating intracellular D-type cyclins resulting in abnormal initiation of stem cell differentiation in a variety of different organ systems. Furthermore, stabilisation of D-type cyclins is observed in a wide range of disorders characterized by cellular over-proliferation, including cancers and overgrowth disorders. In this review, we will summarize and compare the roles played by each D-type cyclin during development and provide examples of how their intracellular dysregulation can be an underlying cause of disease.
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Affiliation(s)
- Mostafa Saleban
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
| | - Erica L Harris
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
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8
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Niazi Y, Paramasivam N, Blocka J, Kumar A, Huhn S, Schlesner M, Weinhold N, Sijmons R, De Jong M, Durie B, Goldschmidt H, Hemminki K, Försti A. Investigation of Rare Non-Coding Variants in Familial Multiple Myeloma. Cells 2022; 12:cells12010096. [PMID: 36611892 PMCID: PMC9818386 DOI: 10.3390/cells12010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Multiple myeloma (MM) is a plasma cell malignancy whereby a single clone of plasma cells over-propagates in the bone marrow, resulting in the increased production of monoclonal immunoglobulin. While the complex genetic architecture of MM is well characterized, much less is known about germline variants predisposing to MM. Genome-wide sequencing approaches in MM families have started to identify rare high-penetrance coding risk alleles. In addition, genome-wide association studies have discovered several common low-penetrance risk alleles, which are mainly located in the non-coding genome. Here, we further explored the genetic basis in familial MM within the non-coding genome in whole-genome sequencing data. We prioritized and characterized 150 upstream, 5' untranslated region (UTR) and 3' UTR variants from 14 MM families, including 20 top-scoring variants. These variants confirmed previously implicated biological pathways in MM development. Most importantly, protein network and pathway enrichment analyses also identified 10 genes involved in mitogen-activated protein kinase (MAPK) signaling pathways, which have previously been established as important MM pathways.
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Affiliation(s)
- Yasmeen Niazi
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Correspondence: (Y.N.); (K.H.)
| | - Nagarajan Paramasivam
- Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Joanna Blocka
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Stefanie Huhn
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg (NCT), 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | - Rolf Sijmons
- University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands
| | - Mirjam De Jong
- University Medical Center Groningen, University of Groningen, 9712 Groningen, The Netherlands
| | - Brian Durie
- Cedars Sinai Cancer Center, Los Angeles, CA 90048, USA
| | - Hartmut Goldschmidt
- Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | - Kari Hemminki
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic
- Correspondence: (Y.N.); (K.H.)
| | - Asta Försti
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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9
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Corpas M, Megy K, Metastasio A, Lehmann E. Implementation of individualised polygenic risk score analysis: a test case of a family of four. BMC Med Genomics 2022; 15:207. [PMID: 36192731 PMCID: PMC9531350 DOI: 10.1186/s12920-022-01331-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Polygenic risk scores (PRS) have been widely applied in research studies, showing how population groups can be stratified into risk categories for many common conditions. As healthcare systems consider applying PRS to keep their populations healthy, little work has been carried out demonstrating their implementation at an individual level. CASE PRESENTATION We performed a systematic curation of PRS sources from established data repositories, selecting 15 phenotypes, comprising an excess of 37 million SNPs related to cancer, cardiovascular, metabolic and autoimmune diseases. We tested selected phenotypes using whole genome sequencing data for a family of four related individuals. Individual risk scores were given percentile values based upon reference distributions among 1000 Genomes Iberians, Europeans, or all samples. Over 96 billion allele effects were calculated in order to obtain the PRS for each of the individuals analysed here. CONCLUSIONS Our results highlight the need for further standardisation in the way PRS are developed and shared, the importance of individual risk assessment rather than the assumption of inherited averages, and the challenges currently posed when translating PRS into risk metrics.
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Affiliation(s)
- Manuel Corpas
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK.
- Institute of Continuing Education, University of Cambridge, Cambridge, UK.
- Facultad de Ciencias de La Salud, Universidad Internacional de La Rioja, Madrid, Spain.
| | - Karyn Megy
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK
- Department of Haematology, University of Cambridge & NHS Blood and Transplant, Cambridge, UK
| | - Antonio Metastasio
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK
- Camden and Islington NHS Foundation Trust, London, UK
| | - Edmund Lehmann
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK
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10
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Canzian F, Piredda C, Macauda A, Zawirska D, Andersen NF, Nagler A, Zaucha JM, Mazur G, Dumontet C, Wątek M, Jamroziak K, Sainz J, Várkonyi J, Butrym A, Beider K, Abildgaard N, Lesueur F, Dudziński M, Vangsted AJ, Pelosini M, Subocz E, Petrini M, Buda G, Raźny M, Gemignani F, Marques H, Orciuolo E, Kadar K, Jurczyszyn A, Druzd-Sitek A, Vogel U, Andersen V, Reis RM, Suska A, Avet-Loiseau H, Kruszewski M, Tomczak W, Rymko M, Minvielle S, Campa D. A polygenic risk score for multiple myeloma risk prediction. Eur J Hum Genet 2022; 30:474-479. [PMID: 34845334 PMCID: PMC8991223 DOI: 10.1038/s41431-021-00986-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
There is overwhelming epidemiologic evidence that the risk of multiple myeloma (MM) has a solid genetic background. Genome-wide association studies (GWAS) have identified 23 risk loci that contribute to the genetic susceptibility of MM, but have low individual penetrance. Combining the SNPs in a polygenic risk score (PRS) is a possible approach to improve their usefulness. Using 2361 MM cases and 1415 controls from the International Multiple Myeloma rESEarch (IMMEnSE) consortium, we computed a weighted and an unweighted PRS. We observed associations with MM risk with OR = 3.44, 95% CI 2.53-4.69, p = 3.55 × 10-15 for the highest vs. lowest quintile of the weighted score, and OR = 3.18, 95% CI 2.1 = 34-4.33, p = 1.62 × 10-13 for the highest vs. lowest quintile of the unweighted score. We found a convincing association of a PRS generated with 23 SNPs and risk of MM. Our work provides additional validation of previously discovered MM risk variants and of their combination into a PRS, which is a first step towards the use of genetics for risk stratification in the general population.
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Affiliation(s)
- Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Chiara Piredda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biology, University of Pisa, Pisa, Italy
| | - Angelica Macauda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biology, University of Pisa, Pisa, Italy
| | - Daria Zawirska
- Department of Hematology, University Hospital of Cracow, Cracow, Poland
| | | | - Arnon Nagler
- Hematology Division, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | | | - Grzegorz Mazur
- Department of Internal and Occupational Diseases, Hypertension and Clinical Oncology, Medical University Wroclaw, Wroclaw, Poland
| | - Charles Dumontet
- Cancer Research Center of Lyon/Hospices Civils de Lyon, Lyon, France
| | - Marzena Wątek
- Hematology Clinic, Holycross Cancer Center, Kielce, Poland
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Juan Sainz
- Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada/Andalusian Regional Government, Granada, Spain
- Hematology department, Virgen de las Nieves University Hospital, Granada, Spain
| | - Judit Várkonyi
- Third Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Aleksandra Butrym
- Department of Internal and Occupational Diseases, Medical University Wroclaw, Wroclaw, Poland
| | - Katia Beider
- Hematology Division, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Niels Abildgaard
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Fabienne Lesueur
- Institut Curie, PSL Research University, Mines ParisTech Inserm, U900, Paris, France
| | - Marek Dudziński
- Hematology Department, Teaching Hospital No 1, Rzeszów, Poland
| | - Annette Juul Vangsted
- Department of Hematology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Matteo Pelosini
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Edyta Subocz
- Department of Haematology, Military Institute of Medicine, Warsaw, Poland
| | - Mario Petrini
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Gabriele Buda
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Małgorzata Raźny
- Department of Hematology, Rydygier Specialistic Hospital, Cracow, Poland
| | | | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences/Molecular Oncology Research Center, University of Minho, Braga, Portugal
| | - Enrico Orciuolo
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Katalin Kadar
- Third Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Artur Jurczyszyn
- Department of Hematology, Jagiellonian University Medical College, Cracow, Poland
| | | | - Ulla Vogel
- National Research Centre for the Working Environment, DK-2100, Copenhagen, Denmark
| | - Vibeke Andersen
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Rui Manuel Reis
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences/Molecular Oncology Research Center, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Molecular Oncology Research Center, Barretos Cancer Hospital, S.Paulo, Brazil
| | - Anna Suska
- Department of Hematology, Jagiellonian University Medical College, Cracow, Poland
| | - Hervé Avet-Loiseau
- Unité de Génomique du Myélome, Institut Universitaire du Cancer Toulouse - Oncopole, Toulouse, France
| | - Marcin Kruszewski
- Department of Hematology, University Hospital Bydgoszcz, Bydgoszcz, Poland
| | | | - Marcin Rymko
- Department of Hematology, N. Copernicus Town Hospital, Torun, Poland
| | - Stephane Minvielle
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
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11
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Ajore R, Niroula A, Pertesi M, Cafaro C, Thodberg M, Went M, Bao EL, Duran-Lozano L, Lopez de Lapuente Portilla A, Olafsdottir T, Ugidos-Damboriena N, Magnusson O, Samur M, Lareau CA, Halldorsson GH, Thorleifsson G, Norddahl GL, Gunnarsdottir K, Försti A, Goldschmidt H, Hemminki K, van Rhee F, Kimber S, Sperling AS, Kaiser M, Anderson K, Jonsdottir I, Munshi N, Rafnar T, Waage A, Weinhold N, Thorsteinsdottir U, Sankaran VG, Stefansson K, Houlston R, Nilsson B. Functional dissection of inherited non-coding variation influencing multiple myeloma risk. Nat Commun 2022; 13:151. [PMID: 35013207 PMCID: PMC8748989 DOI: 10.1038/s41467-021-27666-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/02/2021] [Indexed: 12/16/2022] Open
Abstract
Thousands of non-coding variants have been associated with increased risk of human diseases, yet the causal variants and their mechanisms-of-action remain obscure. In an integrative study combining massively parallel reporter assays (MPRA), expression analyses (eQTL, meQTL, PCHiC) and chromatin accessibility analyses in primary cells (caQTL), we investigate 1,039 variants associated with multiple myeloma (MM). We demonstrate that MM susceptibility is mediated by gene-regulatory changes in plasma cells and B-cells, and identify putative causal variants at six risk loci (SMARCD3, WAC, ELL2, CDCA7L, CEP120, and PREX1). Notably, three of these variants co-localize with significant plasma cell caQTLs, signaling the presence of causal activity at these precise genomic positions in an endogenous chromosomal context in vivo. Our results provide a systematic functional dissection of risk loci for a hematologic malignancy.
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Affiliation(s)
- Ram Ajore
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Abhishek Niroula
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
| | - Maroulio Pertesi
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Caterina Cafaro
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Malte Thodberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Erik L Bao
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Laura Duran-Lozano
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | | | | | - Nerea Ugidos-Damboriena
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Olafur Magnusson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Mehmet Samur
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Caleb A Lareau
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Asta Försti
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
- Hopp Children's Cancer Center, Heidelberg, Germany
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University Hospital of Heidelberg, 69120, Heidelberg, Germany
| | - Kari Hemminki
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Prague, 30605, Czech Republic
| | | | - Scott Kimber
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Adam S Sperling
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Martin Kaiser
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Kenneth Anderson
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Nikhil Munshi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Thorunn Rafnar
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491, Trondheim, Norway
| | - Niels Weinhold
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
- Department of Internal Medicine V, University Hospital of Heidelberg, 69120, Heidelberg, Germany
| | | | - Vijay G Sankaran
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA.
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12
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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13
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Dalland JC, Smadbeck JB, Sharma N, Meyer RG, Pearce KE, Greipp PT, Peterson JF, Kumar S, Ketterling RP, King RL, Baughn LB. Increased complexity of t(11;14) rearrangements in plasma cell neoplasms compared with mantle cell lymphoma. Genes Chromosomes Cancer 2021; 60:678-686. [PMID: 34124820 PMCID: PMC8453742 DOI: 10.1002/gcc.22977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
Plasma cell neoplasms (PCN) and mantle cell lymphoma (MCL) can both harbor t(11;14)(q13;q32) (CCND1/IGH), usually resulting in cyclin D1 overexpression. In some cases, particularly at low levels of disease, it can be morphologically challenging to distinguish between these entities in the bone marrow (BM) since PCN with t(11;14) are often CD20-positive with lymphoplasmacytic cytology, while MCL can rarely have plasmacytic differentiation. We compared the difference in CCND1/IGH by fluorescence in situ hybridization (FISH) in PCN and MCL to evaluate for possible differentiating characteristics. We identified 326 cases of MCL with t(11;14) and 279 cases of PCN with t(11;14) from either formalin-fixed, paraffin-embedded tissue or fresh BM specimens. The "typical," balanced CCND1/IGH FISH signal pattern was defined as three total CCND1 signals, three total IGH signals, and two total fusion signals. Any deviation from the "typical" pattern was defined as an "atypical" pattern, which was further stratified into "gain of fusion" vs "complex" patterns. There was a significantly higher proportion of cases that showed an atypical FISH pattern in PCN compared with MCL (53% vs 27%, P < .0001). There was also a significantly higher proportion of cases that showed a complex FISH pattern in PCN compared with MCL (47% vs 17%, P < .0001). We confirmed these findings using mate-pair sequencing of 25 PCN and MCL samples. PCN more often have a complex CCND1/IGH FISH pattern compared with MCL, suggesting possible differences in the genomic mechanisms underlying these rearrangements in plasma cells compared with B cells.
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Affiliation(s)
- Joanna C. Dalland
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Neeraj Sharma
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Reid G. Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Kathryn E. Pearce
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Patricia T. Greipp
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Jess F. Peterson
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Shaji Kumar
- Division of Hematology, Department of Internal MedicineMayo ClinicRochesterMinnesotaUSA
| | - Rhett P. Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Rebecca L. King
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
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14
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Hemminki K, Försti A, Houlston R, Sud A. Epidemiology, genetics and treatment of multiple myeloma and precursor diseases. Int J Cancer 2021; 149:1980-1996. [PMID: 34398972 DOI: 10.1002/ijc.33762] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 12/17/2022]
Abstract
Multiple myeloma (MM) is a hematological malignancy caused by the clonal expansion of plasma cells. The incidence of MM worldwide is increasing with greater than 140 000 people being diagnosed with MM per year. Whereas 5-year survival after a diagnosis of MM has improved from 28% in 1975 to 56% in 2012, the disease remains essentially incurable. In this review, we summarize our current understanding of MM including its epidemiology, genetics and biology. We will also provide an overview of MM management that has led to improvements in survival, including recent changes to diagnosis and therapies. Areas of unmet need include the management of patients with high-risk MM, those with reduced performance status and those refractory to standard therapies. Ongoing research into the biology and early detection of MM as well as the development of novel therapies, such as immunotherapies, has the potential to influence MM practice in the future.
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Affiliation(s)
- Kari Hemminki
- Biomedical Center, Faculty of Medicine, Charles University in Pilsen, Pilsen, Czech Republic.,Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asta Försti
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.,The Department of Haemato-Oncology, The Royal Marsden Hospital NHS Foundation Trust, London, UK
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15
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Belachew AA, Wu X, Callender R, Waller R, Orlowski RZ, Vachon CM, Camp NJ, Ziv E, Hildebrandt MAT. Genetic determinants of multiple myeloma risk within the Wnt/beta-catenin signaling pathway. Cancer Epidemiol 2021; 73:101972. [PMID: 34216957 DOI: 10.1016/j.canep.2021.101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/17/2021] [Accepted: 06/20/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Aberrant Wnt/beta-catenin pathway activation is implicated in Multiple Myeloma (MM) development, but little is known if genetic variants within this pathway contribute to MM susceptibility. METHODS We performed a discovery candidate pathway analysis in 269 non-Hispanic white MM cases and 272 controls focusing on 171 variants selected from 26 core genes within the Wnt/beta-catenin pathway. Significant candidate variants (P < 0.05) were selected for validation in internal and external non-Hispanic white populations totaling 818 cases and 1209 controls. We also examined significant variants in non-Hispanic black and Hispanic case/control study populations to identify potential differences by race/ethnicity. Possible biological functions of candidate variants were predicted in silico. RESULTS Seven variants were significantly associated with MM risk in non-Hispanic whites in the discovery population, of which LRP6:rs7966410 (OR: 0.57; 95 % CI: 0.38-0.88; P = 9.90 × 10-3) and LRP6:rs7956971 (OR: 0.64; 95 % CI: 0.44-0.95; P = 0.027) remained significant in the internal and external populations. CSNK1D:rs9901910 replicated among all three racial/ethnic groups, with 2-6 fold increased risk of MM (OR: 2.40; 95 % CI: 1.67-3.45; P = 2.43 × 10-6 - non-Hispanic white; OR: 6.42; 95 % CI: 2.47-16.7; P = 3.14 × 10-4 - non-Hispanic black; OR: 4.31; 95 % CI: 1.83-10.1; P = 8.10 × 10-4 - Hispanic). BTRC:rs7916830 was associated with a significant 37 % and 24 % reduced risk of MM in the non-Hispanic white (95 % CI: 0.49-0.82; P = 5.60 × 10-4) and non-Hispanic Black (95 % CI: 0.60-0.97; P = 0.028) population, respectively. In silico tools predicted that these loci altered function through via gene regulation. CONCLUSION We identified several variants within the Wnt/beta-catenin pathway associated with MM susceptibility. Findings of this study highlight the potential genetic role of Wnt/beta-catenin signaling in MM etiology among a diverse patient population.
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Affiliation(s)
- Alem A Belachew
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rashida Callender
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rosalie Waller
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, United States
| | - Robert Z Orlowski
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Celine M Vachon
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, United States
| | - Nicola J Camp
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, United States
| | - Elad Ziv
- Department of Medicine, Division of General Internal Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, 94143, United States
| | - Michelle A T Hildebrandt
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States.
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16
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Waller RG, Klein RJ, Vijai J, McKay JD, Clay-Gilmour A, Wei X, Madsen MJ, Sborov DW, Curtin K, Slager SL, Offit K, Vachon CM, Lipkin SM, Dumontet C, Camp NJ. Sequencing at lymphoid neoplasm susceptibility loci maps six myeloma risk genes. Hum Mol Genet 2021; 30:1142-1153. [PMID: 33751038 PMCID: PMC8188404 DOI: 10.1093/hmg/ddab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/14/2022] Open
Abstract
Inherited genetic risk factors play a role in multiple myeloma (MM), yet considerable missing heritability exists. Rare risk variants at genome-wide association study (GWAS) loci are a new avenue to explore. Pleiotropy between lymphoid neoplasms (LNs) has been suggested in family history and genetic studies, but no studies have interrogated sequencing for pleiotropic genes or rare risk variants. Sequencing genetically enriched cases can help discover rarer variants. We analyzed exome sequencing in familial or early-onset MM cases to identify rare, functionally relevant variants near GWAS loci for a range of LNs. A total of 149 distinct and significant LN GWAS loci have been published. We identified six recurrent, rare, potentially deleterious variants within 5 kb of significant GWAS single nucleotide polymorphisms in 75 MM cases. Mutations were observed in BTNL2, EOMES, TNFRSF13B, IRF8, ACOXL and TSPAN32. All six genes replicated in an independent set of 255 early-onset MM or familial MM or precursor cases. Expansion of our analyses to the full length of these six genes resulted in a list of 39 rare and deleterious variants, seven of which segregated in MM families. Three genes also had significant rare variant burden in 733 sporadic MM cases compared with 935 control individuals: IRF8 (P = 1.0 × 10-6), EOMES (P = 6.0 × 10-6) and BTNL2 (P = 2.1 × 10-3). Together, our results implicate six genes in MM risk, provide support for genetic pleiotropy between LN subtypes and demonstrate the utility of sequencing genetically enriched cases to identify functionally relevant variants near GWAS loci.
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MESH Headings
- Acyl-CoA Oxidase/genetics
- Butyrophilins/genetics
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Hodgkin Disease/genetics
- Hodgkin Disease/pathology
- Humans
- Interferon Regulatory Factors/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphocytes/pathology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Multiple Myeloma/genetics
- Multiple Myeloma/pathology
- Polymorphism, Single Nucleotide/genetics
- Risk Factors
- T-Box Domain Proteins/genetics
- Tetraspanins/genetics
- Transmembrane Activator and CAML Interactor Protein/genetics
- Exome Sequencing
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Affiliation(s)
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY 10029-5674, USA
| | - Joseph Vijai
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - James D McKay
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, 69372 Lyon Cedex 08, France
| | - Alyssa Clay-Gilmour
- Department of Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaomu Wei
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael J Madsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Douglas W Sborov
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Karen Curtin
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Susan L Slager
- Department of Health Sciences, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Celine M Vachon
- Department of Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Charles Dumontet
- INSERM 1052, CNRS 5286, University of Lyon, 69361 Lyon Cedex 07, France
| | - Nicola J Camp
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
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17
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Griffin Waller R, Madsen MJ, Gardner J, Sborov DW, Camp NJ. Duo Shared Genomic Segment analysis identifies a genome-wide significant risk locus at 18q21.33 in myeloma pedigrees. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2021; 5:112-123. [PMID: 34888494 PMCID: PMC8654160 DOI: 10.20517/jtgg.2021.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIM High-risk pedigrees (HRPs) are a powerful design to map highly penetrant risk genes. We previously described Shared Genomic Segment (SGS) analysis, a mapping method for single large extended pedigrees that also addresses genetic heterogeneity inherent in complex diseases. SGS identifies shared segregating chromosomal regions that may inherit in only a subset of cases. However, single large pedigrees that are individually powerful (at least 15 meioses between studied cases) are scarce. Here, we expand the SGS strategy to incorporate evidence from two extended HRPs by identifying the same segregating risk locus in both pedigrees and allowing for some relaxation in the size of each HRP. METHODS Duo-SGS is a procedure to combine single-pedigree SGS evidence. It implements statistically rigorous duo-pedigree thresholding to determine genome-wide significance levels that account for optimization across pedigree pairs. Single-pedigree SGS identifies optimal segments shared by case subsets at each locus across the genome, with nominal significance assessed empirically. Duo-SGS combines the statistical evidence for SGS segments at the same genomic location in two pedigrees using Fisher's method. One pedigree is paired with all others and the best duo-SGS evidence at each locus across the genome is established. Genome-wide significance thresholds are determined through distribution-fitting and the Theory of Large Deviations. We applied the duoSGS strategy to eleven extended, myeloma HRPs. RESULTS We identified one genome-wide significant region at 18q21.33 (0.85 Mb, P = 7.3 × 10-9) which contains one gene, CDH20. Thirteen regions were genome-wide suggestive: 1q42.2, 2p16.1, 3p25.2, 5q21.3, 5q31.1, 6q16.1, 6q26, 7q11.23, 12q24.31, 13q13.3, 18p11.22, 18q22.3 and 19p13.12. CONCLUSION Our results provide novel risk loci with segregating evidence from multiple HRPs and offer compelling targets and specific segment carriers to focus a future search for functional variants involved in inherited risk formyeloma.
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Affiliation(s)
- Rosalie Griffin Waller
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
- University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | | | - John Gardner
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Douglas W. Sborov
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
- University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nicola J. Camp
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
- University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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18
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A meta-analysis of genome-wide association studies of multiple myeloma among men and women of African ancestry. Blood Adv 2021; 4:181-190. [PMID: 31935283 DOI: 10.1182/bloodadvances.2019000491] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Persons of African ancestry (AA) have a twofold higher risk for multiple myeloma (MM) compared with persons of European ancestry (EA). Genome-wide association studies (GWASs) support a genetic contribution to MM etiology in individuals of EA. Little is known about genetic risk factors for MM in individuals of AA. We performed a meta-analysis of 2 GWASs of MM in 1813 cases and 8871 controls and conducted an admixture mapping scan to identify risk alleles. We fine-mapped the 23 known susceptibility loci to find markers that could better capture MM risk in individuals of AA and constructed a polygenic risk score (PRS) to assess the aggregated effect of known MM risk alleles. In GWAS meta-analysis, we identified 2 suggestive novel loci located at 9p24.3 and 9p13.1 at P < 1 × 10-6; however, no genome-wide significant association was noted. In admixture mapping, we observed a genome-wide significant inverse association between local AA at 2p24.1-23.1 and MM risk in AA individuals. Of the 23 known EA risk variants, 20 showed directional consistency, and 9 replicated at P < .05 in AA individuals. In 8 regions, we identified markers that better capture MM risk in persons with AA. AA individuals with a PRS in the top 10% had a 1.82-fold (95% confidence interval, 1.56-2.11) increased MM risk compared with those with average risk (25%-75%). The strongest functional association was between the risk allele for variant rs56219066 at 5q15 and lower ELL2 expression (P = 5.1 × 10-12). Our study shows that common genetic variation contributes to MM risk in individuals with AA.
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19
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Hassan H, Szalat R. Genetic Predictors of Mortality in Patients with Multiple Myeloma. APPLICATION OF CLINICAL GENETICS 2021; 14:241-254. [PMID: 33953598 PMCID: PMC8092627 DOI: 10.2147/tacg.s262866] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/31/2021] [Indexed: 12/19/2022]
Abstract
Multiple myeloma (MM) is a heterogeneous disease featured by clonal plasma cell proliferation and genomic instability. The advent of next-generation sequencing allowed unraveling the complex genomic landscape of the disease. Several recurrent genomic aberrations including immunoglobulin genes translocations, copy number abnormalities, complex chromosomal events, transcriptomic and epigenomic deregulation, and mutations define various molecular subgroups with distinct outcomes. In this review, we describe the recurrent genomic events identified in MM impacting patients’ outcome and survival. These genomic aberrations constitute new markers that could be incorporated into a prognostication model to eventually guide therapy at every stage of the disease.
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Affiliation(s)
- Hamza Hassan
- Department of Hematology and Medical Oncology, Boston University Medical Center, Boston, MA, USA
| | - Raphael Szalat
- Department of Hematology and Medical Oncology, Boston University Medical Center, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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20
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Giaccherini M, Macauda A, Orciuolo E, Rymko M, Gruenpeter K, Dumontet C, Raźny M, Moreno V, Buda G, Beider K, Varkonyi J, Avet-Loiseau H, Martinez-Lopez J, Marques H, Watek M, Sarasquete ME, Andersen V, Karlin L, Suska A, Kruszewski M, Abildgaard N, Dudziński M, Butrym A, Nagler A, Vangsted AJ, Kadar K, Waldemar T, Jamroziak K, Jacobsen SEH, Ebbesen LH, Taszner M, Mazur G, Lesueur F, Pelosini M, Garcia-Sanz R, Jurczyszyn A, Demangel D, Reis RM, Iskierka-Jażdżewska E, Markiewicz M, Gemignani F, Subocz E, Zawirska D, Druzd-Sitek A, Stępień A, Alonso MH, Sainz J, Canzian F, Campa D. Genetically determined telomere length and multiple myeloma risk and outcome. Blood Cancer J 2021; 11:74. [PMID: 33854038 PMCID: PMC8046773 DOI: 10.1038/s41408-021-00462-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 12/16/2022] Open
Abstract
Telomeres are involved in processes like cellular growth, chromosomal stability, and proper segregation to daughter cells. Telomere length measured in leukocytes (LTL) has been investigated in different cancer types, including multiple myeloma (MM). However, LTL measurement is prone to heterogeneity due to sample handling and study design (retrospective vs. prospective). LTL is genetically determined; genome-wide association studies identified 11 SNPs that, combined in a score, can be used as a genetic instrument to measure LTL and evaluate its association with MM risk. This approach has been already successfully attempted in various cancer types but never in MM. We tested the "teloscore" in 2407 MM patients and 1741 controls from the International Multiple Myeloma rESEarch (IMMeNSE) consortium. We observed an increased risk for longer genetically determined telomere length (gdTL) (OR = 1.69; 95% CI 1.36-2.11; P = 2.97 × 10-6 for highest vs. lowest quintile of the score). Furthermore, in a subset of 1376 MM patients we tested the relationship between the teloscore and MM patients survival, observing a better prognosis for longer gdTL compared with shorter gdTL (HR = 0.93; 95% CI 0.86-0.99; P = 0.049). In conclusion, we report convincing evidence that longer gdTL is a risk marker for MM risk, and that it is potentially involved in increasing MM survival.
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Affiliation(s)
| | - Angelica Macauda
- Department of Biology, University of Pisa, Pisa, Italy.,Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Enrico Orciuolo
- Haematology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marcin Rymko
- Department of Hematology, Copernicus Hospital, Torun, Poland
| | - Karolina Gruenpeter
- Department of Haematology and Bone Marrow Transplantation, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | | | - Malgorzata Raźny
- Department of Hematology, Rydygier Specialistic Hospital, Cracow, Poland
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL, CIBERESP and Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Gabriele Buda
- Haematology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Katia Beider
- Hematology Division, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | | | - Hervé Avet-Loiseau
- Laboratory for Genomics in Myeloma, Institut Universitaire du Cancer and University Hospital, Centre de Recherche en Cancerologie de Toulouse, Toulouse, France
| | | | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal and ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Marzena Watek
- Department of Hematology, Holy Cross Cancer Center, Kielce, Poland.,Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | | | - Vibeke Andersen
- Department of Biochemistry, University Hospital of Southern Jutland, Sønderborg, Denmark.,IRS-Center Soenderjylland, University Hospital of Southern Jutland, Aabenraa, Denmark
| | | | - Anna Suska
- Department of Hematology, Jagiellonian University Medical College, Krakow, Poland
| | - Marcin Kruszewski
- Department of Hematology, University Hospital No. 2 in Bydgoszcz, Bydgoszcz, Poland
| | - Niels Abildgaard
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Marek Dudziński
- Department of Hematology, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, Rzeszow, Poland
| | - Aleksandra Butrym
- Department of Internal Diseases, Occupational Medicine, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Arnold Nagler
- Hematology Division, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | | | | | - Tomczak Waldemar
- Department of Haemato-oncology and Bone Marrow Transplantation and Department of Internal Medicine in Nursing, Medical University of Lublin, Lublin, Poland
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | | | | | - Michał Taszner
- Department of Hematology and Transplantology Medical University of Gdansk, Gdańsk, Poland
| | - Grzegorz Mazur
- Department of Internal Diseases, Occupational Medicine, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Matteo Pelosini
- U.O. Dipartimento di Ematologia, Azienda USL Toscana Nord Ovest, Livorno, Italy, currently Ospedale Santa Chiara, Pisa, Italy
| | - Ramon Garcia-Sanz
- Hematology Department, University Hospital of Salamanca, CIBERONC, Salamanca, Spain
| | - Artur Jurczyszyn
- Department of Hematology, Jagiellonian University Medical College, Krakow, Poland
| | | | - Rui Manuel Reis
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal and ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Miroslaw Markiewicz
- Department of Hematology, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, Rzeszow, Poland
| | | | - Edyta Subocz
- Department of Hematology, Military Institute of Medicine, Warsaw, Poland
| | - Daria Zawirska
- Department of Haematology, University Hospital in Cracow, Cracow, Poland
| | - Agnieszka Druzd-Sitek
- Department of Lymphoid Malignancies, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Stępień
- Laboratory of Clinical and Transplant Immunology and Genetics, Copernicus Memorial Hospital, Łódź, Poland
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL, CIBERESP and Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Juan Sainz
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
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21
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Pelizzo G, Chiricosta L, Mazzon E, Zuccotti GV, Avanzini MA, Croce S, Lima M, Bramanti P, Calcaterra V. Discovering Genotype Variants in an Infant with VACTERL through Clinical Exome Sequencing: A Support for Personalized Risk Assessment and Disease Prevention. Pediatr Rep 2021; 13:45-56. [PMID: 33466296 PMCID: PMC7838983 DOI: 10.3390/pediatric13010006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022] Open
Abstract
Congenital anomalies may have an increased risk of noncommunicable diseases (NCDs) We performed a clinical exome analysis in an infant affected by "Vertebral, Anorectal, Cardiac, Tracheoesophageal, Genitourinary, and Limb" (VACTERL) malformation association to identify potential biomarkers that may be helpful for preventing malignancy risk or other chronic processes. Among the variants, six variants that may be linked with VACTERL were identified in the exome analysis. The variants c.501G>C on OLR1 and c.-8C>G on PSMA6 were previously associated with myocardial infarction. The variants c.1936A>G on AKAP10 and c.575A>G on PON1 are linked to defects in cardiac conduction and artery disease, respectively. Alterations in metabolism were also suggested by the variants c.860G>A on EPHX2 and c.214C>A on GHRL. In addition, three variants associated with colon cancer were discovered. Specifically, the reported variants were c.723G>A on CCND1 and c.91T>A on AURKA proto-oncogenes as well as c.827A>C in the tumor suppressor PTPRJ. A further inspection identified 15 rare variants carried by cancer genes. Specifically, these mutations are located on five tumor suppressors (SDHA, RB1CC1, PTCH1, DMBT1, BCR) and eight proto-oncogenes (MERTK, CSF1R, MYB, ROS1, PCM1, FGFR2, MYH11, BRCC3) and have an allele frequency lower than 0.01 in the Genome Aggregation Database (GnomAD). We observed that the cardiac and metabolic phenotypic traits are linked with the genotype of the patient. In addition, the risk of developing neoplasia cannot be excluded a priori. Long-term surgical issues of patients with VATER syndrome could benefit from the clinical exome sequencing of a personalized risk assessment for the appearance of further disease in pubertal timing and adult age.
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Affiliation(s)
- Gloria Pelizzo
- Pediatric Surgery Unit, Ospedale dei Bambini “Vittore Buzzi”, 20154 Milano, Italy
- Department of Biomedical and Clinical Science “L. Sacco”, University of Milano, 20157 Milano, Italy;
- Correspondence:
| | - Luigi Chiricosta
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (L.C.); (E.M.); (P.B.)
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (L.C.); (E.M.); (P.B.)
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Science “L. Sacco”, University of Milano, 20157 Milano, Italy;
- Department of Pediatrics, Ospedale dei Bambini “Vittore Buzzi”, 20154 Milano, Italy;
| | - Maria Antonietta Avanzini
- Immunology and Transplantation Laboratory, Cell Factory, Pediatric Hematology Oncology Unit, Department of Maternal and Children’s Health, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy; (M.A.A.); (S.C.)
| | - Stefania Croce
- Immunology and Transplantation Laboratory, Cell Factory, Pediatric Hematology Oncology Unit, Department of Maternal and Children’s Health, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy; (M.A.A.); (S.C.)
| | - Mario Lima
- Pediatric Surgery Unit, S. Orsola Hospital, University of Bologna, 40138 Bologna, Italy;
| | - Placido Bramanti
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (L.C.); (E.M.); (P.B.)
| | - Valeria Calcaterra
- Department of Pediatrics, Ospedale dei Bambini “Vittore Buzzi”, 20154 Milano, Italy;
- Pediatrics and Adolescentology Unit, Department of Internal Medicine, University of Pavia, 27100 Pavia, Italy
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22
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Da Vià MC, Ziccheddu B, Maeda A, Bagnoli F, Perrone G, Bolli N. A Journey Through Myeloma Evolution: From the Normal Plasma Cell to Disease Complexity. Hemasphere 2020; 4:e502. [PMID: 33283171 PMCID: PMC7710229 DOI: 10.1097/hs9.0000000000000502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
The knowledge of cancer origin and the subsequent tracking of disease evolution represent unmet needs that will soon be within clinical reach. This will provide the opportunity to improve patient's stratification and to personalize treatments based on cancer biology along its life history. In this review, we focus on the molecular pathogenesis of multiple myeloma (MM), a hematologic malignancy with a well-known multi-stage disease course, where such approach can sooner translate into a clinical benefit. We describe novel insights into modes and timing of disease initiation. We dissect the biology of the preclinical and pre-malignant phases, elucidating how knowledge of the genomics of the disease and the composition of the microenvironment allow stratification of patients based on risk of disease progression. Then, we explore cell-intrinsic and cell-extrinsic drivers of MM evolution to symptomatic disease. Finally, we discuss how this may relate to the development of refractory disease after treatment. By integrating an evolutionary view of myeloma biology with the recent acquisitions on its clonal heterogeneity, we envision a way to drive the clinical management of the disease based on its detailed biological features more than surrogates of disease burden.
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Affiliation(s)
- Matteo C. Da Vià
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Bachisio Ziccheddu
- Department of Molecular Biotechnologies and Health Sciences, University of Turin, Turin, Italy
| | - Akihiro Maeda
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Filippo Bagnoli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulia Perrone
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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23
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Zhang S, DuBois W, Zhang K, Simmons JK, Hughitt VK, Gorjifard S, Gaikwad S, Peat TJ, Mock BA. Mouse tumor susceptibility genes identify drug combinations for multiple myeloma. ACTA ACUST UNITED AC 2020; 6. [PMID: 32923678 PMCID: PMC7486007 DOI: 10.20517/2394-4722.2020.40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Long-term genetic studies utilizing backcross and congenic strain analyses coupled with positional cloning strategies and functional studies identified Cdkn2a, Mtor, and Mndal as mouse plasmacytoma susceptibility/resistance genes. Tumor incidence data in congenic strains carrying the resistance alleles of Cdkn2a and Mtor led us to hypothesize that drug combinations affecting these pathways are likely to have an additive, if not synergistic effect in inhibiting tumor cell growth. Traditional and novel systems-level genomic approaches were used to assess combination activity, disease specificity, and clinical potential of a drug combination involving rapamycin/everolimus, an Mtor inhibitor, with entinostat, an histone deacetylase inhibitor. The combination synergistically repressed oncogenic MYC and activated the Cdkn2a tumor suppressor. The identification of MYC as a primary upstream regulator led to the identification of small molecule binders of the G-quadruplex structure that forms in the NHEIII region of the MYC promoter. These studies highlight the importance of identifying drug combinations which simultaneously upregulate tumor suppressors and downregulate oncogenes.
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Affiliation(s)
- Shuling Zhang
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Wendy DuBois
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Ke Zhang
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - John K Simmons
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA.,Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - V Keith Hughitt
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Sayeh Gorjifard
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA.,University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA 98195, USA
| | - Snehal Gaikwad
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Tyler J Peat
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
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24
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Clay-Gilmour AI, Hildebrandt MAT, Brown EE, Hofmann JN, Spinelli JJ, Giles GG, Cozen W, Bhatti P, Wu X, Waller RG, Belachew AA, Robinson DP, Norman AD, Sinnwell JP, Berndt SI, Rajkumar SV, Kumar SK, Chanock SJ, Machiela MJ, Milne RL, Slager SL, Camp NJ, Ziv E, Vachon CM. Coinherited genetics of multiple myeloma and its precursor, monoclonal gammopathy of undetermined significance. Blood Adv 2020; 4:2789-2797. [PMID: 32569378 PMCID: PMC7322948 DOI: 10.1182/bloodadvances.2020001435] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/22/2020] [Indexed: 12/28/2022] Open
Abstract
So far, 23 germline susceptibility loci have been associated with multiple myeloma (MM) risk. It is unclear whether the genetic variation associated with MM susceptibility also predisposes to its precursor, monoclonal gammopathy of undetermined significance (MGUS). Leveraging 2434 MM cases, 754 MGUS cases, and 2 independent sets of controls (2567/879), we investigated potential shared genetic susceptibility of MM and MGUS by (1) performing MM and MGUS genome-wide association studies (GWAS); (2) validating the association of a polygenic risk score (PRS) based on 23 established MM loci (MM-PRS) with risk of MM, and for the first time with MGUS; and (3) examining genetic correlation of MM and MGUS. Heritability and genetic estimates yielded 17% (standard error [SE] ±0.04) and 15% (SE ±0.11) for MM and MGUS risk, respectively, and a 55% (SE ±0.30) genetic correlation. The MM-PRS was associated with risk of MM when assessed continuously (odds ratio [OR], 1.17 per SD; 95% confidence interval [CI], 1.13-1.21) or categorically (OR, 1.70; 95% CI, 1.38-2.09 for highest; OR, 0.71; 95% CI, 0.55-0.90 for lowest compared with middle quintile). The MM-PRS was similarly associated with MGUS (OR, 1.19 per SD; 95% CI, 1.14-1.26 as a continuous measure, OR, 1.77, 95%CI: 1.29-2.43 for highest and OR, 0.70, 95%CI: 0.50-0.98 for lowest compared with middle quintile). MM and MGUS associations did not differ by age, sex, or MM immunoglobulin isotype. We validated a 23-SNP MM-PRS in an independent series of MM cases and provide evidence for its association with MGUS. Our results suggest shared common genetic susceptibility to MM and MGUS.
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Affiliation(s)
- Alyssa I Clay-Gilmour
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
- Department of Biostatistics and Epidemiology, Arnold School of Public Health, University of South Carolina, Greenville, SC
| | - Michelle A T Hildebrandt
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elizabeth E Brown
- Department of Pathology, School of Medicine at the; University of Alabama, Birmingham, AL
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institues of Health, Bethesda, MD
| | - John J Spinelli
- Division of Population Oncology, BC Cancer, BC, Canada
- School of Population and Public Health, University of British Columbia, BC, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Wendy Cozen
- Department of Preventive Medicine, Keck School of Medicine at University of Southern California, Los Angeles, CA
| | - Parveen Bhatti
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rosalie G Waller
- Division of Hematology and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Alem A Belachew
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dennis P Robinson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, and
| | - Aaron D Norman
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, and
| | - Jason P Sinnwell
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, and
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institues of Health, Bethesda, MD
| | - S Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN; and
| | - Shaji K Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN; and
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institues of Health, Bethesda, MD
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institues of Health, Bethesda, MD
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Susan L Slager
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, and
| | - Nicola J Camp
- Division of Hematology and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Elad Ziv
- Department of Medicine, University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Celine M Vachon
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
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25
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Thomsen H, Chattopadhyay S, Hoffmann P, Nöthen MM, Kalirai H, Coupland SE, Jonas JB, Hemminki K, Försti A. Genome-wide study on uveal melanoma patients finds association to DNA repair gene TDP1. Melanoma Res 2020; 30:166-172. [PMID: 31626034 DOI: 10.1097/cmr.0000000000000641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Uveal melanoma is a life-threatening disease for which data on germline predisposition are essentially limited to mutations in the BAP1 gene. Many risk factors are shared between uveal melanoma and cutaneous melanoma, and these include fair skin color and light eye color. We carried out a genome-wide association study on 590 uveal melanoma patients and 5199 controls. Using a P-value limit of 10 we identified 11 loci with related odds ratios for the risk alleles ranging from 1.32 to 1.78. The smallest P-value in the overall analysis reached 1.07 × 10 for rs3759710 at 14q32.11, which is intronic to TDP1 (tyrosyl-DNA phosphodiesterase 1). This locus emerged as a genome-wide significant association for uveal melanoma clinical subtypes with any chromosomal aberrations (P = 10) and presence of epithelioid cells (P = 10). TDP1 is a DNA repair enzyme capable of repairing many types of DNA damage, including oxidative DNA lesions which may be relevant for uveal melanoma. We additionally wanted to replicate the previous candidate locus for uveal melanoma at chromosome 5p15.33 intronic to the CLPTM1L gene. Our analysis gave an odds ratio of 1.23 (95% confidence interval: 1.09-1.38; P = 0.0008) for the C allele of rs421284 and 1.21 (95% confidence interval: 1.07-1.36; P = 0.002) for the C allele of rs452932. Our data thus replicated the association of uveal melanoma with the CLPTM1L locus. Our data on TDP1 offer an attractive model positing that oxidative damage in pigmented tissue may be an initiation event in uveal melanoma and the level of damage may be regulated by the degree and type of iris pigmentation.
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Affiliation(s)
- Hauke Thomsen
- Division of Molecular Genetic Epidemiology of German Cancer Research Center (DKFZ), Heidelberg
| | - Subhayan Chattopadhyay
- Division of Molecular Genetic Epidemiology of German Cancer Research Center (DKFZ), Heidelberg
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Research Center, University of Bonn, Bonn, Germany
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular & Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool
| | - Sarah E Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular & Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool
- Department of Cellular Pathology, Royal Liverpool University Hospital, Liverpool, UK
| | - Jost B Jonas
- Department of Ophthalmology of the Medical Faculty Mannheim of the Ruprecht-Karls-University, Heidelberg, Germany
- Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology of German Cancer Research Center (DKFZ), Heidelberg
| | - Asta Försti
- Division of Molecular Genetic Epidemiology of German Cancer Research Center (DKFZ), Heidelberg
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26
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Baughn LB, Li Z, Pearce K, Vachon CM, Polley MY, Keats J, Elhaik E, Baird M, Therneau T, Cerhan JR, Bergsagel PL, Dispenzieri A, Rajkumar SV, Asmann YW, Kumar S. The CCND1 c.870G risk allele is enriched in individuals of African ancestry with plasma cell dyscrasias. Blood Cancer J 2020; 10:39. [PMID: 32179748 PMCID: PMC7075993 DOI: 10.1038/s41408-020-0294-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/07/2020] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhuo Li
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Kathryn Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Celine M Vachon
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mei-Yin Polley
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jonathan Keats
- Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | | | - Terry Therneau
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - James R Cerhan
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - P Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Angela Dispenzieri
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - S Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yan W Asmann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Shaji Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA.
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27
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Bolli N, Genuardi E, Ziccheddu B, Martello M, Oliva S, Terragna C. Next-Generation Sequencing for Clinical Management of Multiple Myeloma: Ready for Prime Time? Front Oncol 2020; 10:189. [PMID: 32181154 PMCID: PMC7057289 DOI: 10.3389/fonc.2020.00189] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/04/2020] [Indexed: 12/22/2022] Open
Abstract
Personalized treatment is an attractive strategy that promises increased efficacy with reduced side effects in cancer. The feasibility of such an approach has been greatly boosted by next-generation sequencing (NGS) techniques, which can return detailed information on the genome and on the transcriptome of each patient's tumor, thus highlighting biomarkers of response or druggable targets that may differ from case to case. However, while the number of cancers sequenced is growing exponentially, much fewer cases are amenable to a molecularly-guided treatment outside of clinical trials to date. In multiple myeloma, genomic analysis shows a variety of gene mutations, aneuploidies, segmental copy-number changes, translocations that are extremely heterogeneous, and more numerous than other hematological malignancies. Currently, in routine clinical practice we employ reduced FISH panels that only capture three high-risk features as part of the R-ISS. On the contrary, recent advances have suggested that extending genomic analysis to the full spectrum of recurrent mutations and structural abnormalities in multiple myeloma may have biological and clinical implications. Furthermore, increased efficacy of novel treatments can now produce deeper responses, and standard methods do not have enough sensitivity to stratify patients in complete biochemical remission. Consequently, NGS techniques have been developed to monitor the size of the clone to a sensitivity of up to a cell in a million after treatment. However, even these techniques are not within reach of standard laboratories. In this review we will recapitulate recent advances in multiple myeloma genomics, with special focus on the ones that may have immediate translational impact. We will analyze the benefits and pitfalls of NGS-based diagnostics, highlighting crucial aspects that will need to be taken into account before this can be implemented in most laboratories. We will make the point that a new era in myeloma diagnostics and minimal residual disease monitoring is close and conventional genetic testing will not be able to return the required information. This will mandate that even in routine practice NGS should soon be adopted owing to a higher informative potential with increasing clinical benefits.
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Affiliation(s)
- Niccolo Bolli
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy
| | - Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences, University of Turin, Turin, Italy
| | - Bachisio Ziccheddu
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Department of Molecular Biotechnologies and Health Sciences, University of Turin, Turin, Italy
| | - Marina Martello
- Seràgnoli Institute of Hematology, Bologna University School of Medicine, Bologna, Italy
| | - Stefania Oliva
- Department of Molecular Biotechnologies and Health Sciences, University of Turin, Turin, Italy
| | - Carolina Terragna
- Seràgnoli Institute of Hematology, Azienda Ospedaliero-Universitaria Sant'Orsola-Malpighi, Bologna, Italy
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28
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Pertesi M, Went M, Hansson M, Hemminki K, Houlston RS, Nilsson B. Genetic predisposition for multiple myeloma. Leukemia 2020; 34:697-708. [PMID: 31913320 DOI: 10.1038/s41375-019-0703-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 12/24/2019] [Indexed: 12/14/2022]
Abstract
Multiple myeloma (MM) is the second most common blood malignancy. Epidemiological family studies going back to the 1920s have provided evidence for familial aggregation, suggesting a subset of cases have an inherited genetic background. Recently, studies aimed at explaining this phenomenon have begun to provide direct evidence for genetic predisposition to MM. Genome-wide association studies have identified common risk alleles at 24 independent loci. Sequencing studies of familial cases and kindreds have begun to identify promising candidate genes where variants with strong effects on MM risk might reside. Finally, functional studies are starting to give insight into how identified risk alleles promote the development of MM. Here, we review recent findings in MM predisposition field, and highlight open questions and future directions.
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Affiliation(s)
- Maroulio Pertesi
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Kari Hemminki
- Department of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld, Heidelberg, Germany.,Faculty of Medicine and Biomedical Center, Charles University in Prague, 30605, Pilsen, Czech Republic
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden. .,Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.
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29
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Ali M, Lemonakis K, Wihlborg AK, Veskovski L, Turesson I, Mellqvist UH, Gullberg U, Hansson M, Nilsson B. Sequence variation at the MTHFD1L-AKAP12 and FOPNL loci does not influence multiple myeloma survival in Sweden. Blood Cancer J 2019; 9:57. [PMID: 31363079 PMCID: PMC6667490 DOI: 10.1038/s41408-019-0222-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/22/2019] [Accepted: 04/30/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Mina Ali
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Konstantinos Lemonakis
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden.,Hematology Clinic, Skåne University Hospital, 221 85, Lund, Sweden
| | - Anna-Karin Wihlborg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Ljupco Veskovski
- Section of Hematology, South Elvsborg Hospital, SE 501 83, Borås, Sweden
| | - Ingemar Turesson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | | | - Urban Gullberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden.,Hematology Clinic, Skåne University Hospital, 221 85, Lund, Sweden.,Wallenberg Center for Molecular Medicine, 221 84, Lund, Sweden
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden. .,Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA.
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30
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Lu HF, Hung KS, Chu HW, Wong HSC, Kim J, Kim MK, Choi BY, Tai YT, Ikegawa S, Cho EC, Chang WC. Meta-Analysis of Genome-Wide Association Studies Identifies Three Loci Associated With Stiffness Index of the Calcaneus. J Bone Miner Res 2019; 34:1275-1283. [PMID: 30779856 DOI: 10.1002/jbmr.3703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/27/2019] [Accepted: 02/12/2019] [Indexed: 01/11/2023]
Abstract
The stiffness index (SI) from quantitative ultrasound measurements is a good indicator of BMD and may be used to predict the risk of osteoporotic fracture. We conducted a genomewide association study (GWAS) for SI using 7742 individuals from the Taiwan Biobank, followed by a replication study in a Korean population (n = 2955). Approximately 6.1 million SNPs were subjected to association analysis, and SI-associated variants were identified. We further conducted a meta-analysis of Taiwan Biobank significant SNPs with a Korean population-based cohort. Candidate genes were prioritized according to epigenetic annotations, gene ontology, protein-protein interaction, GWAS catalog, and expression quantitative trait loci analyses. Our results revealed seven significant single-nucleotide polymorphisms (SNPs) within three loci: 7q31.31, 17p13.3, and 11q14.2. Conditional analysis showed that three SNPs, rs2536195 (CPED1/WNT16), rs1231207 (SMG6), and rs4944661 (LOC10050636/TMEM135), were the most important signals within these regions. The associations for the three SNPs were confirmed in a UK Biobank estimated BMD GWAS; these three cytobands were replicated successfully after a meta-analysis with a Korean population cohort as well. However, two SNPs were not replicated. After prioritization, we identified two novel genes, RAB15 and FNTB, as strong candidates for association with SI. Our study identified three SI-associated SNPs and two novel SI-related genes. Overall, these results provide further insight into the genetic architecture of osteoporosis. Further studies in larger East Asian populations are needed. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Hsing-Fang Lu
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kuo-Sheng Hung
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Neurosurgery, Taipei Medical University-Wan Fang Hospital, Taipei, Taiwan.,Graduate Institute of Injury, Prevention and Control, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Henry Sung-Ching Wong
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jihye Kim
- Department of Preventive Medicine, College of Medicine, Hanyang University, Seoul, South Korea.,Institute for Health and Society, Hanyang University, Seoul, South Korea
| | - Mi Kyung Kim
- Department of Preventive Medicine, College of Medicine, Hanyang University, Seoul, South Korea.,Institute for Health and Society, Hanyang University, Seoul, South Korea
| | - Bo Youl Choi
- Department of Preventive Medicine, College of Medicine, Hanyang University, Seoul, South Korea.,Institute for Health and Society, Hanyang University, Seoul, South Korea
| | - Yu-Ting Tai
- Department of Anesthesiology, Taipei Medical University, Taipei, Taiwan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Er-Chieh Cho
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chiao Chang
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Pharmacy, Taipei Medical University-Wanfang Hospital, Taipei, Taiwan.,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medicine Research, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
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31
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Janz S, Zhan F, Sun F, Cheng Y, Pisano M, Yang Y, Goldschmidt H, Hari P. Germline Risk Contribution to Genomic Instability in Multiple Myeloma. Front Genet 2019; 10:424. [PMID: 31139207 PMCID: PMC6518313 DOI: 10.3389/fgene.2019.00424] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/17/2019] [Indexed: 12/14/2022] Open
Abstract
Genomic instability, a well-established hallmark of human cancer, is also a driving force in the natural history of multiple myeloma (MM) - a difficult to treat and in most cases fatal neoplasm of immunoglobulin producing plasma cells that reside in the hematopoietic bone marrow. Long recognized manifestations of genomic instability in myeloma at the cytogenetic level include abnormal chromosome numbers (aneuploidy) caused by trisomy of odd-numbered chromosomes; recurrent oncogene-activating chromosomal translocations that involve immunoglobulin loci; and large-scale amplifications, inversions, and insertions/deletions (indels) of genetic material. Catastrophic genetic rearrangements that either shatter and illegitimately reassemble a single chromosome (chromotripsis) or lead to disordered segmental rearrangements of multiple chromosomes (chromoplexy) also occur. Genomic instability at the nucleotide level results in base substitution mutations and small indels that affect both the coding and non-coding genome. Sometimes this generates a distinctive signature of somatic mutations that can be attributed to defects in DNA repair pathways, the DNA damage response (DDR) or aberrant activity of mutator genes including members of the APOBEC family. In addition to myeloma development and progression, genomic instability promotes acquisition of drug resistance in patients with myeloma. Here we review recent findings on the genetic predisposition to myeloma, including newly identified candidate genes suggesting linkage of germline risk and compromised genomic stability control. The role of ethnic and familial risk factors for myeloma is highlighted. We address current research gaps that concern the lack of studies on the mechanism by which germline risk alleles promote genomic instability in myeloma, including the open question whether genetic modifiers of myeloma development act in tumor cells, the tumor microenvironment (TME), or in both. We conclude with a brief proposition for future research directions, which concentrate on the biological function of myeloma risk and genetic instability alleles, the potential links between the germline genome and somatic changes in myeloma, and the need to elucidate genetic modifiers in the TME.
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Affiliation(s)
- Siegfried Janz
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Fenghuang Zhan
- Department of Internal Medicine, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, United States.,Holden Comprehensive Cancer Center, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, United States
| | - Fumou Sun
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Yan Cheng
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael Pisano
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States.,Interdisciplinary Graduate Program in Immunology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, United States
| | - Ye Yang
- The Third Affiliated Hospital, Nanjing University of Chinese Medicine, Nanjing, China.,Ministry of Education's Key Laboratory of Acupuncture and Medicine Research, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hartmut Goldschmidt
- Medizinische Klinik V, Universitätsklinikum Heidelberg, Heidelberg, Germany.,Nationales Centrum für Tumorerkrankungen, Heidelberg, Germany
| | - Parameswaran Hari
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
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32
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Rasche L, Kortüm KM, Raab MS, Weinhold N. The Impact of Tumor Heterogeneity on Diagnostics and Novel Therapeutic Strategies in Multiple Myeloma. Int J Mol Sci 2019; 20:ijms20051248. [PMID: 30871078 PMCID: PMC6429294 DOI: 10.3390/ijms20051248] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 12/31/2022] Open
Abstract
Myeloma is characterized by extensive inter-patient genomic heterogeneity due to multiple different initiating events. A recent multi-region sequencing study demonstrated spatial differences, with progression events, such as TP53 mutations, frequently being restricted to focal lesions. In this review article, we describe the clinical impact of these two types of tumor heterogeneity. Target mutations are often dominant at one site but absent at other sites, which poses a significant challenge to personalized therapy in myeloma. The same holds true for high-risk subclones, which can be locally restricted, and as such not detectable at the iliac crest, which is the usual sampling site. Imaging can improve current risk classifiers and monitoring of residual disease, but does not allow for deciphering the molecular characteristics of tumor clones. In the era of novel immunotherapies, the clinical impact of heterogeneity certainly needs to be re-defined. Yet, preliminary observations indicate an ongoing impact of spatial heterogeneity on the efficacy of monoclonal antibodies. In conclusion, we recommend combining molecular tests with imaging to improve risk prediction and monitoring of residual disease. Overcoming intra-tumor heterogeneity is the prerequisite for curing myeloma. Novel immunotherapies are promising but research addressing their impact on the spatial clonal architecture is highly warranted.
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Affiliation(s)
- Leo Rasche
- Department of Internal Medicine 2, University Hospital of Würzburg, 97080 Würzburg, Germany.
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - K Martin Kortüm
- Department of Internal Medicine 2, University Hospital of Würzburg, 97080 Würzburg, Germany.
| | - Marc S Raab
- Department of Internal Medicine V, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
| | - Niels Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
- Department of Internal Medicine V, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
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33
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Campa D, Martino A, Macauda A, Dudziński M, Suska A, Druzd-Sitek A, Raab MS, Moreno V, Huhn S, Butrym A, Sainz J, Szombath G, Rymko M, Marques H, Lesueur F, Vangsted AJ, Vogel U, Kruszewski M, Subocz E, Buda G, Iskierka-Jażdżewska E, Ríos R, Merz M, Schöttker B, Mazur G, Perrial E, Martinez-Lopez J, Butterbach K, García Sanz R, Goldschmidt H, Brenner H, Jamroziak K, Reis RM, Kadar K, Dumontet C, Wątek M, Haastrup EK, Helbig G, Jurczyszyn A, Jerez A, Varkonyi J, Barington T, Grzasko N, Zaucha JM, Andersen V, Zawirska D, Canzian F. Genetic polymorphisms in genes of class switch recombination and multiple myeloma risk and survival: an IMMEnSE study. Leuk Lymphoma 2019; 60:1803-1811. [PMID: 30633655 DOI: 10.1080/10428194.2018.1551536] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genetic variants in genes acting during the maturation process of immature B-cell to differentiated plasma cell could influence the risk of developing multiple myeloma (MM). During B-cell maturation, several programmed genetic rearrangements occur to increase the variation of the immunoglobulin chains. Class switch recombination (CSR) is one of the most important among these mechanisms. Germline polymorphisms altering even subtly this process could play a role in the etiology and outcome of MM. We performed an association study of 30 genetic variants in the key CSR genes, using 2632 MM patients and 2848 controls from the International Multiple Myeloma rESEarch (IMMEnSE) consortium, the Heidelberg MM Group and the ESTHER cohort. We found an association between LIG4-rs1555902 and decreased MM risk, which approached statistical significance, as well as significant associations between AICDA-rs3794318 and better outcome. Our results add to our knowledge on the genetic component of MM risk and survival.
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Affiliation(s)
- Daniele Campa
- a Department of Biology , University of Pisa , Pisa , Italy
| | - Alessandro Martino
- b Genomic Epidemiology Group, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Angelica Macauda
- a Department of Biology , University of Pisa , Pisa , Italy.,b Genomic Epidemiology Group, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Marek Dudziński
- c Hematology Department , Teaching Hospital No 1 , Rzeszów , Poland
| | - Anna Suska
- d Department of Hematology , Jagiellonian University Medical College , Cracow , Poland
| | - Agnieszka Druzd-Sitek
- e Lymphoma Department , Centre of Oncology-Institute of Maria Skłodowska-Curie , Warsaw , Poland
| | - Marc-Steffen Raab
- f Department of Internal Medicine V , Heidelberg University Hospital , Heidelberg , Germany.,g Max-Eder Research Group Experimental Therapies for Hematologic Malignancies, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Victor Moreno
- h Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL, CIBERESP and Department of Clinical Sciences, Faculty of Medicine , University of Barcelona , Barcelona , Spain
| | - Stefanie Huhn
- i Molecular Biology Laboratory, Section of Multiple Myeloma, Department of Internal Medicine V , Heidelberg University Hospital , Heidelberg , Germany
| | - Aleksandra Butrym
- j Department of Internal and Occupational Diseases, Hypertension and Clinical Oncology , Wroclaw Medical University , Wroclaw , Poland
| | - Juan Sainz
- k PTS Granada , Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government , Granada , Spain.,l Monoclonal Gammopathies Unit, University Hospital Virgen de las Nieves , Granada , Spain.,m Pharmacogenetics Unit. Instituto de Investigación Biosanitaria de Granada (Ibs. Granada) , Hospitales Universitarios de Granada / Universidad de Granada , Granada , Spain
| | - Gergely Szombath
- n Department of Intrenal Medicine , Semmelweis University , Budapest , Hungary
| | - Marcin Rymko
- o Department of Haematology , Copernicus Town Hospital of Torun , Torun , Poland
| | - Herlander Marques
- p Life and Health Sciences Research Institute (ICVS), School of Health Sciences , University of Minho , Braga , Portugal
| | - Fabienne Lesueur
- q INSERM U900 , Paris , France.,r Institut Curie , Paris , France.,s Mines ParisTech , Fontainebleau , France.,t PSL University , Paris , France
| | - Annette Juul Vangsted
- u Department of Hematology , Copenhagen University Hospital , Rigshospitalet , Denmark
| | - Ulla Vogel
- v National Research Centre for the Working Environment , Denmark
| | - Marcin Kruszewski
- w Department of Hematology , University Hospital , Bydgoszcz , Poland
| | - Edyta Subocz
- x Department of Haematology , Military Institute of Medicine , Warsaw , Poland
| | - Gabriele Buda
- y Hematology Unit, Department of Clinical and Experimental Medicine , University of Pisa , Pisa , Italy
| | | | - Rafael Ríos
- k PTS Granada , Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government , Granada , Spain.,l Monoclonal Gammopathies Unit, University Hospital Virgen de las Nieves , Granada , Spain.,m Pharmacogenetics Unit. Instituto de Investigación Biosanitaria de Granada (Ibs. Granada) , Hospitales Universitarios de Granada / Universidad de Granada , Granada , Spain
| | - Maximilian Merz
- f Department of Internal Medicine V , Heidelberg University Hospital , Heidelberg , Germany
| | - Ben Schöttker
- aa Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,ab Network Aging Research (NAR) , University of Heidelberg , Heidelberg , Germany
| | - Grzegorz Mazur
- j Department of Internal and Occupational Diseases, Hypertension and Clinical Oncology , Wroclaw Medical University , Wroclaw , Poland
| | - Emeline Perrial
- ac Cancer Research Center of Lyon, INSERM 1052/CNRS 5286 , University of Lyon , Lyon , France
| | | | - Katja Butterbach
- ab Network Aging Research (NAR) , University of Heidelberg , Heidelberg , Germany
| | - Ramón García Sanz
- ae Department of Hematology , University Hospital of Salamanca , Salamanca , Spain
| | - Hartmut Goldschmidt
- f Department of Internal Medicine V , Heidelberg University Hospital , Heidelberg , Germany.,af National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Hermann Brenner
- aa Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,ab Network Aging Research (NAR) , University of Heidelberg , Heidelberg , Germany.,ag Division of Preventive Oncology , National Center for Tumor Diseases (NCT) German Cancer Research Center (DKFZ) , Heidelberg , Germany.,ah German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Krzysztof Jamroziak
- ai Department of Hematology , Institute of Hematology and Transfusion Medicine , Warsaw , Poland
| | - Rui Manuel Reis
- p Life and Health Sciences Research Institute (ICVS), School of Health Sciences , University of Minho , Braga , Portugal.,aj ICVS/3B's - PT Government Associate Laboratory , Braga/Guimarães , Portugal.,ak Barretos Cancer Hospital , Molecular Oncology Research Center , S. Paulo , Brazil
| | - Katalin Kadar
- n Department of Intrenal Medicine , Semmelweis University , Budapest , Hungary
| | - Charles Dumontet
- ac Cancer Research Center of Lyon, INSERM 1052/CNRS 5286 , University of Lyon , Lyon , France
| | - Marzena Wątek
- al Department of Hematology , Holy Cross Oncology Center , Kielce , Poland
| | - Eva Kannik Haastrup
- am Department of Clinical Immunology , Copenhagen University Hospital , Rigshospitalet, Copenhagen , Denmark
| | - Grzegorz Helbig
- an Department of Hematology and Bone Marrow Transplantation , Medical University of Silesia , Katowice , Poland
| | - Artur Jurczyszyn
- d Department of Hematology , Jagiellonian University Medical College , Cracow , Poland
| | - Andrés Jerez
- ao Department of Hematology , University Hospital Morales Meseguer, IMIB , Murcia , Spain
| | - Judit Varkonyi
- n Department of Intrenal Medicine , Semmelweis University , Budapest , Hungary
| | - Torben Barington
- ap Department of Clinical Immunology , Odense University Hospital , Odense , Denmark
| | - Norbert Grzasko
- aq Department of Hematology , St. John's Cancer Center , Lublin , Poland.,ar Department of Experimental Hematooncology , Medical University of Lublin , Lublin , Poland
| | | | - Vibeke Andersen
- at IRS-Center Sønderjylland , Aabenraa , Denmark.,au Institute of Molecular Biology, University of Southern Denmark , Odense , Denmark
| | - Daria Zawirska
- av Department of Haematology , University Hospital of Cracow , Cracow , Poland
| | - Federico Canzian
- b Genomic Epidemiology Group, German Cancer Research Center (DKFZ) , Heidelberg , Germany
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34
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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] [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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35
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Risk of MGUS in relatives of multiple myeloma cases by clinical and tumor characteristics. Leukemia 2018; 33:499-507. [PMID: 30201985 DOI: 10.1038/s41375-018-0246-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/13/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022]
Abstract
We and others have shown increased risk of monoclonal gammopathy of undetermined significance (MGUS) in first-degree relatives of patients with multiple myeloma (MM). Whether familial risk of MGUS differs by the MM proband's age at onset, tumor or clinical characteristics is unknown. MM and smoldering MM (SMM) cases (N = 430) were recruited from the Mayo Clinic in Rochester, Minnesota between 2005-2015. First-degree relatives over age 40 provided serum samples for evaluation of MGUS (N = 1179). Age and sex specific rates of MGUS among first-degree relatives were compared to a population-based sample. Cytogenetic subtypes were classified by Fluorescence in situ hybridization. MGUS was detected in 75 first-degree relatives for an age- and sex- adjusted prevalence of 5.8% (95% CI: 4.5-7.2). Prevalence of MGUS in first-degree relatives was 2.4 fold (95% CI: 1.9-2.9) greater than expected rates. Familial risk did not differ by proband's age at diagnosis, gender, isotype, IgH translocation, or trisomy. This study confirms first-degree relatives of MM cases have a significantly higher risk of MGUS compared to the general population, regardless of age, gender, or tumor characteristics. In selected situations, such as multiple affected first-degree relatives, screening of first-degree relatives of MM cases could be considered for follow-up and prevention strategies.
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Vodicka P, Musak L, Vodickova L, Vodenkova S, Catalano C, Kroupa M, Naccarati A, Polivkova Z, Vymetalkova V, Försti A, Hemminki K. Genetic variation of acquired structural chromosomal aberrations. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:13-21. [PMID: 30389156 DOI: 10.1016/j.mrgentox.2018.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/24/2018] [Accepted: 05/10/2018] [Indexed: 12/21/2022]
Abstract
Human malignancies are often hallmarked with genomic instability, which itself is also considered a causative event in malignant transformation. Genomic instability may manifest itself as genetic changes in the nucleotide sequence of DNA, or as structural or numerical changes of chromosomes. Unrepaired or insufficiently repaired DNA double-strand breaks, as well as telomere shortening, are important contributors in the formation of structural chromosomal aberrations (CAs). In the present review, we discuss potential mechanisms behind the formation of CAs and their relation to cancer. Based on our own studies, we also illustrate how inherited genetic variation may modify the frequency and types of CAs occurring in humans. Recently, we published a series of studies on variations in genes relevant to maintaining genomic integrity, such as those encoding xenobiotic-metabolising enzymes, DNA repair, the tumour suppressor TP53, the spindle assembly checkpoint, and cyclin D1 (CCND1). While individually genetic variation in these genes exerted small modulating effects, in interactions they were associated with CA frequencies in peripheral blood lymphocytes of healthy volunteers. Moreover, we observed opposite associations between the CCND1 splice site polymorphism rs9344 G870A and the frequency of CAs compared to their association with translocation t(11,14). We discuss the functional consequences of the CCND1 gene in interplay with DNA damage response and DNA repair during malignant transformation. Our review summarizes existing evidence that gene variations in relevant cellular pathways modulate the frequency of CAs, predominantly in a complex interaction. More functional/mechanistic studies elucidating these observations are required. Several questions emerge, such as the role of CAs in malignancies with respect to a particular phenotype and heterogeneity, the formation of CAs during the process of malignant transformation, and the formation of CAs in individual types of lymphocytes in relation to the immune response.
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Affiliation(s)
- Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic.
| | - Ludovit Musak
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, 03601, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, 10000, Czech Republic
| | - Calogerina Catalano
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, D69120, Germany
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Italian Institute for Genomic Medicine (IIGM), Torino, 10126, Italy
| | - Zdena Polivkova
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, 10000, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, D69120, Germany; Center for Primary Health Care Research, Lund University, Malmö, 214 28, Sweden
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, D69120, Germany; Center for Primary Health Care Research, Lund University, Malmö, 214 28, Sweden
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Genetic Predisposition to Multiple Myeloma at 5q15 Is Mediated by an ELL2 Enhancer Polymorphism. Cell Rep 2018; 20:2556-2564. [PMID: 28903037 PMCID: PMC5608969 DOI: 10.1016/j.celrep.2017.08.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/07/2017] [Accepted: 08/18/2017] [Indexed: 01/08/2023] Open
Abstract
Multiple myeloma (MM) is a malignancy of plasma cells. Genome-wide association studies have shown that variation at 5q15 influences MM risk. Here, we have sought to decipher the causal variant at 5q15 and the mechanism by which it influences tumorigenesis. We show that rs6877329 G > C resides in a predicted enhancer element that physically interacts with the transcription start site of ELL2. The rs6877329-C risk allele is associated with reduced enhancer activity and lowered ELL2 expression. Since ELL2 is critical to the B cell differentiation process, reduced ELL2 expression is consistent with inherited genetic variation contributing to arrest of plasma cell development, facilitating MM clonal expansion. These data provide evidence for a biological mechanism underlying a hereditary risk of MM at 5q15.
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Search for rare protein altering variants influencing susceptibility to multiple myeloma. Oncotarget 2018; 8:36203-36210. [PMID: 28404951 PMCID: PMC5482649 DOI: 10.18632/oncotarget.15874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/28/2017] [Indexed: 12/12/2022] Open
Abstract
The genetic basis underlying the inherited risk of developing multiple myeloma (MM) is largely unknown. To examine the impact of rare protein altering variants on the risk of developing MM we analyzed high-coverage exome sequencing data on 513 MM cases and 1,569 healthy controls, performing both single variant and gene burden tests. We did not identify any recurrent coding low-frequency alleles (1–5%) with moderate effect that were statistically associated with MM. In a gene burden analysis we did however identify a promising relationship between variation in the marrow kinetochore microtubule stromal gene KIF18A, which plays a role in control mitotic chromosome positioning dynamics, and risk of MM (P =3.6×10−6). Further analysis showed KIF18A displays a distinct pattern of expression across molecular subgroups of MM as well as being associated with patient survival. Our results inform future study design and provide a resource for contextualizing the impact of candidate MM susceptibility genes.
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Waller RG, Darlington TM, Wei X, Madsen MJ, Thomas A, Curtin K, Coon H, Rajamanickam V, Musinsky J, Jayabalan D, Atanackovic D, Rajkumar SV, Kumar S, Slager S, Middha M, Galia P, Demangel D, Salama M, Joseph V, McKay J, Offit K, Klein RJ, Lipkin SM, Dumontet C, Vachon CM, Camp NJ. Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk. PLoS Genet 2018; 14:e1007111. [PMID: 29389935 PMCID: PMC5794067 DOI: 10.1371/journal.pgen.1007111] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/10/2017] [Indexed: 01/10/2023] Open
Abstract
The high-risk pedigree (HRP) design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS) method in 11 extended, Utah, multiple myeloma (MM) HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM) cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu), a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val), a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.
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Affiliation(s)
- Rosalie G. Waller
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Todd M. Darlington
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Xiaomu Wei
- Weill Cornell Medical College, New York, New York, United States of America
| | - Michael J. Madsen
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Alun Thomas
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Karen Curtin
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Hilary Coon
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | | | - Justin Musinsky
- Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - David Jayabalan
- Weill Cornell Medical College, New York, New York, United States of America
| | - Djordje Atanackovic
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | | | - Shaji Kumar
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - Susan Slager
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mridu Middha
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | | | - Mohamed Salama
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Vijai Joseph
- Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Robert J. Klein
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Steven M. Lipkin
- Weill Cornell Medical College, New York, New York, United States of America
| | | | | | - Nicola J. Camp
- University of Utah School of Medicine, Salt Lake City, Utah, United States of America
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40
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Kinnersley B, Houlston RS, Bondy ML. Genome-Wide Association Studies in Glioma. Cancer Epidemiol Biomarkers Prev 2018; 27:418-428. [PMID: 29382702 DOI: 10.1158/1055-9965.epi-17-1080] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 01/23/2023] Open
Abstract
Since the first reports in 2009, genome-wide association studies (GWAS) have been successful in identifying germline variants associated with glioma susceptibility. In this review, we describe a chronological history of glioma GWAS, culminating in the most recent study comprising 12,496 cases and 18,190 controls. We additionally summarize associations at the 27 glioma-risk SNPs that have been reported so far. Future efforts are likely to be principally focused on assessing association of germline-risk SNPs with particular molecular subgroups of glioma, as well as investigating the functional basis of the risk loci in tumor formation. These ongoing studies will be important to maximize the impact of research into glioma susceptibility, both in terms of insight into tumor etiology as well as opportunities for clinical translation. Cancer Epidemiol Biomarkers Prev; 27(4); 418-28. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Melissa L Bondy
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.
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41
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A common variant within the HNF1B gene is associated with overall survival of multiple myeloma patients: results from the IMMEnSE consortium and meta-analysis. Oncotarget 2018; 7:59029-59048. [PMID: 27437873 PMCID: PMC5312293 DOI: 10.18632/oncotarget.10665] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/19/2016] [Indexed: 01/01/2023] Open
Abstract
Diabetogenic single nucleotide polymorphisms (SNPs) have recently been associated with multiple myeloma (MM) risk but their impact on overall survival (OS) of MM patients has not been analysed yet. In order to investigate the impact of 58 GWAS-identified variants for type 2 diabetes (T2D) on OS of patients with MM, we analysed genotyping data of 936 MM patients collected by the International Multiple Myeloma rESEarch (IMMENSE) consortium and an independent set of 700 MM patients recruited by the University Clinic of Heidelberg. A meta-analysis of the cox regression results of the two sets showed that rs7501939 located in the HNF1B gene negatively impacted OS (HRRec= 1.44, 95% CI = 1.18-1.76, P = 0.0001). The meta-analysis also showed a noteworthy gender-specific association of the SLC30A8rs13266634 SNP with OS. The presence of each additional copy of the minor allele at rs13266634 was associated with poor OS in men whereas no association was seen in women (HRMen-Add = 1.32, 95% CI 1.13-1.54, P = 0.0003). In conclusion, these data suggest that the HNF1Brs7501939 SNP confers poor OS in patients with MM and that a SNP in SLC30A8 affect OS in men.
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42
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Iordache PD, Mates D, Gunnarsson B, Eggertsson HP, Sulem P, Guðmundsson J, Benónísdóttir S, Csiki IE, Rascu S, Radavoi D, Ursu R, Staicu C, Calota V, Voinoiu A, Jinga M, Rosoga G, Danau R, Sima SC, Badescu D, Suciu N, Radoi V, Manolescu A, Rafnar T, Halldórsson BV, Jinga V, Stefánsson K. Profile of common prostate cancer risk variants in an unscreened Romanian population. J Cell Mol Med 2017; 22:1574-1582. [PMID: 29266682 PMCID: PMC5824401 DOI: 10.1111/jcmm.13433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
To find sequence variants affecting prostate cancer (PCA) susceptibility in an unscreened Romanian population we use a genome‐wide association study (GWAS). The study population included 990 unrelated pathologically confirmed PCA cases and 1034 male controls. DNA was genotyped using Illumina SNP arrays, and 24.295.558 variants were imputed using the 1000 Genomes data set. An association test was performed between the imputed markers and PCA. A systematic literature review for variants associated with PCA risk identified 115 unique variants that were tested in the Romanian sample set. Thirty of the previously reported SNPs replicated (P‐value < 0.05), with the strongest associations observed at: 8q24.21, 11q13.3, 6q25.3, 5p15.33, 22q13.2, 17q12 and 3q13.2. The replicated variants showing the most significant association in Romania are rs1016343 at 8q24.21 (P = 2.2 × 10−4), rs7929962 at 11q13.3 (P = 2.7 × 10−4) and rs9364554 at 6q25.2 (P = 4.7 × 10−4). None of the variants tested in the Romanian GWAS reached genome‐wide significance (P‐value <5 × 10−8) but 807 markers had P‐values <1 × 10−4. Here, we report the results of the first GWAS of PCA performed in a Romanian population. Our study provides evidence that a substantial fraction of previously validated PCA variants associate with risk in this unscreened Romanian population.
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Affiliation(s)
- Paul D Iordache
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | | | | | | | | | | | | | - Stefan Rascu
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Daniel Radavoi
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Radu Ursu
- Department of Medical Genetics, Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | | | | | | | - Mariana Jinga
- Carol Davila University of Medicine and Pharmacy, Dr. Carol Davila Central University Emergency Military Hospital, Bucharest, Romania
| | - Gabriel Rosoga
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Razvan Danau
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Sorin Cristian Sima
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Daniel Badescu
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | | | - Viorica Radoi
- Department of Medical Genetics, Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Andrei Manolescu
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | - Bjarni V Halldórsson
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.,deCODE genetics/AMGEN, Reykjavik, Iceland
| | - Viorel Jinga
- Urology Department, 'Prof. Dr. Th. Burghele' Clinical Hospital, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Kári Stefánsson
- deCODE genetics/AMGEN, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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43
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Kim EE, Lee S, Lee CH, Oh H, Song K, Han B. FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects. Bioinformatics 2017; 33:3947-3954. [PMID: 29036405 PMCID: PMC5860085 DOI: 10.1093/bioinformatics/btx463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 07/19/2017] [Indexed: 11/26/2022] Open
Abstract
Motivation In genetic association studies, meta-analyses are widely used to increase the statistical power by aggregating information from multiple studies. In meta-analyses, participating studies often share the same individuals due to the shared use of publicly available control data or accidental recruiting of the same subjects. As such overlapping can inflate false positive rate, overlapping subjects are traditionally split in the studies prior to meta-analysis, which requires access to genotype data and is not always possible. Fortunately, recently developed meta-analysis methods can systematically account for overlapping subjects at the summary statistics level. Results We identify and report a phenomenon that these methods for overlapping subjects can yield low power. For instance, in our simulation involving a meta-analysis of five studies that share 20% of individuals, whereas the traditional splitting method achieved 80% power, none of the new methods exceeded 32% power. We found that this low power resulted from the unaccounted differences between shared and unshared individuals in terms of their contributions towards the final statistic. Here, we propose an optimal summary-statistic-based method termed as FOLD that increases the power of meta-analysis involving studies with overlapping subjects. Availability and implementation Our method is available at http://software.buhmhan.com/FOLD. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emma E Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea.,Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | | | - Hyunjung Oh
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Buhm Han
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea.,Department of Convergence Medicine
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44
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Sud A, Kinnersley B, Houlston RS. Genome-wide association studies of cancer: current insights and future perspectives. Nat Rev Cancer 2017; 17:692-704. [PMID: 29026206 DOI: 10.1038/nrc.2017.82] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWAS) provide an agnostic approach for investigating the genetic basis of complex diseases. In oncology, GWAS of nearly all common malignancies have been performed, and over 450 genetic variants associated with increased risks have been identified. As well as revealing novel pathways important in carcinogenesis, these studies have shown that common genetic variation contributes substantially to the heritable risk of many common cancers. The clinical application of GWAS is starting to provide opportunities for drug discovery and repositioning as well as for cancer prevention. However, deciphering the functional and biological basis of associations is challenging and is in part a barrier to fully unlocking the potential of GWAS.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
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45
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Wang W, Zhang Y, Chen R, Tian Z, Zhai Y, Janz S, Gu C, Yang Y. Chromosomal instability and acquired drug resistance in multiple myeloma. Oncotarget 2017; 8:78234-78244. [PMID: 29100463 PMCID: PMC5652852 DOI: 10.18632/oncotarget.20829] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/26/2017] [Indexed: 12/29/2022] Open
Abstract
Chromosomal instability (CIN) is an important hallmark of human cancer. CIN not only contributes to all stages of tumor development (initiation, promotion and progression) but also drives, in large measure, the acquisition of drug resistance by cancer cells. Although CIN is a cornerstone of the complex mutational architecture that underlies neoplastic cell development and tumor heterogeneity and has been tightly associated with treatment responses and survival of cancer patients, it may be one of the least understood features of the malignant phenotype in terms of genetic pathways and molecular mechanisms. Here we review new insights into the type of CIN seen in multiple myeloma (MM), a blood cancer of terminally differentiated, immunoglobulin-producing B-lymphocytes called plasma cells that remains incurable in the great majority of cases. We will consider bona fide myeloma CIN genes, methods for measuring CIN in myeloma cells, and novel approaches to CIN-targeted treatments of patients with myeloma. The new findings generate optimism that enhanced understanding of CIN will lead to the design and testing of new therapeutic strategies to overcome drug resistance in MM in the not-so-distant future.
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Affiliation(s)
- Wang Wang
- The Third Affiliated Hospital, Nanjing University of Chinese Medicine, Nanjing, 210023, China.,School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yi Zhang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Ruini Chen
- School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhidan Tian
- Department of Pathology, Nanjing First Hospital, Nanjing, 210006, China
| | - Yongpin Zhai
- Department of Hematology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, China
| | - Siegfried Janz
- Department of Pathology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, 52242, USA
| | - Chunyan Gu
- The Third Affiliated Hospital, Nanjing University of Chinese Medicine, Nanjing, 210023, China.,School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ye Yang
- The Third Affiliated Hospital, Nanjing University of Chinese Medicine, Nanjing, 210023, China.,School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023, China
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Abstract
The outcomes for the majority of patients with myeloma have improved over recent decades, driven by treatment advances. However, there is a subset of patients considered to have high-risk disease who have not benefited. Understanding how high-risk disease evolves from more therapeutically tractable stages is crucial if we are to improve outcomes. This can be accomplished by identifying the genetic mechanisms and mutations driving the transition of a normal plasma cell to one with the features of the following disease stages: monoclonal gammopathy of undetermined significance, smouldering myeloma, myeloma and plasma cell leukaemia. Although myeloma initiating events are clonal, subsequent driver lesions often occur in a subclone of cells, facilitating progression by Darwinian selection processes. Understanding the co-evolution of the clones within their microenvironment will be crucial for therapeutically manipulating the process. The end stage of progression is the generation of a state associated with treatment resistance, increased proliferation, evasion of apoptosis and an ability to grow independently of the bone marrow microenvironment. In this Review, we discuss these end-stage high-risk disease states and how new information is improving our understanding of their evolutionary trajectories, how they may be diagnosed and the biological behaviour that must be addressed if they are to be treated effectively.
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Affiliation(s)
- Charlotte Pawlyn
- The Institute of Cancer Research, 15 Cotswold Road, Sutton SM2 5NG, UK
| | - Gareth J Morgan
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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47
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Bolli N, Barcella M, Salvi E, D'Avila F, Vendramin A, De Philippis C, Munshi NC, Avet-Loiseau H, Campbell PJ, Mussetti A, Carniti C, Maura F, Barlassina C, Corradini P, Montefusco V. Next-generation sequencing of a family with a high penetrance of monoclonal gammopathies for the identification of candidate risk alleles. Cancer 2017; 123:3701-3708. [DOI: 10.1002/cncr.30777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/04/2017] [Accepted: 04/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Niccolo Bolli
- Department of Oncology and Hemato-Oncology; University of Milan; Milan Italy
- Department of Hematology and Pediatric Onco-Hematology; IRCCS Foundation National Cancer Institute; Milan Italy
- The Cancer Genome Project; Wellcome Trust Sanger Institute; Cambridge United Kingdom
| | - Matteo Barcella
- Genomic and Bioinformatics Unit; Department of Health Sciences, University of Milan; Milan Italy
| | - Erika Salvi
- Genomic and Bioinformatics Unit; Department of Health Sciences, University of Milan; Milan Italy
| | - Francesca D'Avila
- Genomic and Bioinformatics Unit; Department of Health Sciences, University of Milan; Milan Italy
| | - Antonio Vendramin
- Department of Oncology and Hemato-Oncology; University of Milan; Milan Italy
- Department of Hematology and Pediatric Onco-Hematology; IRCCS Foundation National Cancer Institute; Milan Italy
| | - Chiara De Philippis
- Department of Oncology and Hemato-Oncology; University of Milan; Milan Italy
- Department of Hematology and Pediatric Onco-Hematology; IRCCS Foundation National Cancer Institute; Milan Italy
| | - Nikhil C. Munshi
- LeBow Institute for Myeloma Therapeutics; Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School; Boston Massachusetts
| | - Herve Avet-Loiseau
- Laboratory for Genomics in Myeloma; University Cancer Center of Toulouse; CRCT INSERM 1037, Toulouse France
| | - Peter J. Campbell
- The Cancer Genome Project; Wellcome Trust Sanger Institute; Cambridge United Kingdom
| | - Alberto Mussetti
- Department of Hematology and Pediatric Onco-Hematology; IRCCS Foundation National Cancer Institute; Milan Italy
| | - Cristiana Carniti
- Department of Hematology and Pediatric Onco-Hematology; IRCCS Foundation National Cancer Institute; Milan Italy
| | - Francesco Maura
- Department of Oncology and Hemato-Oncology; University of Milan; Milan Italy
| | - Cristina Barlassina
- Genomic and Bioinformatics Unit; Department of Health Sciences, University of Milan; Milan Italy
| | - Paolo Corradini
- Department of Oncology and Hemato-Oncology; University of Milan; Milan Italy
- Department of Hematology and Pediatric Onco-Hematology; IRCCS Foundation National Cancer Institute; Milan Italy
| | - Vittorio Montefusco
- Department of Hematology and Pediatric Onco-Hematology; IRCCS Foundation National Cancer Institute; Milan Italy
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48
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Direct evidence for a polygenic etiology in familial multiple myeloma. Blood Adv 2017; 1:619-623. [PMID: 29296704 DOI: 10.1182/bloodadvances.2016003111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/04/2017] [Indexed: 11/20/2022] Open
Abstract
Although common risk alleles for multiple myeloma (MM) were recently identified, their contribution to familial MM is unknown. Analyzing 38 familial cases identified primarily by linking Swedish nationwide registries, we demonstrate an enrichment of common MM risk alleles in familial compared with 1530 sporadic cases (P = 4.8 × 10-2 and 6.0 × 10-2, respectively, for 2 different polygenic risk scores) and 10 171 population-based controls (P = 1.5 × 10-4 and 1.3 × 10-4, respectively). Using mixture modeling, we estimate that about one-third of familial cases result from such enrichments. Our results provide the first direct evidence for a polygenic etiology in a familial hematologic malignancy.
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49
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Campo C, da Silva Filho MI, Weinhold N, Mahmoudpour SH, Goldschmidt H, Hemminki K, Merz M, Försti A. Bortezomib-induced peripheral neuropathy: A genome-wide association study on multiple myeloma patients. Hematol Oncol 2017; 36:232-237. [PMID: 28317148 DOI: 10.1002/hon.2391] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 01/02/2023]
Abstract
The proteasome-inhibitor bortezomib was introduced into the treatment of multiple myeloma more than a decade ago. It is clinically beneficial, but peripheral neuropathy (PNP) is a side effect that may limit its use in some patients. To examine the possible genetic predisposing factors to PNP, we performed a genome-wide association study on 646 bortezomib-treated German multiple myeloma patients. Our aim was to identify genetic risk variants associated with the development of PNP as a serious side effect of the treatment. We identified 4 new promising loci for bortezomib-induced PNP at 4q34.3 (rs6552496), 5q14.1 (rs12521798), 16q23.3 (rs8060632), and 18q21.2 (rs17748074). Even though the results did not reach genome-wide significance level, they support the idea of previous studies, suggesting a genetic basis for neurotoxicity. The identified single nucleotide polymorphisms map to genes or next to genes involved in the development and function of the nervous system (CDH13, DCC, and TENM3). As possible functional clues, 2 of the variants, rs12521798 and rs17748074, affect enhancer histone marks in the brain. The rs12521798 may also impact expression of THBS4, which affects specific signal trasduction pathways in the nervous system. Further research is needed to clarify the mechanism of action of the identified single nucleotide polymorphisms in the development of drug-induced PNP and to functionally validate our in silico predictions.
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Affiliation(s)
- Chiara Campo
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.,Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.,National Centre of Tumor Diseases, Heidelberg, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Maximilian Merz
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.,Department of Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
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50
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Peng M, Zhao G, Yang F, Cheng G, Huang J, Qin X, Liu Y, Wang Q, Li Y, Qin D. NCOA1 is a novel susceptibility gene for multiple myeloma in the Chinese population: A case-control study. PLoS One 2017; 12:e0173298. [PMID: 28264017 PMCID: PMC5338790 DOI: 10.1371/journal.pone.0173298] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
Multiple myeloma (MM) is an incurable malignancy of mature B-lymphoid cells, and its pathogenesis is only partially understood. Previous studies have demonstrated that a number of Non-Hodgkin Lymphoma (NHL) associated genes also show susceptibility to MM, suggesting malignancies originating from B cells may share similar genetic susceptibility. Several recent large-scale genome-wide association studies (GWAS) have identified HLA-I, HLA-II, CXCR5, ETS1, LPP and NCOA1 genes as genetic risk factors associated with NHL, and this study aimed to investigate whether these genes polymorphisms confer susceptibility with MM in the Chinese Han population. In 827 MM cases and 709 healthy controls of Chinese Han, seven single nucleotide polymorphisms (SNPs) in the HLA–I region (rs6457327), the HLA–II region (rs2647012 and rs7755224), the CXCR5 gene (rs4938573), the ETS1 gene (rs4937362), the LPP gene (rs6444305), and the NCOA1 region (rs79480871) were genotyped using the Sequenom platform. Our study indicated that genotype and allele frequencies of rs79480871 showed strong associations with MM patients (pa = 3.5×10−4 and pa = 1.5×10−4), and the rs6457327 genotype was more readily associated with MM patients than with controls (pa = 4.9×10−3). This study was the first to reveal the correlation between NCOA1 gene polymorphisms and MM patients, indicating that NCOA1 might be a novel susceptibility gene for MM patients in the Chinese Han population.
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Affiliation(s)
- Mengle Peng
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, Henan, China
| | - Guanfei Zhao
- Department of Clinical Laboratory, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Funing Yang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin, China
| | - Guixue Cheng
- Department of Clinical Laboratory, Shengjing Hospital Affiliated to China Medical University, Shenyang, Liaoning, China
| | - Jing Huang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin, China
| | - Xiaosong Qin
- Department of Clinical Laboratory, Shengjing Hospital Affiliated to China Medical University, Shenyang, Liaoning, China
| | - Yong Liu
- Department of Clinical Laboratory, Shengjing Hospital Affiliated to China Medical University, Shenyang, Liaoning, China
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yongzhe Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
- * E-mail: (DQ); (YZL)
| | - Dongchun Qin
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, Henan, China
- * E-mail: (DQ); (YZL)
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