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1. Genome-Wide Somatic Alterations in Multiple Myeloma Reveal a Superior Outcome Group

Author

Stephane Minvielle, Jill Corre, Raphael Szalat, Hervé Avet-Loiseau, Masood A. Shammas, Anjan Thakurta, Anil Aktas Samur, Mehmet Kemal Samur, Paul G. Richardson, Kenneth C. Anderson, Giovanni Parmigiani, Florence Magrangeas, Mariateresa Fulciniti, Nikhil C. Munshi, Tessa Han, Philippe Moreau, Dana-Farber Cancer Institute [Boston], Harvard T.H. Chan School of Public Health, Harvard Medical School [Boston] (HMS), Integrative Oncogenomics of Multiple Myeloma Pathogenesis and Progression (CRCINA-ÉQUIPE 11), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Celgene Corporation [Summit, NJ, USA], Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), VA Boston Healthcare System [Boston, MA], Bernardo, Elizabeth, Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Adult, Male, Cancer Research, Somatic cell, DNA Mutational Analysis, MEDLINE, [SDV.CAN]Life Sciences [q-bio]/Cancer, Bioinformatics, Genome, Dexamethasone, GTP Phosphohydrolases, Bortezomib, 03 medical and health sciences, 0302 clinical medicine, INDEL Mutation, [SDV.CAN] Life Sciences [q-bio]/Cancer, Antineoplastic Combined Chemotherapy Protocols, Biomarkers, Tumor, Hematologic Malignancy, Humans, Medicine, Lenalidomide, Multiple myeloma, Aged, 030304 developmental biology, 0303 health sciences, Whole Genome Sequencing, business.industry, Membrane Proteins, DNA, Neoplasm, ORIGINAL REPORTS, Middle Aged, medicine.disease, Combined Modality Therapy, Progression-Free Survival, 3. Good health, Survival Rate, Treatment Outcome, Oncology, 030220 oncology & carcinogenesis, Female, Multiple Myeloma, business, Stem Cell Transplantation
Abstract

PURPOSE Multiple myeloma (MM) is accompanied by heterogeneous somatic alterations. The overall goal of this study was to describe the genomic landscape of myeloma using deep whole-genome sequencing (WGS) and develop a model that identifies patients with long survival. METHODS We analyzed deep WGS data from 183 newly diagnosed patients with MM treated with lenalidomide, bortezomib, and dexamethasone (RVD) alone or RVD + autologous stem cell transplant (ASCT) in the IFM/DFCI 2009 study (ClinicalTrials.gov identifier: NCT01191060 ). We integrated genomic markers with clinical data. RESULTS We report significant variability in mutational load and processes within MM subgroups. The timeline of observed activation of mutational processes provides the basis for 2 distinct models of acquisition of mutational changes detected at the time of diagnosis of myeloma. Virtually all MM subgroups have activated DNA repair–associated signature as a prominent late mutational process, whereas APOBEC signature targeting C>G is activated in the intermediate phase of disease progression in high-risk MM. Importantly, we identify a genomically defined MM subgroup (17% of newly diagnosed patients) with low DNA damage (low genomic scar score with chromosome 9 gain) and a superior outcome (100% overall survival at 69 months), which was validated in a large independent cohort. This subgroup allowed us to distinguish patients with low- and high-risk hyperdiploid MM and identify patients with prolongation of progression-free survival. Genomic characteristics of this subgroup included lower mutational load with significant contribution from age-related mutations as well as frequent NRAS mutation. Surprisingly, their overall survival was independent of International Staging System and minimal residual disease status. CONCLUSION This is a comprehensive study identifying genomic markers of a good-risk group with prolonged survival. Identification of this patient subgroup will affect future therapeutic algorithms and research planning.

Published
2020

2. Deciphering the chronology of copy number alterations in Multiple Myeloma

Author

Kenneth C. Anderson, Nikhil C. Munshi, Masood A. Shammas, Michel Attal, Florence Magrangeas, Paul G. Richardson, Mariateresa Fulciniti, Anil Aktas Samur, Mehmet Kemal Samur, Philippe Moreau, Stephane Minvielle, Giovanni Parmigiani, Hervé Avet-Loiseau, Dana-Farber Cancer Institute [Boston], Department of Biostatistics [Boston, MA, USA], Harvard T.H. Chan School of Public Health, Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), Department of Medical Oncology [Boston, MA, USA], Harvard Medical School [Boston] (HMS)-Dana-Farber Cancer Institute [Boston], VA Boston Healthcare System, Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de génomique du myélome [IUCT Oncopole, Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), This work was supported by Department of Veterans Affairs Merit Review Award I01BX001584-01, NIH grants PO1-155258 and National Cancer Institute Spore 5P50CA100707-13 (N.C.M., M.K.S., K.C.A., H.A.-L., M.F., M.S.), and Leukemia and Lymphoma Society Translational Research Grant (N.C.M., M.S.)., Bernardo, Elizabeth, Pôle Institut Universitaire du Cancer - Oncopole [CHU Toulouse] (Pôle IUC - Oncopole), CHU Toulouse [Toulouse]-Oncopole de Toulouse, CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
DNA Copy Number Variations, Chromosomal translocation, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, lcsh:RC254-282, Clonal deletion, Article, 03 medical and health sciences, 0302 clinical medicine, Copy Number Alteration, [SDV.CAN] Life Sciences [q-bio]/Cancer, immune system diseases, hemic and lymphatic diseases, medicine, Humans, cardiovascular diseases, 10. No inequality, Multiple myeloma, Extramural, Hematology, medicine.disease, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Oncology, 030220 oncology & carcinogenesis, Cancer research, Multiple Myeloma, 030215 immunology
Abstract

Multiple myeloma (MM) and its precursor condition MGUS are characterized by chromosomal aberrations. Here, we comprehensively characterize the order of occurrence of these complex genomic events underlying MM development using 500 MGUS, and MM samples. We identify hyperdiploid MM (HMM) and non-HMM as genomically distinct entities with different evolution of the copy number alterations. In HMM, gains of 9,15 or 19 are the first and clonal events observed as clonal even at MGUS stage. These events are thus early and may underlie initial transformation of normal plasma cells to MGUS cells. However, CNAs may not be adequate for progression to MM except in 15% of the patients in whom the complex subclonal deletion events are observed in MM but not MGUS. In NHMM, besides the driver translocations, clonal deletion of 13 and 1q gain are early events also observed in MGUS. We combined this information to propose a timeline for copy number alteration.

Published
2019

3. Deciphering the Chronology of Copy Number Alterations in Multiple Myeloma (MM): What Comes First?

Author

Nikhil C. Munshi, Masood A. Shammas, Anil Aktas Samur, Mehmet Kemal Samur, Hervé Avet-Loiseau, Philippe Moreau, Kenneth C. Anderson, Florence Magrangeas, Mariateresa Fulciniti, Michel Attal, Giovanni Parmigiani, Stephane Minvielle, Integrative Oncogenomics of Multiple Myeloma Pathogenesis and Progression (CRCINA-ÉQUIPE 11), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), and Bernardo, Elizabeth

Subjects
Idiopathic guttate hypomelanosis, 0303 health sciences, business.industry, Immunology, Disease progression, Chromosomal translocation, [SDV.CAN]Life Sciences [q-bio]/Cancer, Cell Biology, Hematology, medicine.disease, Biochemistry, Malignant transformation, 03 medical and health sciences, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, Cancer research, Medicine, Immunoglobulin heavy chain, business, Trisomy, Multiple myeloma, Monoclonal gammopathy of undetermined significance, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 030215 immunology
Abstract

Multiple Myeloma (MM) is characterized by genomic heterogeneity with copy number alterations (CNA) as one of the most prominent genomic perturbation. Hyperdiploidy involving chromosomes 3,5,7,9,11,15,19, and 21 is observed in nearly half of the patients, however the chronological sequence of their occurrence during MM development remains unknown. Here, we have acquired one of the largest genomic datasets from 647 patients that combines data from monoclonal gammopathy of undermined significance (MGUS) to newly diagnosed MM (336 newly diagnosed MM, 147 smoldering MM (SMM) and 164 MGUS) to characterize when and in what sequence CNA occurs in MM development. We deduce the order of CNA events by identifying their pattern of clonality basically inferring that clonal genomic change suggest its origin at an earlier stage of the disease. In hyperdiploid MM (HMM), gains in chromosome 19 (95%), 15 (90%) and 9 (90%) are the most frequent events, followed by gains in 5,11,3,7 and 21. Based on the clonality assessment the gain of chromosome 15 is the first and most frequent clonal/near clonal event, observed in 95% of HMM patients followed by Chromosome 9. Surprisingly, although chromosome 19 gain is the most frequent event overall, its clonal occurrence was lower than clonal chromosome 15 gain. More than 96% of HMM samples had concurrent gains in at least 2 of the 3 most frequent chromosomes (9,15 and 19). Moreover, less frequent events such as chromosome 21 gain, 18p gain, and 1q gain showed higher frequency of clonal/near clonal occurrence compared to other events indicating that when these events occur they are early events. Majority of the deletions occur as late subclonal events with few or none observed as clonal events. In the nonhyperdiploid MM (NHMM), del13, gain of 1q and gain of 11 had the highest frequency of clonal occurrence. Most were clonal events signifying its importance in the early stages of the disease. As all MM originates from its precursor conditions, MGUS and SMM, clonal and likely early CNAs in MM, must also exist in MGUS and SMM. So, we next investigated genomic data from SMM and MGUS for the occurrence of clonal events observed in MM. We confirmed same patterns for top MM-related CNA events in SMM and MGUS and observed no significant difference (p=0.1) between the number of events in hyperdiploid groups in MM (median=10, IQR= [8-12]) and SMM (median=9, IQR= [7-11]).To further confirm the analysis, we calculated an average clonality score for each chromosomal alteration using a 1 to 5 clonality index (1 being clonal 5 being low subclonal) in MM, SMM and MGUS and observed that similar clonal trisomies median=5, IQR=[4-6] are observed in both HMM and hyperdiploid MGUS; and that not all trisomies are required or occur at the same time. With occurrence in over 96% of cases trisomy involving chromosome 15 is central to the development of MGUS and later on MM. This is closely followed by trisomy of 9, and 19. Gain of chromosome 21 is also an early event. Major events like deletion 13 and 1q gain occur relatively later than first hyperdiploid events. NHMM on the other hand is well known to have clonal IgH-associated translocation as an initiating feature which is also observed in SMM and MGUS. However, different from HMM, it shows only few CNAs at an early stage and does not accumulate frequent additional alterations. The only exception to this rule is a deletion group observed in HMM, NHMM and SMM but not MGUS. In this deletion in over 10 whole chromosome or its p or q arm are involved as subclonal events. Its absence in MGUS suggests them to be a later event in MM development. On the other hand, number of deletions are observed at the same locations in both hyperdiploid and non-hyperdiploid groups with similar frequency. Moreover, similarity of events in this deletion groups strongly suggest that in sub group of both HMM and NHMM a similar process may be operative to induce such deletions. Our results also highlight that for both HMM and NHMM groups the major copy number events are not adequate for eventual malignant transformation since only a small fraction of MGUS patients progress to MM. Here, we describe the time line of initial copy number alterations observed in MM and confirm their early occurrence using data from a unique early stage plasma cell cases. Similarities between stages show that large scale DNA alterations happen early however some copy number hotspots are enriched over the time which could be important for disease progression. Disclosures Moreau: Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees. Anderson:Bristol Myers Squibb: Consultancy; C4 Therapeutics: Equity Ownership, Other: Scientific founder; Gilead: Membership on an entity's Board of Directors or advisory committees; OncoPep: Equity Ownership, Other: Scientific founder; Millennium Takeda: Consultancy; Celgene: Consultancy. Munshi:OncoPep: Other: Board of director.

Published
2018

4. Long intergenic non-coding RNAs have an independent impact on survival in multiple myeloma

Author

Kenneth C. Anderson, Jonathan J Keats, Paul G. Richardson, Florence Magrangeas, Mariateresa Fulciniti, Annamaria Gulla, Stephane Minvielle, Yu-Tzu Tai, Giovanni Parmigiani, Philippe Moreau, Mehmet Kemal Samur, Nikhil C. Munshi, Daniel Auclair, Raphael Szalat, Hervé Avet-Loiseau, Michel Attal, Masood A. Shammas, Anil Aktas Samur, Alice Cleynen, Dana-Farber Cancer Institute [Boston, USA], Harvard Medical School [Boston] (HMS), Integrative Oncogenomics of Multiple Myeloma Pathogenesis and Progression (CRCINA-ÉQUIPE 11), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Université de Montpellier (UM), Multiple Myeloma Research Foundation [Norwalk, CT, USA], The Translational Genomics Research Institute (TGen), Pôle Institut Universitaire du Cancer - Oncopole [CHU Toulouse] (Pôle IUC - Oncopole), CHU Toulouse [Toulouse]-Oncopole de Toulouse, VA Boston Healthcare System, NIH grants P01-155258 and P50-100707, Department of Veterans Affairs Merit Review Award I01 BX001584-01., Harvard Medical School [Boston] ( HMS ), Integrative oncogenomics of multiple myeloma pathogenesis and progression ( CRCINA - Département NOHMAD - Equipe 11 ), Centre de recherche de Cancérologie et d'Immunologie / Nantes - Angers ( CRCINA ), Université d'Angers ( UA ) -Université de Nantes ( UN ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche en Santé de l'Université de Nantes ( IRS-UN ) -Centre hospitalier universitaire de Nantes ( CHU Nantes ) -Université d'Angers ( UA ) -Université de Nantes ( UN ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche en Santé de l'Université de Nantes ( IRS-UN ) -Centre hospitalier universitaire de Nantes ( CHU Nantes ), Université de Montpellier ( UM ), The Translational Genomics Research Institute - TGen [Phoenix, AZ, USA], Pôle Institut Universitaire du Cancer - Oncopole [CHU Toulouse] ( Pôle IUC - Oncopole ), Centre Hospitalier Universitaire de Toulouse - CHU Toulouse (FRANCE)-Oncopole de Toulouse, Veterans Administration Boston Healthcare System [West Roxbury, MA, USA], Bernardo, Elizabeth, Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Adult, Male, 0301 basic medicine, Oncology, Cancer Research, medicine.medical_specialty, [SDV.CAN]Life Sciences [q-bio]/Cancer, Newly diagnosed, Article, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 03 medical and health sciences, 0302 clinical medicine, Text mining, Intergenic region, [SDV.CAN] Life Sciences [q-bio]/Cancer, Standard Risk, Internal medicine, Humans, Medicine, Clinical significance, Multiple myeloma, Aged, Framingham Risk Score, Sequence Analysis, RNA, business.industry, Hematology, Middle Aged, medicine.disease, MRD Negative, 3. Good health, 030104 developmental biology, 030220 oncology & carcinogenesis, Female, RNA, Long Noncoding, Multiple Myeloma, business
Abstract

International audience; Although long intergenic non-coding RNAs (lincRNA) role in various cancers is described, their significance in Multiple Myeloma (MM) remains poorly defined. Here we have studied the lincRNA profile and their clinical impact in MM. We performed RNA-seq on MM cells from 308 newly diagnosed and uniformly treated patients, 16 normal plasma cells and utilized RNA-seq data from 532 newly diagnosed patients from CoMMpass study to analyze for lincRNAs. We observed 869 differentially expressed lincRNAs in MM compared to normal plasma cells. We identified 14 lincRNAs associated with PFS and calculated a risk score to stratify patients. The median PFS between high vs low-risk groups was 17 months vs not-reached (NR); and OS 30 months vs NR, respectively (p < 0.0001 for both). In the independent validation dataset between high and low-risk groups, PFS was 27 vs 42 months (HR 2.06 [1.44−2.96]; p < 0.0005); and 4-year OS 62% vs 86% (HR 2.76 [1.51–5.05]; p < 0.0005) confirming significant clinical relevance of lincRNA in MM. Importantly, lincRNA signature was able to further identify patients with significant differential outcomes within each low and high-risk categories identified using standard risk categorization including cytogenetic/FISH, ISS, and MRD negative or positive. Our results suggest that lincRNAs have an independent effect on MM outcome and provide a rationale to evaluate its molecular and biological impact.

Published
2018

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