1
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Minvielle S, Letouzé E. Role and timing of chromosome deletions in multiple myeloma. Blood 2024; 144:688-689. [PMID: 39145940 DOI: 10.1182/blood.2024025269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
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2
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Cirrincione AM, Poos AM, Ziccheddu B, Kaddoura M, Bärtsch MA, Maclachlan K, Chojnacka M, Diamond B, John L, Reichert P, Huhn S, Blaney P, Gagler D, Rippe K, Zhang Y, Dogan A, Lesokhin AM, Davies F, Goldschmidt H, Fenk R, Weisel KC, Mai EK, Korde N, Morgan GJ, Usmani S, Landgren O, Raab MS, Weinhold N, Maura F. The biological and clinical impact of deletions before and after large chromosomal gains in multiple myeloma. Blood 2024; 144:771-783. [PMID: 38728430 DOI: 10.1182/blood.2024024299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/16/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
ABSTRACT Acquisition of a hyperdiploid (HY) karyotype or immunoglobulin heavy chain (IgH) translocations are considered key initiating events in multiple myeloma (MM). To explore if other genomic events can precede these events, we analyzed whole-genome sequencing data from 1173 MM samples. By integrating molecular time and structural variants within early chromosomal duplications, we indeed identified pregain deletions in 9.4% of patients with an HY karyotype without IgH translocations, challenging acquisition of an HY karyotype as the earliest somatic event. Remarkably, these deletions affected tumor suppressor genes (TSGs) and/or oncogenes in 2.4% of patients with an HY karyotype without IgH translocations, supporting their role in MM pathogenesis. Furthermore, our study points to postgain deletions as novel driver mechanisms in MM. Using multiomics approaches to investigate their biologic impact, we found associations with poor clinical outcome in newly diagnosed patients and profound effects on both the oncogene and TSG activity despite the diploid gene status. Overall, this study provides novel insights into the temporal dynamics of genomic alterations in MM.
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Affiliation(s)
- Anthony M Cirrincione
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Alexandra M Poos
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital and Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Bachisio Ziccheddu
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Marcella Kaddoura
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Marc-Andrea Bärtsch
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital and Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Monika Chojnacka
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Benjamin Diamond
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Lukas John
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital and Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Philipp Reichert
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Stefanie Huhn
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Patrick Blaney
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Dylan Gagler
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexander M Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Faith Davies
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Roland Fenk
- Department of Hematology, Oncology and Clinical Immunology, University-Hospital Duesseldorf, Duesseldorf, Germany
| | - Katja C Weisel
- Department of Oncology, Hematology, and Blood and Marrow Transplant, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elias K Mai
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Neha Korde
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gareth J Morgan
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Saad Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ola Landgren
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Marc S Raab
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital and Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Niels Weinhold
- Heidelberg Myeloma Center, Department of Medicine V, University Hospital and Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Francesco Maura
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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3
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Lazzaroni F, Matera A, Marella A, Maeda A, Castellano G, Marchetti A, Fabris S, Pioggia S, Silvestris I, Ronchetti D, Lonati S, Fabbiano G, Traini V, Taiana E, Porretti L, Colombo F, De Magistris C, Scopetti M, Barbieri M, Pettine L, Torricelli F, Neri A, Passamonti F, Lionetti M, Da Vià MC, Bolli N. Inference of genomic lesions from single-cell RNA-seq in myeloma improves functional intraclonal and interclonal analysis. Blood Adv 2024; 8:3972-3984. [PMID: 38830132 PMCID: PMC11331727 DOI: 10.1182/bloodadvances.2023012409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/30/2024] [Accepted: 05/23/2024] [Indexed: 06/05/2024] Open
Abstract
ABSTRACT Smoldering multiple myeloma (SMM) is an asymptomatic plasma cell (PC) neoplasm that may evolve with variable frequency into multiple myeloma (MM). SMM is initiated by chromosomal translocations involving the immunoglobulin heavy-chain locus or by hyperdiploidy and evolves through acquisition of additional genetic lesions. In this scenario, we aimed at establishing a reliable analysis pipeline to infer genomic lesions from transcriptomic analysis, by combining single-cell RNA sequencing (scRNA-seq) with B-cell receptor sequencing and copy number abnormality (CNA) analysis to identify clonal PCs at the genetic level along their specific transcriptional landscape. We profiled 20 465 bone marrow PCs derived from 5 patients with SMM/MM and unbiasedly identified clonal and polyclonal PCs. Hyperdiploidy, t(11;14), and t(6;14) were identified at the scRNA level by analysis of chimeric reads. Subclone functional analysis was improved by combining transcriptome with CNA analysis. As examples, we illustrate the different functional properties of a light-chain escape subclone in SMM and of different B-cell and PC subclones in a patient affected by Wäldenstrom macroglobulinemia and SMM. Overall, our data provide a proof of principle for inference of clinically relevant genotypic data from scRNA-seq, which in turn will refine functional annotation of the clonal architecture of PC dyscrasias.
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Affiliation(s)
- Francesca Lazzaroni
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Matera
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Alessio Marella
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Akihiro Maeda
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giancarlo Castellano
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alfredo Marchetti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Pioggia
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Ilaria Silvestris
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Domenica Ronchetti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Silvia Lonati
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppina Fabbiano
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Traini
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Taiana
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Porretti
- Flow Cytometry Laboratory, Clinical Pathology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Federico Colombo
- Flow Cytometry Laboratory, Clinical Pathology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Claudio De Magistris
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Margherita Scopetti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Marzia Barbieri
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Loredana Pettine
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Antonino Neri
- Scientific Directorate, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Passamonti
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Marta Lionetti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Matteo Claudio Da Vià
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Niccolò Bolli
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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4
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Ziccheddu B, Giannotta C, D'Agostino M, Bertuglia G, Saraci E, Oliva S, Genuardi E, Papadimitriou M, Diamond B, Corradini P, Coffey D, Landgren O, Bolli N, Bruno B, Boccadoro M, Massaia M, Maura F, Larocca A. Genomic and immune determinants of resistance to daratumumab-based therapy in relapsed refractory multiple myeloma. Blood Cancer J 2024; 14:117. [PMID: 39030183 PMCID: PMC11271515 DOI: 10.1038/s41408-024-01096-6] [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: 02/13/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/21/2024] Open
Abstract
Targeted immunotherapy combinations, including the anti-CD38 monoclonal antibody (MoAb) daratumumab, have shown promising results in patients with relapsed/refractory multiple myeloma (RRMM), leading to a considerable increase in progression-free survival. However, a large fraction of patients inevitably relapse. To understand this, we investigated 32 relapsed MM patients treated with daratumumab, lenalidomide, and dexamethasone (Dara-Rd; NCT03848676). We conducted an integrated analysis using whole-genome sequencing (WGS) and flow cytometry in patients with RRMM. WGS before and after treatment pinpointed genomic drivers associated with early progression, including RPL5 loss, APOBEC mutagenesis, and gain of function structural variants involving MYC and chromothripsis. Flow cytometry on 202 blood samples, collected every 3 months until progression for 31 patients, revealed distinct immune changes significantly impacting clinical outcomes. Progressing patients exhibited significant depletion of CD38-positive NK cells, persistence of T-cell exhaustion, and reduced depletion of regulatory T cells over time. These findings underscore the influence of immune composition and daratumumab-induced immune changes in promoting MM resistance. Integrating genomics and flow cytometry unveiled associations between adverse genomic features and immune patterns. Overall, this study sheds light on the intricate interplay between genomic complexity and the immune microenvironment driving resistance to Dara-Rd in patients with RRMM.
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Affiliation(s)
- Bachisio Ziccheddu
- Myeloma Division, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Claudia Giannotta
- Laboratory of Blood Tumor Immunology, Molecular Biotechnology Center "Guido Tarone", Department of Molecular Biotechnology and Health Sciences, Università di Torino, Torino, Italy
| | - Mattia D'Agostino
- Division of Hematology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Torino, Torino, Italy
| | - Giuseppe Bertuglia
- Division of Hematology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Torino, Torino, Italy
| | - Elona Saraci
- Division of Hematology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Torino, Torino, Italy
| | - Stefania Oliva
- Division of Hematology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Torino, Torino, Italy
| | - Elisa Genuardi
- Division of Hematology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Torino, Torino, Italy
| | - Marios Papadimitriou
- Myeloma Division, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Benjamin Diamond
- Myeloma Division, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Paolo Corradini
- Division of Hematology and Bone Marrow Transplant, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - David Coffey
- Myeloma Division, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Ola Landgren
- Myeloma Division, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Niccolò Bolli
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy
| | - Benedetto Bruno
- Division of Hematology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Torino, Torino, Italy
| | | | - Massimo Massaia
- Laboratory of Blood Tumor Immunology, Molecular Biotechnology Center "Guido Tarone", Department of Molecular Biotechnology and Health Sciences, Università di Torino, Torino, Italy
- SC Ematologia, AO S. Croce e Carle, Cuneo, Italy
| | - Francesco Maura
- Myeloma Division, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA.
| | - Alessandra Larocca
- Division of Hematology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Torino, Torino, Italy
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5
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Lorincz-Comi N, Yang Y, Li G, Zhu X. MRBEE: A bias-corrected multivariable Mendelian randomization method. HGG ADVANCES 2024; 5:100290. [PMID: 38582968 PMCID: PMC11053334 DOI: 10.1016/j.xhgg.2024.100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024] Open
Abstract
Mendelian randomization (MR) is an instrumental variable approach used to infer causal relationships between exposures and outcomes, which is becoming increasingly popular because of its ability to handle summary statistics from genome-wide association studies. However, existing MR approaches often suffer the bias from weak instrumental variables, horizontal pleiotropy and sample overlap. We introduce MRBEE (MR using bias-corrected estimating equation), a multivariable MR method capable of simultaneously removing weak instrument and sample overlap bias and identifying horizontal pleiotropy. Our extensive simulations and real data analyses reveal that MRBEE provides nearly unbiased estimates of causal effects, well-controlled type I error rates and higher power than comparably robust methods and is computationally efficient. Our real data analyses result in consistent causal effect estimates and offer valuable guidance for conducting multivariable MR studies, elucidating the roles of pleiotropy, and identifying total 42 horizontal pleiotropic loci missed previously that are associated with myopia, schizophrenia, and coronary artery disease.
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Affiliation(s)
- Noah Lorincz-Comi
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yihe Yang
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Gen Li
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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6
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Uryu H, Saeki K, Haeno H, Kapadia CD, Furudate K, Nangalia J, Chapman MS, Zhao L, Hsu JI, Zhao C, Chen S, Tanaka T, Li Z, Yang H, DiNardo C, Daver N, Pemmaraju N, Jain N, Ravandi F, Zhang J, Song X, Thompson E, Tang H, Little L, Gumbs C, Orlowski RZ, Qazilbash M, Bhalla K, Colla S, Kantarjian H, Shamanna RK, Ramos CB, Nakada D, Futreal PA, Shpall E, Goodell M, Garcia-Manero G, Takahashi K. Clonal evolution of hematopoietic stem cells after cancer chemotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595594. [PMID: 38826462 PMCID: PMC11142159 DOI: 10.1101/2024.05.23.595594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Normal hematopoietic stem and progenitor cells (HSPCs) inherently accumulate somatic mutations and lose clonal diversity with age, processes implicated in the development of myeloid malignancies 1 . The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal HSPCs is not well defined. We conducted whole-genome sequencing on 1,032 single-cell-derived HSPC colonies from 10 patients with multiple myeloma (MM), who had undergone various chemotherapy regimens. Our findings reveal that melphalan treatment distinctly increases mutational burden with a unique mutation signature, whereas other MM chemotherapies do not significantly affect the normal mutation rate of HSPCs. Among these therapy-induced mutations were several oncogenic drivers such as TET2 and PPM1D . Phylogenetic analysis showed a clonal architecture in post-treatment HSPCs characterized by extensive convergent evolution of mutations in genes such as TP53 and PPM1D . Consequently, the clonal diversity and structure of post-treatment HSPCs mirror those observed in normal elderly individuals, suggesting an accelerated clonal aging due to chemotherapy. Furthermore, analysis of matched therapy-related myeloid neoplasm (t-MN) samples, which occurred 1-8 years later, enabled us to trace the clonal origin of t-MNs to a single HSPC clone among a group of clones with competing malignant potential, indicating the critical role of secondary mutations in dictating clonal dominance and malignant transformation. Our findings suggest that cancer chemotherapy promotes an oligoclonal architecture with multiple HSPC clones possessing competing leukemic potentials, setting the stage for the selective emergence of a singular clone that evolves into t-MNs after acquiring secondary mutations. These results underscore the importance of further systematic research to elucidate the long-term hematological consequences of cancer chemotherapy.
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7
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Zhuk AS, Stepchenkova EI, Zotova IV, Belopolskaya OB, Pavlov YI, Kostroma II, Gritsaev SV, Aksenova AY. G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients. Int J Mol Sci 2024; 25:5269. [PMID: 38791307 PMCID: PMC11121618 DOI: 10.3390/ijms25105269] [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: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy, which remains incurable despite recent advances in treatment strategies. Like other forms of cancer, MM is characterized by genomic instability, caused by defects in DNA repair. Along with mutations in DNA repair genes and genotoxic drugs used to treat MM, non-canonical secondary DNA structures (four-stranded G-quadruplex structures) can affect accumulation of somatic mutations and chromosomal abnormalities in the tumor cells of MM patients. Here, we tested the hypothesis that G-quadruplex structures may influence the distribution of somatic mutations in the tumor cells of MM patients. We sequenced exomes of normal and tumor cells of 11 MM patients and analyzed the data for the presence of G4 context around points of somatic mutations. To identify molecular mechanisms that could affect mutational profile of tumors, we also analyzed mutational signatures in tumor cells as well as germline mutations for the presence of specific SNPs in DNA repair genes or in genes regulating G-quadruplex unwinding. In several patients, we found that sites of somatic mutations are frequently located in regions with G4 context. This pattern correlated with specific germline variants found in these patients. We discuss the possible implications of these variants for mutation accumulation and specificity in MM and propose that the extent of G4 context enrichment around somatic mutation sites may be a novel metric characterizing mutational processes in tumors.
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Affiliation(s)
- Anna S. Zhuk
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Institute of Applied Computer Science, ITMO University, 197101 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Irina V. Zotova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
| | - Olesya B. Belopolskaya
- Resource Center “Bio-Bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia;
- The Laboratory of Genogeography, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - 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
| | - Ivan I. Kostroma
- City Hospital No. 15, 198205 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | | | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
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8
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Maura F, Coffey DG, Stein CK, Braggio E, Ziccheddu B, Sharik ME, Du MT, Tafoya Alvarado Y, Shi CX, Zhu YX, Meermeier EW, Morgan GJ, Landgren O, Bergsagel PL, Chesi M. The genomic landscape of Vk*MYC myeloma highlights shared pathways of transformation between mice and humans. Nat Commun 2024; 15:3844. [PMID: 38714690 PMCID: PMC11076575 DOI: 10.1038/s41467-024-48091-w] [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: 07/12/2023] [Accepted: 04/15/2024] [Indexed: 05/10/2024] Open
Abstract
Multiple myeloma (MM) is a heterogeneous disease characterized by frequent MYC translocations. Sporadic MYC activation in the germinal center of genetically engineered Vk*MYC mice is sufficient to induce plasma cell tumors in which a variety of secondary mutations are spontaneously acquired and selected over time. Analysis of 119 Vk*MYC myeloma reveals recurrent copy number alterations, structural variations, chromothripsis, driver mutations, apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identify frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent on MYC. In summary, here we credential the Vk*MYC mouse as a unique resource to explore MM genomic evolution and describe a fully annotated collection of diverse and immortalized murine MM tumors.
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Affiliation(s)
| | - David G Coffey
- Division of Myeloma, University of Miami, Miami, FL, USA
| | - Caleb K Stein
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Esteban Braggio
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | | | - Meaghen E Sharik
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Megan T Du
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Yuliza Tafoya Alvarado
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Chang-Xin Shi
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Yuan Xiao Zhu
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Erin W Meermeier
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Gareth J Morgan
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Ola Landgren
- Division of Myeloma, University of Miami, Miami, FL, USA
| | - P Leif Bergsagel
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Marta Chesi
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA.
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9
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Grasedieck S, Panahi A, Jarvis MC, Borzooee F, Harris RS, Larijani M, Avet-Loiseau H, Samur M, Munshi N, Song K, Rouhi A, Kuchenbauer F. Redefining high risk multiple myeloma with an APOBEC/Inflammation-based classifier. Leukemia 2024; 38:1172-1177. [PMID: 38461190 PMCID: PMC11073955 DOI: 10.1038/s41375-024-02210-0] [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: 07/26/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/11/2024]
Affiliation(s)
- Sarah Grasedieck
- Department of Microbiology and Immunology, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada
| | - Afsaneh Panahi
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, NC, USA
| | - Faezeh Borzooee
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | | | - Mehmet Samur
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nikhil Munshi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kevin Song
- Leukemia/Bone Marrow Transplant Program of British Columbia, Vancouver General Hospital, BC Cancer, Vancouver, BC, Canada
| | - Arefeh Rouhi
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Florian Kuchenbauer
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC, Canada.
- Leukemia/Bone Marrow Transplant Program of British Columbia, Vancouver General Hospital, BC Cancer, Vancouver, BC, Canada.
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10
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Song JH, Dávalos LM, MacCarthy T, Damaghi M. Evolvability of cancer-associated genes under APOBEC3A/B selection. iScience 2024; 27:109433. [PMID: 38550998 PMCID: PMC10972820 DOI: 10.1016/j.isci.2024.109433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/08/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and genetic variation. Mutations generated by APOBEC3 contribute to genetic variation and tumor evolvability. However, the influence of APOBEC3 on the evolvability of the genome and its differential impact on cancer genes versus non-cancer genes remains unclear. Analyzing over 40,000 human protein-coding transcripts, we identified distinct distribution patterns of APOBEC3A/B TC motifs between cancer and non-cancer genes, suggesting unique associations with cancer. Studying a bat species with numerous APOBEC3 genes, we found distinct motif patterns in orthologs of cancer genes compared to non-cancer genes, as in humans, suggesting APOBEC3 evolution to reduce impacts on the genome rather than the converse. Simulations confirmed that APOBEC3-induced heterogeneity enhances cancer evolution through bimodal patterns of mutations in certain classes of genes. Our results suggest the bimodal distribution of APOBEC-induced mutations can significantly increase cancer heterogeneity.
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Affiliation(s)
- Joon-Hyun Song
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY 11794, USA
| | - Thomas MacCarthy
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Mehdi Damaghi
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
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11
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Dhodapkar MV. Immune-Pathogenesis of Myeloma. Hematol Oncol Clin North Am 2024; 38:281-291. [PMID: 38195307 DOI: 10.1016/j.hoc.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
This research indicates that monoclonal gammopathy of undetermined significance (MGUS) and myeloma may stem from chronic immune activation and inflammation, causing immune dysfunction and spatial immune exclusion. As the conditions progress, a shift toward myeloma involves ongoing immune impairment, affecting both innate and adaptive immunity. Intriguingly, even in advanced myeloma stages, susceptibility to immune effector cells persists. This insight highlights the intricate interplay between immune responses and the development of these conditions, paving the way for potential therapeutic interventions targeting immune modulation in the management of MGUS and myeloma.
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Affiliation(s)
- Madhav V Dhodapkar
- Department of Hematology/Medical Oncology, Emory University, Winship Cancer Institute, 1365 Clifton Road, Atlanta, GA 30332, USA.
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12
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Maura F, Bergsagel PL. Molecular Pathogenesis of Multiple Myeloma: Clinical Implications. Hematol Oncol Clin North Am 2024; 38:267-279. [PMID: 38199896 DOI: 10.1016/j.hoc.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Multiple myeloma is a malignancy of bone-marrow-localized, isotype-switched plasma cells that secrete a monoclonal immunoglobulin and cause hyperCalcemia, Anemia, Renal failure, and lytic Bone disease. It is preceded, often for decades, by a relatively stable monoclonal gammopathy lacking these clinical and malignant features. Both conditions are characterized by the presence of types of immunoglobulin heavy gene translocations that dysregulate a cyclin D family gene on 11q13 (CCND1), 6p21 (CCND3), or 12q11 (CCND2), a maf family gene on 16q23 (MAF), 20q11 (MAFB), or 8q24 (MAFA), or NSD2/FGFR3 on 4p16, or the presence of hyperdiploidy. Subsequent loss of function of tumor suppressor genes and mutations activating MYC, RAS, NFkB, and cell cycle pathways are associated with the progression to malignant disease.
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Affiliation(s)
- Francesco Maura
- University of Miami, 1120 Northwest 14th Street, Miami, FL 33136, USA.
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13
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Chen X, Varma G, Davies F, Morgan G. Approach to High-Risk Multiple Myeloma. Hematol Oncol Clin North Am 2024; 38:497-510. [PMID: 38195306 DOI: 10.1016/j.hoc.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Improving the outcome of high-risk myeloma (HRMM) is a key therapeutic aim for the next decade. To achieve this aim, it is necessary to understand in detail the genetic drivers underlying this clinical behavior and to target its biology therapeutically. Advances have already been made, with a focus on consensus guidance and the application of novel immunotherapeutic approaches. Cases of HRMM are likely to have impaired prognosis even with novel strategies. However, if disease eradication and minimal disease states are achieved, then cure may be possible.
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Affiliation(s)
- Xiaoyi Chen
- Center Blood Cancer, Perlmutter Cancer Center, New York University, NYCLangone, Room# 496, Medical Science Building 4th Floor, 540 1st Avenue, New York, NY 10016, USA
| | - Gaurav Varma
- Center Blood Cancer, Perlmutter Cancer Center, New York University, NYCLangone, Room# 496, Medical Science Building 4th Floor, 540 1st Avenue, New York, NY 10016, USA
| | - Faith Davies
- Center Blood Cancer, Perlmutter Cancer Center, New York University, NYCLangone, Room# 496, Medical Science Building 4th Floor, 540 1st Avenue, New York, NY 10016, USA
| | - Gareth Morgan
- Center Blood Cancer, Perlmutter Cancer Center, New York University, NYCLangone, Room# 496, Medical Science Building 4th Floor, 540 1st Avenue, New York, NY 10016, USA.
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14
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Yamada M, Keller RR, Gutierrez RL, Cameron D, Suzuki H, Sanghrajka R, Vaynshteyn J, Gerwin J, Maura F, Hooper W, Shah M, Robine N, Demarest P, Bayin NS, Zapater LJ, Reed C, Hébert S, Masilionis I, Chaligne R, Socci ND, Taylor MD, Kleinman CL, Joyner AL, Raju GP, Kentsis A. Childhood cancer mutagenesis caused by transposase-derived PGBD5. SCIENCE ADVANCES 2024; 10:eadn4649. [PMID: 38517960 PMCID: PMC10959420 DOI: 10.1126/sciadv.adn4649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, some of which carry PGBD5-specific sequences at their breakpoints. Similar sequence breakpoints recurrently affect somatic DNA rearrangements of known tumor suppressors and oncogenes in medulloblastomas in 329 children. This identifies PGBD5 as a medulloblastoma mutator and provides a genetic mechanism for the generation of oncogenic DNA rearrangements in childhood cancer.
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Affiliation(s)
- Makiko Yamada
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Ross R. Keller
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Daniel Cameron
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Reeti Sanghrajka
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Jake Vaynshteyn
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Gerwin
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - William Hooper
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Minita Shah
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Nicolas Robine
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Phillip Demarest
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge, UK
| | - Luz Jubierre Zapater
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Casie Reed
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ignas Masilionis
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D. Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael D. Taylor
- Department of Pediatrics—Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, USA
- Hematology-Oncology Section, Texas Children’s Cancer Center, Houston, TX, USA
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Claudia L. Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program and Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - G. Praveen Raju
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Kentsis
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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15
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Bravo-Perez C, Gurnari C. A tower of babel of acronyms? The shadowlands of MGUS/MBL/CHIP/TCUS. Semin Hematol 2024; 61:43-50. [PMID: 38350765 DOI: 10.1053/j.seminhematol.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
With the advent of outperforming and massive laboratory tools, such as multiparameter flow cytometry and next-generation sequencing, hematopoietic cell clones with putative abnormalities for a variety of blood malignancies have been appreciated in otherwise healthy individuals. These conditions do not fulfill the criteria of their presumed cancer counterparts, and thus have been recognized as their precursor states. This is the case of monoclonal gammopathy of unknown significance (MGUS), the first blood premalignancy state described, preceding multiple myeloma (MM) or Waldenström macroglobulinemia (WM). However, in the last 2 decades, an increasing list of clonopathies has been recognized, including monoclonal B cell lymphocytosis (MBL), which antecedes chronic lymphocytic leukemia (CLL), clonal hematopoiesis of indeterminate potential (CHIP) for myeloid neoplasms (MN), and T-cell clones of uncertain significance (TCUS) for T-cell large chronic lymphocytic leukemia (LGLL). While for some of these entities diagnostic boundaries are precisely set, for others these are yet to be fully defined. Moreover, despite mostly considered of "uncertain significance," they have not only appeared to predispose to malignancy, but also to be capable of provoking set of immunological and cardiovascular complications that may require specialized management. The clinical implications of the aberrant clones, together with the extensive knowledge generated on the pathogenetic events driving their evolution, raises the question whether earlier interventions may alter the natural history of the disease. Herein, we review this Tower of Babel of acronyms pinpointing diagnostic definitions, differential diagnosis, and the role of genomic profiling of these precursor states, as well as potential interventional strategies.
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Affiliation(s)
- Carlos Bravo-Perez
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Department of Hematology and Medical Oncology, Hospital Universitario Morales Meseguer, University of Murcia, IMIB-Pascual Parrilla, CIBERER - Instituto de Salud Carlos III, Murcia, Spain
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy.
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16
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Gong L, Qiu L, Hao M. Novel Insights into the Initiation, Evolution, and Progression of Multiple Myeloma by Multi-Omics Investigation. Cancers (Basel) 2024; 16:498. [PMID: 38339250 PMCID: PMC10854875 DOI: 10.3390/cancers16030498] [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: 12/05/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
The evolutionary history of multiple myeloma (MM) includes malignant transformation, followed by progression to pre-malignant stages and overt malignancy, ultimately leading to more aggressive and resistant forms. Over the past decade, large effort has been made to identify the potential therapeutic targets in MM. However, MM remains largely incurable. Most patients experience multiple relapses and inevitably become refractory to treatment. Tumor-initiating cell populations are the postulated population, leading to the recurrent relapses in many hematological malignancies. Clonal evolution of tumor cells in MM has been identified along with the disease progression. As a consequence of different responses to the treatment of heterogeneous MM cell clones, the more aggressive populations survive and evolve. In addition, the tumor microenvironment is a complex ecosystem which plays multifaceted roles in supporting tumor cell evolution. Emerging multi-omics research at single-cell resolution permits an integrative and comprehensive profiling of the tumor cells and microenvironment, deepening the understanding of biological features of MM. In this review, we intend to discuss the novel insights into tumor cell initiation, clonal evolution, drug resistance, and tumor microenvironment in MM, as revealed by emerging multi-omics investigations. These data suggest a promising strategy to unravel the pivotal mechanisms of MM progression and enable the improvement in treatment, both holistically and precisely.
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Affiliation(s)
- Lixin Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin 300020, China;
- Tianjin Institutes of Health Science, Tianjin 300020, China
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin 300020, China;
- Tianjin Institutes of Health Science, Tianjin 300020, China
- Gobroad Healthcare Group, Beijing 100072, China
| | - Mu Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin 300020, China;
- Tianjin Institutes of Health Science, Tianjin 300020, China
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17
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Song JH, Dávalos LM, MacCarthy T, Damaghi M. Evolvability of cancer-associated genes under APOBEC3A/B selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.27.554991. [PMID: 38106028 PMCID: PMC10723265 DOI: 10.1101/2023.08.27.554991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and, ultimately, genetic variation. Mutations generated by APOBEC3 cytidine deaminases can contribute to genetic variation and the consequences of APOBEC activation differ depending on the stage of cancer, with the most significant impact observed during the early stages. However, how APOBEC activity shapes evolutionary patterns of genes in the host genome and differential impacts on cancer-associated and non-cancer genes remain unclear. Analyzing over 40,000 human protein-coding transcripts, we identified distinct distribution patterns of APOBEC3A/B TC motifs between cancer-related genes and controls, suggesting unique associations with cancer. Studying a bat species with many more APOBEC3 genes, we found diverse motif patterns in orthologs of cancer genes compared to controls, similar to humans and suggesting APOBEC evolution to reduce impacts on the genome rather than the converse. Simulations confirmed that APOBEC-induced heterogeneity enhances cancer evolution, shaping clonal dynamics through bimodal introduction of mutations in certain classes of genes. Our results suggest that a major consequence of the bimodal distribution of APOBEC affects greater cancer heterogeneity.
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Affiliation(s)
- Joon-Hyun Song
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Liliana M. Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Thomas MacCarthy
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Mehdi Damaghi
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
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18
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Mo CC, Hartley-Brown MA, Midha S, Richardson PG. Upfront or Deferred Autologous Stem Cell Transplantation for Newly Diagnosed Multiple Myeloma in the Era of Triplet and Quadruplet Induction and Minimal Residual Disease/Risk-Adapted Therapy. Cancers (Basel) 2023; 15:5709. [PMID: 38136255 PMCID: PMC10741557 DOI: 10.3390/cancers15245709] [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: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
The standards of care for the initial treatment of patients with newly diagnosed multiple myeloma (NDMM) who are eligible for high-dose melphalan and autologous stem cell transplantation (HDM-ASCT) include highly active triplet and quadruplet regimens based on proteasome inhibitors, immunomodulatory drugs, and monoclonal antibodies. These regimens are resulting in improved outcomes and increasingly high rates of minimal residual disease (MRD)-negative responses without HDM-ASCT as part of the upfront therapy. Furthermore, recent randomized studies have shown that, while transplant-based approaches as a frontline therapy result in significantly longer progression-free survival compared to non-transplant approaches, this has not translated into an overall survival benefit. Given these developments, and in the context of the treatment burden of undergoing HDM-ASCT, in addition to the acute toxicities and long-term sequelae of HDM, which are associated with the genotoxicity of melphalan, there is an increasing rationale for considering deferring upfront HDM-ASCT in select transplant-eligible patients and saving it as a treatment option for later salvage therapy. Here, we review the latest clinical trial data on upfront or deferred HDM-ASCT and on the activity of quadruplet induction regimens, including rates of MRD-negative responses, and summarize emerging treatment approaches in the upfront setting such as the use of MRD-directed therapy and alternatives to HDM-ASCT.
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Affiliation(s)
| | | | | | - Paul G. Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Jerome Lipper Center for Multiple Myeloma Research, Harvard Medical School, 450 Brookline Avenue, Dana 1B02, Boston, MA 02115, USA; (C.C.M.); (M.A.H.-B.); (S.M.)
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19
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Ziccheddu B, Giannotta C, D'Agostino M, Bertuglia G, Saraci E, Oliva S, Genuardi E, Papadimitriou M, Diamond B, Corradini P, Coffey D, Landgren O, Bolli N, Bruno B, Boccadoro M, Massaia M, Maura F, Larocca A. Genomic and immune determinants of resistance to anti-CD38 monoclonal antibody-based therapy in relapsed refractory multiple myeloma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.04.23299287. [PMID: 38106151 PMCID: PMC10723485 DOI: 10.1101/2023.12.04.23299287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Anti-CD38 antibody therapies have transformed multiple myeloma (MM) treatment. However, a large fraction of patients inevitably relapses. To understand this, we investigated 32 relapsed MM patients treated with daratumumab, lenalidomide, and dexamethasone (Dara-Rd; NCT03848676 ). Whole genome sequencing (WGS) before and after treatment pinpointed genomic drivers associated with early progression, including RPL5 loss and APOBEC mutagenesis. Flow cytometry on 202 blood samples, collected every three months until progression for 31 patients, revealed distinct immune changes significantly impacting clinical outcomes. Progressing patients exhibited significant depletion of CD38+ NK cells, persistence of T cell exhaustion, and reduced depletion of T-reg cells over time. These findings underscore the influence of immune composition and daratumumab-induced immune changes in promoting MM resistance. Integrating genomics and flow cytometry unveiled associations between adverse genomic features and immune patterns. Overall, this study sheds light on the intricate interplay between genomic complexity and the immune microenvironment driving resistance to Dara-Rd.
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20
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Köhrer S, Dittrich T, Schorb M, Weinhold N, Haberbosch I, Börmel M, Pajor G, Goldschmidt H, Müller-Tidow C, Raab MS, John L, Seckinger A, Brobeil A, Dreger P, Tornóczky T, Pajor L, Hegenbart U, Schönland SO, Schwab Y, Krämer A. High-throughput electron tomography identifies centriole over-elongation as an early event in plasma cell disorders. Leukemia 2023; 37:2468-2478. [PMID: 37821581 PMCID: PMC10681902 DOI: 10.1038/s41375-023-02056-y] [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: 08/02/2023] [Revised: 09/14/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023]
Abstract
Plasma cell disorders are clonal outgrowths of pre-malignant or malignant plasma cells, characterized by extensive chromosomal aberrations. Centrosome abnormalities are a major driver of chromosomal instability in cancer but their origin, incidence, and composition in primary tumor cells is poorly understood. Using cutting-edge, semi-automated high-throughput electron tomography, we characterized at nanoscale 1386 centrioles in CD138pos plasma cells from eight healthy donors and 21 patients with plasma cell disorders, and 722 centrioles from different control populations. In plasma cells from healthy individuals, over-elongated centrioles accumulated with age. In plasma cell disorders, centriole over-elongation was notably frequent in early, pre-malignant disease stages, became less pronounced in overt multiple myeloma, and almost entirely disappeared in aggressive plasma cell leukemia. Centrioles in other types of patient-derived B cell neoplasms showed no over-elongation. In contrast to current belief, centriole length appears to be highly variable in long-lived, healthy plasma cells, and over-elongation and structural aberrations are common in this cell type. Our data suggest that structural centrosome aberrations accumulate with age in healthy CD138pos plasma cells and may thus play an important role in early aneuploidization as an oncogenic driver in plasma cell disorders.
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Affiliation(s)
- Sebastian Köhrer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tobias Dittrich
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Isabella Haberbosch
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Mandy Börmel
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Gabor Pajor
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Pathology, University of Pécs Medical School and Clinic, Pécs, Hungary
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, GMMG-Studygroup at University of Heidelberg, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Marc S Raab
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Lukas John
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Anja Seckinger
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Alexander Brobeil
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Peter Dreger
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Tamás Tornóczky
- Department of Pathology, University of Pécs Medical School and Clinic, Pécs, Hungary
| | - László Pajor
- Department of Pathology, University of Pécs Medical School and Clinic, Pécs, Hungary
| | - Ute Hegenbart
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Stefan O Schönland
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
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21
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Maura F, Boyle EM, Coffey D, Maclachlan K, Gagler D, Diamond B, Ghamlouch H, Blaney P, Ziccheddu B, Cirrincione A, Chojnacka M, Wang Y, Siegel A, Hoffman JE, Kazandjian D, Hassoun H, Guzman E, Mailankody S, Shah UA, Tan C, Hultcrantz M, Scordo M, Shah GL, Landau H, Chung DJ, Giralt S, Zhang Y, Arbini A, Gao Q, Roshal M, Dogan A, Lesokhin AM, Davies FE, Usmani SZ, Korde N, Morgan GJ, Landgren O. Genomic and immune signatures predict clinical outcome in newly diagnosed multiple myeloma treated with immunotherapy regimens. NATURE CANCER 2023; 4:1660-1674. [PMID: 37945755 DOI: 10.1038/s43018-023-00657-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 09/20/2023] [Indexed: 11/12/2023]
Abstract
Despite improving outcomes, 40% of patients with newly diagnosed multiple myeloma treated with regimens containing daratumumab, a CD38-targeted monoclonal antibody, progress prematurely. By integrating tumor whole-genome and microenvironment single-cell RNA sequencing from upfront phase 2 trials using carfilzomib, lenalidomide and dexamethasone with daratumumab ( NCT03290950 ), we show how distinct genomic drivers including high APOBEC mutational activity, IKZF3 and RPL5 deletions and 8q gain affect clinical outcomes. Furthermore, evaluation of paired bone marrow profiles, taken before and after eight cycles of carfilzomib, lenalidomide and dexamethasone with daratumumab, shows that numbers of natural killer cells before treatment, high T cell receptor diversity before treatment, the disappearance of sustained immune activation (that is, B cells and T cells) and monocyte expansion over time are all predictive of sustained minimal residual disease negativity. Overall, this study provides strong evidence of a complex interplay between tumor cells and the immune microenvironment that is predictive of clinical outcome and depth of treatment response in patients with newly diagnosed multiple myeloma treated with highly effective combinations containing anti-CD38 antibodies.
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Affiliation(s)
- Francesco Maura
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
| | - Eileen M Boyle
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - David Coffey
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dylan Gagler
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Benjamin Diamond
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Hussein Ghamlouch
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Patrick Blaney
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Bachisio Ziccheddu
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Anthony Cirrincione
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Monika Chojnacka
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Yubao Wang
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Ariel Siegel
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - James E Hoffman
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Dickran Kazandjian
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Hani Hassoun
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Guzman
- Genome Technology Center, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Sham Mailankody
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Urvi A Shah
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Carlyn Tan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Malin Hultcrantz
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Michael Scordo
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunjan L Shah
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Heather Landau
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J Chung
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergio Giralt
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaldo Arbini
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Qi Gao
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander M Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Faith E Davies
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Saad Z Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Neha Korde
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Gareth J Morgan
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA.
| | - Ola Landgren
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
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22
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Poos AM, Prokoph N, Przybilla MJ, Mallm JP, Steiger S, Seufert I, John L, Tirier SM, Bauer K, Baumann A, Rohleder J, Munawar U, Rasche L, Kortüm KM, Giesen N, Reichert P, Huhn S, Müller-Tidow C, Goldschmidt H, Stegle O, Raab MS, Rippe K, Weinhold N. Resolving therapy resistance mechanisms in multiple myeloma by multiomics subclone analysis. Blood 2023; 142:1633-1646. [PMID: 37390336 PMCID: PMC10733835 DOI: 10.1182/blood.2023019758] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/17/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023] Open
Abstract
Intratumor heterogeneity as a clinical challenge becomes most evident after several treatment lines, when multidrug-resistant subclones accumulate. To address this challenge, the characterization of resistance mechanisms at the subclonal level is key to identify common vulnerabilities. In this study, we integrate whole-genome sequencing, single-cell (sc) transcriptomics (scRNA sequencing), and chromatin accessibility (scATAC sequencing) together with mitochondrial DNA mutations to define subclonal architecture and evolution for longitudinal samples from 15 patients with relapsed or refractory multiple myeloma. We assess transcriptomic and epigenomic changes to resolve the multifactorial nature of therapy resistance and relate it to the parallel occurrence of different mechanisms: (1) preexisting epigenetic profiles of subclones associated with survival advantages, (2) converging phenotypic adaptation of genetically distinct subclones, and (3) subclone-specific interactions of myeloma and bone marrow microenvironment cells. Our study showcases how an integrative multiomics analysis can be applied to track and characterize distinct multidrug-resistant subclones over time for the identification of molecular targets against them.
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Affiliation(s)
- Alexandra M. Poos
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Nina Prokoph
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Moritz J. Przybilla
- Division Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Isabelle Seufert
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Lukas John
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Stephan M. Tirier
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Katharina Bauer
- Single Cell Open Lab, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Anja Baumann
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Jennifer Rohleder
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Umair Munawar
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Leo Rasche
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
| | - K. Martin Kortüm
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Nicola Giesen
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Philipp Reichert
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefanie Huhn
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, Heidelberg, Germany
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, GMMG-Study Group at University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver Stegle
- Division Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc S. Raab
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, University Hospital Heidelberg, Heidelberg, Germany
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23
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Sharma NS, Choudhary B. Good Cop, Bad Cop: Profiling the Immune Landscape in Multiple Myeloma. Biomolecules 2023; 13:1629. [PMID: 38002311 PMCID: PMC10669790 DOI: 10.3390/biom13111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/26/2023] Open
Abstract
Multiple myeloma (MM) is a dyscrasia of plasma cells (PCs) characterized by abnormal immunoglobulin (Ig) production. The disease remains incurable due to a multitude of mutations and structural abnormalities in MM cells, coupled with a favorable microenvironment and immune suppression that eventually contribute to the development of drug resistance. The bone marrow microenvironment (BMME) is composed of a cellular component comprising stromal cells, endothelial cells, osteoclasts, osteoblasts, and immune cells, and a non-cellular component made of the extracellular matrix (ECM) and the liquid milieu, which contains cytokines, growth factors, and chemokines. The bone marrow stromal cells (BMSCs) are involved in the adhesion of MM cells, promote the growth, proliferation, invasion, and drug resistance of MM cells, and are also crucial in angiogenesis and the formation of lytic bone lesions. Classical immunophenotyping in combination with advanced immune profiling using single-cell sequencing technologies has enabled immune cell-specific gene expression analysis in MM to further elucidate the roles of specific immune cell fractions from peripheral blood and bone marrow (BM) in myelomagenesis and progression, immune evasion and exhaustion mechanisms, and development of drug resistance and relapse. The review describes the role of BMME components in MM development and ongoing clinical trials using immunotherapeutic approaches.
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Affiliation(s)
- Niyati Seshagiri Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic City, Bengaluru 560100, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic City, Bengaluru 560100, India
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24
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Huber JH, Ji M, Shih YH, Wang M, Colditz G, Chang SH. Disentangling age, gender, and racial/ethnic disparities in multiple myeloma burden: a modeling study. Nat Commun 2023; 14:5768. [PMID: 37730703 PMCID: PMC10511740 DOI: 10.1038/s41467-023-41223-8] [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: 12/17/2022] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy that is consistently preceded by an asymptomatic condition, monoclonal gammopathy of undetermined significance (MGUS). Disparities by age, gender, and race/ethnicity in both MGUS and MM are well-established. However, it remains unclear whether these disparities can be explained by increased incidence of MGUS and/or accelerated progression from MGUS to MM. Here, we fit a mathematical model to nationally representative data from the United States and showed that the difference in MM incidence can be explained by an increased incidence of MGUS among male and non-Hispanic Black populations. We did not find evidence showing differences in the rate of progression from MGUS to MM by either gender or race/ethnicity. Our results suggest that screening for MGUS among high-risk groups (e.g., non-Hispanic Black men) may hold promise as a strategy to reduce the burden and MM health disparities.
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Affiliation(s)
- John H Huber
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA.
| | - Mengmeng Ji
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi-Hsuan Shih
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Mei Wang
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Graham Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Su-Hsin Chang
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
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25
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Coffey DG, Maura F, Gonzalez-Kozlova E, Diaz-Mejia JJ, Luo P, Zhang Y, Xu Y, Warren EH, Dawson T, Lee B, Xie H, Smith E, Ciardiello A, Cho HJ, Rahman A, Kim-Schulze S, Diamond B, Lesokhin A, Kazandjian D, Pugh TJ, Green DJ, Gnjatic S, Landgren O. Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma. Nat Commun 2023; 14:5335. [PMID: 37660077 PMCID: PMC10475030 DOI: 10.1038/s41467-023-40966-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/18/2023] [Indexed: 09/04/2023] Open
Abstract
The role of the immune microenvironment in maintaining disease remission in patients with multiple myeloma (MM) is not well understood. In this study, we comprehensively profile the immune system in patients with newly diagnosed MM receiving continuous lenalidomide maintenance therapy with the aim of discovering correlates of long-term treatment response. Leveraging single-cell RNA sequencing and T cell receptor β sequencing of the peripheral blood and CyTOF mass cytometry of the bone marrow, we longitudinally characterize the immune landscape in 23 patients before and one year after lenalidomide exposure. We compare patients achieving sustained minimal residual disease (MRD) negativity to patients who never achieved or were unable to maintain MRD negativity. We observe that the composition of the immune microenvironment in both the blood and the marrow varied substantially according to both MRD negative status and history of autologous stem cell transplant, supporting the hypothesis that the immune microenvironment influences the depth and duration of treatment response.
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Affiliation(s)
- David G Coffey
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Francesco Maura
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | | | - J Javier Diaz-Mejia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yong Zhang
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Yuexin Xu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Edus H Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Travis Dawson
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Lee
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Smith
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Ciardiello
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hearn J Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Multiple Myeloma Research Foundation, Norwalk, USA
| | - Adeeb Rahman
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Benjamin Diamond
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Alexander Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dickran Kazandjian
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Damian J Green
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ola Landgren
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
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26
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Liu J, Yan W, Fan H, Xu J, Li L, Du C, Mao X, Yan Y, Xu Y, Sui W, Deng S, Yi S, Anderson KC, Qiu L, Zou D, An G. Clinical Benefit of Autologous Stem Cell Transplantation for Patients with Multiple Myeloma Achieving Undetectable Minimal Residual Disease after Induction Treatment. CANCER RESEARCH COMMUNICATIONS 2023; 3:1770-1780. [PMID: 37680953 PMCID: PMC10481879 DOI: 10.1158/2767-9764.crc-23-0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 09/09/2023]
Abstract
Attaining undetectable minimal residual disease (MRD) is the current therapeutic goal for multiple myeloma. But there is a current lack of data regarding the clinical benefit of autologous stem cell transplantation (ASCT) for patients with myeloma achieving early MRD-negative status after induction treatment, in addition to the interaction of longitudinal MRD status with ASCT. The current study included 407 patients with transplant-eligible multiple myeloma with available MRD status from the National Longitudinal Cohort of Hematological Diseases in China (NCT04645199), of whom 147 (34.4%) achieved early undetectable MRD and 182 (44.7%) received ASCT. Early MRD-negative status was associated with a lower risk of disease progression [HR = 0.447; 95% confidence interval (CI), 0.333-0.600; P < 0.001] and death (HR = 0.473; 95% CI, 0.320-0.700; P < 0.001). Of note, patients who achieved undetectable MRD early still benefitted from ASCT, with a remarkable improvement in the median MRD-negative duration (33.5-58.0 months, P < 0.001), progression-free survival (PFS; 46.0-88.3 months, P < 0.001), and overall survival (OS; 76.4 months to not reached, P = 0.003). These clinical benefits were more pronounced in patients with aggressive features (high-risk cytogenetic abnormalities or high tumor burden) compared with standard-risk patients. Similar results were observed in patients with detectable MRD after induction treatment. In addition, we identified four MRD-status transformation patterns following ASCT, which were strongly correlated with diverse survival outcomes (P < 0.001). Our study revealed the enhanced clinical significance of ASCT in patients with transplant-eligible myeloma, regardless of early MRD status, particularly for high-risk patients. Subsequent prospective trials are essential to validate these observations. Significance Achieving and maintaining undetectable MRD is the current treatment goal for multiple myeloma. Our results emphasized the remarkable clinical benefit of ASCT on MRD-negative duration, PFS, and OS in patients with multiple myeloma regardless of early MRD status. These favorable impacts were more evident in patients with aggressive features. Importantly, dynamic MRD monitoring among ASCT could facilitate personalized stratification of therapeutic approaches.
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Affiliation(s)
- Jiahui Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, P.R. China
| | - Wenqiang Yan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Huishou Fan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Jingyu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Lingna Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Chenxing Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Xuehan Mao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Yuting Yan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Yan Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Weiwei Sui
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Shuhui Deng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Shuhua Yi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Kenneth C. Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Dehui Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
| | - Gang An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
- Tianjin Institutes of Health Science, Tianjin, P.R. China
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27
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Maura F, Coffey DG, Stein CK, Braggio E, Ziccheddu B, Sharik ME, Du M, Alvarado YT, Shi CX, Zhu YX, Meermeier EW, Morgan GJ, Landgren O, Leif Bergsagel P, Chesi M. The Vk*MYC Mouse Model recapitulates human multiple myeloma evolution and genomic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550482. [PMID: 37546905 PMCID: PMC10402028 DOI: 10.1101/2023.07.25.550482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Despite advancements in profiling multiple myeloma (MM) and its precursor conditions, there is limited information on mechanisms underlying disease progression. Clincal efforts designed to deconvolute such mechanisms are challenged by the long lead time between monoclonal gammopathy and its transformation to MM. MM mouse models represent an opportunity to overcome this temporal limitation. Here, we profile the genomic landscape of 118 genetically engineered Vk*MYC MM and reveal that it recapitulates the genomic heterogenenity and life history of human MM. We observed recurrent copy number alterations, structural variations, chromothripsis, driver mutations, APOBEC mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identified frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent on MYC expression, that drives the progression of monoclonal gammopathy to MM.
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28
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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29
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Semenzato G, Ghobrial IM, Ghia P. Monoclonal B-cell lymphocytosis, monoclonal gammopathy of undetermined significance, and T-cell clones of uncertain significance: are these premalignant conditions sharing a common identity? Lancet Haematol 2023; 10:e549-e556. [PMID: 37407144 DOI: 10.1016/s2352-3026(23)00086-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 07/07/2023]
Abstract
Monoclonal B-cell lymphocytosis, monoclonal gammopathy of undetermined significance, and T-cell clones of uncertain significance are three premalignant conditions characterised by the presence of small clonal cell expansions in individuals without symptoms or signs that distinguish the related overt malignancies (chronic lymphocytic leukaemia, multiple myeloma, and T-cell large granular lymphocytic leukaemia). As most individuals with these precursor states never progress to malignancies, considerable interest has arisen in comprehending the steps involved in the progression to malignancy, providing more accurate models to investigate potential mechanisms of early blood cancer identification, prevention, and, possibly, intervention. Single-cell technologies and recent progress in high-throughput sequencing and multiomics approaches have contributed to a better definition of the pathophysiological mechanisms of these premalignant conditions, moving our knowledge in the field forward. In this Viewpoint, we analyse the seemingly shared biological trajectories in these precursor haematological malignancies in search of common pathogenetic events. In particular, we address the issue of interactions between expanding clones and their immune ecosystem, offering new clues that might prompt innovative ideas and inspire further investigations to understand the cellular and molecular dynamics entailing progression into overt malignant disease. The relationships between the non-leukaemic microenvironmental cells and the leukaemic counterpart, and the primary drivers of their initial clonal expansion, represent shared biologies that suggest a common identity among the premalignant conditions considered in this Viewpoint.
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Affiliation(s)
- Gianpietro Semenzato
- Haematology Section, Department of Medicine, University of Padova, Padua, Italy; Veneto Institute of Molecular Medicine, Padua, Italy.
| | | | - Paolo Ghia
- Vita-Salute San Raffaele University, Milan, Italy; IRCCS San Raffaele Hospital, Milan, Italy
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30
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Zhang Q, Duan H, Yang W, Liu H, Tao X, Zhang Y. Circ_0005615 restrains the progression of multiple myeloma through modulating miR-331-3p and IGF1R regulatory cascade. J Orthop Surg Res 2023; 18:356. [PMID: 37173768 PMCID: PMC10176712 DOI: 10.1186/s13018-023-03832-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Circular RNAs are implicated in modulating the progression of various malignant tumors. However, the function and underlying mechanisms of circ_0005615 in multiple myeloma (MM) remain unclear. METHODS The expression levels of circ_0005615, miR-331-3p and IGF1R were tested by quantitative real-time polymerase chain reaction or western blot assay. Cell counting kit-8 and 5-ethynyl-2'-deoxyuridine (EdU) assay were performed for cell proliferation detection. Cell apoptosis and cell cycle were measured by flow cytometry. The protein expressions of Bax and Bcl-2 were detected by western blot assay. Glucose consumption, lactate production and ATP/ADP ratios were estimated to disclose cell glycolysis. The interaction relationship among miR-331-3p and circ_0005615 or IGF1R was proved by dual-luciferase reporter assay. RESULTS The abundance of circ_0005615 and IGF1R was increased in MM patients and cells, while the expression of miR-331-3p was decreased. Circ_0005615 inhibition retarded the proliferation and cell cycle progression, while reinforced the apoptosis of MM cells. Molecularly, circ_0005615 could sponge miR-331-3p, and the repressive trends of circ_0005615 deficiency on MM progression could be alleviated by anti-miR-331-3p introduction. Additionally, IGF1R was validated to be targeted by miR-331-3p, and IGF1R overexpression mitigated the suppressive function of miR-331-3p on MM development. Furthermore, IGF1R was mediated by circ_0005615/miR-331-3p axis in MM cells. CONCLUSION Circ_0005615 downregulation blocked MM development by targeting miR-331-3p/IGF1R axis.
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Affiliation(s)
- Qinxin Zhang
- Department of Spinal Surgery, Ordos Central Hospital, Ordos, 017000, Inner Mongolia, China
| | - Hui Duan
- Center for Local Diseases and Chronic Diseases, Dongsheng District Center for Disease Control and Preventio, Ordos, 017000, Inner Mongolia, China
| | - Wupeng Yang
- Department of Spinal Surgery, Ordos Central Hospital, Ordos, 017000, Inner Mongolia, China
| | - Hao Liu
- Department of Spinal Surgery, Ordos Central Hospital, Ordos, 017000, Inner Mongolia, China
| | - Xiaoyang Tao
- Department of Spinal Surgery, Ordos Central Hospital, Ordos, 017000, Inner Mongolia, China
| | - Yan Zhang
- Department of Medical Imaging, Ordos Central Hospital, No. 23, Yijinhuoluoxi Street, Dongsheng District, Ordos, 017000, Inner Mongolia, China.
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31
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Diamond B, Ziccheddu B, Maclachlan K, Taylor J, Boyle E, Ossa JA, Jahn J, Affer M, Totiger TM, Coffey D, Chandhok N, Watts J, Cimmino L, Lu SX, Bolli N, Bolton K, Landau H, Park JH, Ganesh K, McPherson A, Sekeres MA, Lesokhin A, Chung DJ, Zhang Y, Ho C, Roshal M, Tyner J, Nimer S, Papaemmanuil E, Usmani S, Morgan G, Landgren O, Maura F. Tracking the evolution of therapy-related myeloid neoplasms using chemotherapy signatures. Blood 2023; 141:2359-2371. [PMID: 36626250 PMCID: PMC10273163 DOI: 10.1182/blood.2022018244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms (tMN). Preleukemic clones (ie, clonal hematopoiesis [CH]) are detectable years before the development of these aggressive malignancies, although the genomic events leading to transformation and expansion are not well defined. Here, by leveraging distinctive chemotherapy-associated mutational signatures from whole-genome sequencing data and targeted sequencing of prechemotherapy samples, we reconstructed the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy was revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan were hypermutated and enriched for complex structural variants (ie, chromothripsis), whereas neoplasms with nonmutagenic chemotherapy exposures were genomically similar to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as temporal barcodes linked to discrete clinical exposure in each patient's life, we estimated that several complex events and genomic drivers were acquired after chemotherapy was administered. For patients with prior multiple myeloma who were treated with high-dose melphalan and autologous stem cell transplantation, we demonstrate that tMN can develop from either a reinfused CH clone that escapes melphalan exposure and is selected after reinfusion, or from TP53-mutant CH that survives direct myeloablative conditioning and acquires melphalan-induced DNA damage. Overall, we revealed a novel mode of tMN progression that is not reliant on direct mutagenesis or even exposure to chemotherapy. Conversely, for tMN that evolve under the influence of chemotherapy-induced mutagenesis, distinct chemotherapies not only select preexisting CH but also promote the acquisition of recurrent genomic drivers.
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Affiliation(s)
- Benjamin Diamond
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | | | - Kylee Maclachlan
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Eileen Boyle
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Juan Arango Ossa
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacob Jahn
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Maurizio Affer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | | | - David Coffey
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Namrata Chandhok
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Justin Watts
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Luisa Cimmino
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Sydney X. Lu
- Division of Hematology, Stanford Hospital and Clinics, Stanford University, Stanford, CA
| | - Niccolò Bolli
- Department of Oncology and Onco-Hematology, Università degli Studi di Milano, Milan, Italy
- Hematology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Kelly Bolton
- Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Heather Landau
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jae H. Park
- Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karuna Ganesh
- Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew McPherson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Alexander Lesokhin
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David J. Chung
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caleb Ho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeffrey Tyner
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR
| | - Stephen Nimer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Saad Usmani
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gareth Morgan
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Ola Landgren
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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32
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Gundem G, Levine MF, Roberts SS, Cheung IY, Medina-Martínez JS, Feng Y, Arango-Ossa JE, Chadoutaud L, Rita M, Asimomitis G, Zhou J, You D, Bouvier N, Spitzer B, Solit DB, Dela Cruz F, LaQuaglia MP, Kushner BH, Modak S, Shukla N, Iacobuzio-Donahue CA, Kung AL, Cheung NKV, Papaemmanuil E. Clonal evolution during metastatic spread in high-risk neuroblastoma. Nat Genet 2023:10.1038/s41588-023-01395-x. [PMID: 37169874 DOI: 10.1038/s41588-023-01395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/12/2023] [Indexed: 05/13/2023]
Abstract
Patients with high-risk neuroblastoma generally present with widely metastatic disease and often relapse despite intensive therapy. As most studies to date focused on diagnosis-relapse pairs, our understanding of the genetic and clonal dynamics of metastatic spread and disease progression remain limited. Here, using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease-defining loci (MYCN, TERT, MDM2-CDK4) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.
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Affiliation(s)
- Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Max F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irene Y Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan S Medina-Martínez
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Feng
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loic Chadoutaud
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathieu Rita
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Georgios Asimomitis
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe Zhou
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, New York, NY, USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael P LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian H Kushner
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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33
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Lee YS, van Galen P. Mutation signatures reveal clonal evolution. Blood 2023; 141:2292-2293. [PMID: 37166926 DOI: 10.1182/blood.2022019510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
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34
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Maura F, Ziccheddu B, Xiang JZ, Bhinder B, Rosiene J, Abascal F, Maclachlan KH, Eng KW, Uppal M, He F, Zhang W, Gao Q, Yellapantula VD, Trujillo-Alonso V, Park SI, Oberley MJ, Ruckdeschel E, Lim MS, Wertheim GB, Barth MJ, Horton TM, Derkach A, Kovach AE, Forlenza CJ, Zhang Y, Landgren O, Moskowitz CH, Cesarman E, Imielinski M, Elemento O, Roshal M, Giulino-Roth L. Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells. Blood Cancer Discov 2023; 4:208-227. [PMID: 36723991 PMCID: PMC10150291 DOI: 10.1158/2643-3230.bcd-22-0128] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/21/2022] [Accepted: 01/26/2023] [Indexed: 02/02/2023] Open
Abstract
The rarity of malignant Hodgkin and Reed Sternberg (HRS) cells in classic Hodgkin lymphoma (cHL) limits the ability to study the genomics of cHL. To circumvent this, our group has previously optimized fluorescence-activated cell sorting to purify HRS cells. Using this approach, we now report the whole-genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events leading to cHL. We identified alterations in driver genes not previously described in cHL, APOBEC mutational activity, and the presence of complex structural variants including chromothripsis. We found that high ploidy in cHL is often acquired through multiple, independent chromosomal gains events including whole-genome duplication. Evolutionary timing analyses revealed that structural variants enriched for RAG motifs, driver mutations in B2M, BCL7A, GNA13, and PTPN1, and the onset of AID-driven mutagenesis usually preceded large chromosomal gains. This study provides a temporal reconstruction of cHL pathogenesis. SIGNIFICANCE Previous studies in cHL were limited to coding sequences and therefore not able to comprehensively decipher the tumor complexity. Here, leveraging cHL whole-genome characterization, we identify driver events and reconstruct the tumor evolution, finding that structural variants, driver mutations, and AID mutagenesis precede chromosomal gains. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Bachisio Ziccheddu
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Jenny Z. Xiang
- Weill Cornell Medical College, New York, New York
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medical College, New York, New York
| | - Bhavneet Bhinder
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medical College, New York, New York
| | - Joel Rosiene
- Weill Cornell Medical College, New York, New York
| | - Federico Abascal
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Kylee H. Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Wha Eng
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medical College, New York, New York
| | - Manik Uppal
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medical College, New York, New York
| | - Feng He
- Weill Cornell Medical College, New York, New York
| | - Wei Zhang
- Weill Cornell Medical College, New York, New York
| | - Qi Gao
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkata D. Yellapantula
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine at Children's Hospital Los Angeles, Los Angeles, California
| | | | - Sunita I. Park
- Department of Pathology, Children's Hospital of Atlanta, Atlanta, Georgia
| | | | | | - Megan S. Lim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Philadelphia
| | - Gerald B. Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Philadelphia
| | - Matthew J. Barth
- Department of Pediatrics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Terzah M. Horton
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Andriy Derkach
- Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Yanming Zhang
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ola Landgren
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Craig H. Moskowitz
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | | | - Marcin Imielinski
- Weill Cornell Medical College, New York, New York
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medical College, New York, New York
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivier Elemento
- Weill Cornell Medical College, New York, New York
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medical College, New York, New York
| | - Mikhail Roshal
- Memorial Sloan Kettering Cancer Center, New York, New York
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35
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Körber V, Stainczyk SA, Kurilov R, Henrich KO, Hero B, Brors B, Westermann F, Höfer T. Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome. Nat Genet 2023; 55:619-630. [PMID: 36973454 PMCID: PMC10101850 DOI: 10.1038/s41588-023-01332-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
AbstractNeuroblastoma, the most frequent solid tumor in infants, shows very diverse outcomes from spontaneous regression to fatal disease. When these different tumors originate and how they evolve are not known. Here we quantify the somatic evolution of neuroblastoma by deep whole-genome sequencing, molecular clock analysis and population-genetic modeling in a comprehensive cohort covering all subtypes. We find that tumors across the entire clinical spectrum begin to develop via aberrant mitoses as early as the first trimester of pregnancy. Neuroblastomas with favorable prognosis expand clonally after short evolution, whereas aggressive neuroblastomas show prolonged evolution during which they acquire telomere maintenance mechanisms. The initial aneuploidization events condition subsequent evolution, with aggressive neuroblastoma exhibiting early genomic instability. We find in the discovery cohort (n = 100), and validate in an independent cohort (n = 86), that the duration of evolution is an accurate predictor of outcome. Thus, insight into neuroblastoma evolution may prospectively guide treatment decisions.
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36
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Dhodapkar MV. The immune system in multiple myeloma and precursor states: Lessons and implications for immunotherapy and interception. Am J Hematol 2023; 98 Suppl 2:S4-S12. [PMID: 36194782 PMCID: PMC9918687 DOI: 10.1002/ajh.26752] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Abstract
Multiple myeloma (MM) and its precursor monoclonal gammopathy of undetermined significance (MGUS) are distinct disorders that likely originate in the setting of chronic immune activation. Evolution of these lesions is impacted by cross-talk with both innate and adaptive immune systems of the host. Harnessing the immune system may, therefore, be an attractive strategy to prevent clinical malignancy. While clinical MM is characterized by both regional and systemic immune suppression and paresis, immune-based approaches, particularly redirecting T cells have shown remarkable efficacy in MM patients. Optimal application and sequencing of these new immune therapies and their integration into clinical MM management may depend on the underlying immune status, in turn impacted by host, tumor, and environmental features. Immune therapies carry the potential to achieve durable unmaintained responses and cures in MM.
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Affiliation(s)
- Madhav V Dhodapkar
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
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37
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Jahn J, Diamond B, Hsu J, Montoya S, Totiger TM, Landgren O, Maura F, Taylor J. Therapy-selected clonal hematopoiesis and its role in myeloid neoplasms. Leuk Res 2023; 126:107020. [PMID: 36696829 PMCID: PMC11305114 DOI: 10.1016/j.leukres.2023.107020] [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: 11/22/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
Therapy-related myeloid neoplasms (t-MN) account for approximately 10-15% of all myeloid neoplasms and are associated with poor prognosis. Genomic characterization of t-MN to date has been limited in comparison to the considerable sequencing efforts performed for de novo myeloid neoplasms. Until recently, targeted deep sequencing (TDS) or whole exome sequencing (WES) have been the primary technologies utilized and thus limited the ability to explore the landscape of structural variants and mutational signatures. In the past decade, population-level studies have identified clonal hematopoiesis as a risk factor for the development of myeloid neoplasms. However, emerging research on clonal hematopoiesis as a risk factor for developing t-MN is evolving, and much is unknown about the progression of CH to t-MN. In this work, we will review the current knowledge of the genomic landscape of t-MN, discuss background knowledge of clonal hematopoiesis gained from studies of de novo myeloid neoplasms, and examine the recent literature studying the role of therapeutic selection of CH and its evolution under the effects of antineoplastic therapy. Finally, we will discuss the potential implications on current clinical practice and the areas of focus needed for future research into therapy-selected clonal hematopoiesis in myeloid neoplasms.
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Affiliation(s)
- Jacob Jahn
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Benjamin Diamond
- Myeloma Division, Department of Medicine, University of Miami Miller School of Medicine, United States
| | - Jeffrey Hsu
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Skye Montoya
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Tulasigeri M Totiger
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Ola Landgren
- Myeloma Division, Department of Medicine, University of Miami Miller School of Medicine, United States
| | - Francesco Maura
- Myeloma Division, Department of Medicine, University of Miami Miller School of Medicine, United States
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States; Leukemia Program, Department of Medicine, University of Miami Miller School of Medicine, United States.
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38
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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39
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Ansari-Pour N, Samur M, Flynt E, Gooding S, Towfic F, Stong N, Estevez MO, Mavrommatis K, Walker B, Morgan G, Munshi N, Avet-Loiseau H, Thakurta A. Whole-genome analysis identifies novel drivers and high-risk double-hit events in relapsed/refractory myeloma. Blood 2023; 141:620-633. [PMID: 36223594 PMCID: PMC10163277 DOI: 10.1182/blood.2022017010] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Large-scale analyses of genomic data from patients with newly diagnosed multiple myeloma (ndMM) have been undertaken, however, large-scale analysis of relapsed/refractory MM (rrMM) has not been performed. We hypothesize that somatic variants chronicle the therapeutic exposures and clonal structure of myeloma from ndMM to rrMM stages. We generated whole-genome sequencing (WGS) data from 418 tumors (386 patients) derived from 6 rrMM clinical trials and compared them with WGS from 198 unrelated patients with ndMM in a population-based case-control fashion. We identified significantly enriched events at the rrMM stage, including drivers (DUOX2, EZH2, TP53), biallelic inactivation (TP53), noncoding mutations in bona fide drivers (TP53BP1, BLM), copy number aberrations (CNAs; 1qGain, 17pLOH), and double-hit events (Amp1q-ISS3, 1qGain-17p loss-of-heterozygosity). Mutational signature analysis identified a subclonal defective mismatch repair signature enriched in rrMM and highly active in high mutation burden tumors, a likely feature of therapy-associated expanding subclones. Further analysis focused on the association of genomic aberrations enriched at different stages of resistance to immunomodulatory agent (IMiD)-based therapy. This analysis revealed that TP53, DUOX2, 1qGain, and 17p loss-of-heterozygosity increased in prevalence from ndMM to lenalidomide resistant (LENR) to pomalidomide resistant (POMR) stages, whereas enrichment of MAML3 along with immunoglobulin lambda (IGL) and MYC translocations distinguished POM from the LEN subgroup. Genomic drivers associated with rrMM are those that confer clonal selective advantage under therapeutic pressure. Their role in therapy evasion should be further evaluated in longitudinal patient samples, to confirm these associations with the evolution of clinical resistance and to identify molecular subsets of rrMM for the development of targeted therapies.
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Affiliation(s)
- Naser Ansari-Pour
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mehmet Samur
- Dana-Farber Cancer Institute, Boston, MA
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, NJ
| | - Sarah Gooding
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | | | | | - Maria Ortiz Estevez
- Predictive Sciences, BMS Center for Innovation and Translational Research Europe, A Bristol Myers Squibb Company, Sevilla, Spain
| | | | - Brian Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN
| | - Gareth Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY
| | - Nikhil Munshi
- Dana-Farber Cancer Institute, Boston, MA
- VA Boston Healthcare System, West Roxbury, MA
- Harvard Medical School, Boston, MA
| | | | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Bristol Myers Squibb, Summit, NJ
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Disease, University of Oxford, Oxford, United Kingdom
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40
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Ovejero S, Viziteu E, Dutrieux L, Devin J, Lin YL, Alaterre E, Jourdan M, Basbous J, Requirand G, Robert N, de Boussac H, Seckinger A, Hose D, Vincent L, Herbaux C, Constantinou A, Pasero P, Moreaux J. The BLM helicase is a new therapeutic target in multiple myeloma involved in replication stress survival and drug resistance. Front Immunol 2022; 13:983181. [PMID: 36569948 PMCID: PMC9780552 DOI: 10.3389/fimmu.2022.983181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Multiple myeloma (MM) is a hematologic cancer characterized by accumulation of malignant plasma cells in the bone marrow. To date, no definitive cure exists for MM and resistance to current treatments is one of the major challenges of this disease. The DNA helicase BLM, whose depletion or mutation causes the cancer-prone Bloom's syndrome (BS), is a central factor of DNA damage repair by homologous recombination (HR) and genomic stability maintenance. Using independent cohorts of MM patients, we identified that high expression of BLM is associated with a poor outcome with a significant enrichment in replication stress signature. We provide evidence that chemical inhibition of BLM by the small molecule ML216 in HMCLs (human myeloma cell lines) leads to cell cycle arrest and increases apoptosis, likely by accumulation of DNA damage. BLM inhibition synergizes with the alkylating agent melphalan to efficiently inhibit growth and promote cell death in HMCLs. Moreover, ML216 treatment re-sensitizes melphalan-resistant cell lines to this conventional therapeutic agent. Altogether, these data suggest that inhibition of BLM in combination with DNA damaging agents could be of therapeutic interest in the treatment of MM, especially in those patients with high BLM expression and/or resistance to melphalan.
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Affiliation(s)
- Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France,Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Elena Viziteu
- Department of Biological Hematology, CHU Montpellier, Montpellier, France,Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Laure Dutrieux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France,Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Julie Devin
- Department of Biological Hematology, CHU Montpellier, Montpellier, France,Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Yea-Lih Lin
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Elina Alaterre
- Department of Biological Hematology, CHU Montpellier, Montpellier, France,Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Michel Jourdan
- Department of Biological Hematology, CHU Montpellier, Montpellier, France,Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jihane Basbous
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Guilhem Requirand
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | - Nicolas Robert
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | | | | | - Dirk Hose
- Department of Hematology and Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Laure Vincent
- Department of Hematology and Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Charles Herbaux
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France,Department of Hematology and Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Philippe Pasero
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France,Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France,Department of Clinical Hematology, CHU Montpellier, Montpellier, France,*Correspondence: Jérôme Moreaux,
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41
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Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response. NPJ Precis Oncol 2022; 6:89. [PMID: 36456685 PMCID: PMC9715662 DOI: 10.1038/s41698-022-00331-2] [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: 05/26/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
Activation-induced cytidine deaminase, AICDA or AID, is a driver of somatic hypermutation and class-switch recombination in immunoglobulins. In addition, this deaminase belonging to the APOBEC family may have off-target effects genome-wide, but its effects at pan-cancer level are not well elucidated. Here, we used different pan-cancer datasets, totaling more than 50,000 samples analyzed by whole-genome, whole-exome, or targeted sequencing. AID mutations are present at pan-cancer level with higher frequency in hematological cancers and higher presence at transcriptionally active TAD domains. AID synergizes initial hotspot mutations by a second composite mutation. AID mutational load was found to be independently associated with a favorable outcome in immune-checkpoint inhibitors (ICI) treated patients across cancers after analyzing 2000 samples. Finally, we found that AID-related neoepitopes, resulting from mutations at more frequent hotspots if compared to other mutational signatures, enhance CXCL13/CCR5 expression, immunogenicity, and T-cell exhaustion, which may increase ICI sensitivity.
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42
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Maclachlan KH, Lesokhin AM. Are we ready to look beyond plasma cells in assessing high-risk smoldering myeloma? Cancer Cell 2022; 40:1270-1272. [PMID: 36379204 DOI: 10.1016/j.ccell.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sklavenitis-Pistofidis et al. report clinical and correlative results of a single-arm phase II trial of elotuzumab, lenalidomide, and dexamethasone in patients with high-risk smoldering myeloma. The authors explore the interactions between the genetics of the plasma cell clone and the immune microenvironment as potential biomarkers of treatment susceptibility and efficacy.
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Affiliation(s)
- Kylee H Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill-Cornell Medical College, New York, NY, USA
| | - Alexander M Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill-Cornell Medical College, New York, NY, USA.
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43
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Landgren O, Kazandjian D. Modern Myeloma Therapy + Sustained Minimal Residual Disease-Negative = (Functional) Cure! J Clin Oncol 2022; 40:2863-2866. [PMID: 35772041 PMCID: PMC9426854 DOI: 10.1200/jco.22.00622] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/10/2022] [Accepted: 05/07/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Ola Landgren
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Dickran Kazandjian
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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44
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Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. Nat Med 2022; 28:1662-1671. [PMID: 35953718 PMCID: PMC9388377 DOI: 10.1038/s41591-022-01927-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
Abstract
Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT. Single-cell genomic and transcriptomic analyses of longitudinal samples of patients with Richter syndrome reveal the presence and dynamics of clones driving transformation from chronic lymphocytic leukemia years before clinical manifestation
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ramon Massoni-Badosa
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Beatriz Garcia-Torre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Neus Villamor
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Vicente Chapaprieta
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Sara Ruiz-Gil
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Núria Verdaguer-Dot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica Romo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maria Rozman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Alfredo Rivas-Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Tycho Baumann
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Marcos González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fina Climent
- Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellví
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Bosch
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Anna Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sílvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Armando López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Pedro Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | | | - Josep Ll Gelpí
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Pablo M Garcia-Roves
- Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Maura
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. .,Hospital Clínic of Barcelona, Barcelona, Spain. .,Universitat de Barcelona, Barcelona, Spain.
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45
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Jain MD, Ziccheddu B, Coughlin CA, Faramand R, Griswold AJ, Reid KM, Menges M, Zhang Y, Cen L, Wang X, Hussaini M, Landgren O, Davila ML, Schatz JH, Locke FL, Maura F. Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma. Blood 2022; 140:491-503. [PMID: 35476848 PMCID: PMC9353150 DOI: 10.1182/blood.2021015008] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/20/2022] Open
Abstract
CD19-directed chimeric antigen receptor (CAR-19) T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. Although host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients with relapsed disease retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 patients with CAR-19-treated large B-cell lymphoma. We found that the pretreatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients for whom CAR T-cell therapy failed. Pretreatment reduced expression or monoallelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are related to multiple mechanisms. Our study showed that tumor-intrinsic genomic alterations are key among the complex interplay of factors that underlie CAR-19 efficacy and resistance for large B-cell lymphomas.
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Affiliation(s)
- Michael D Jain
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Bachisio Ziccheddu
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
| | - Caroline A Coughlin
- Medical Scientist Training Program
- Sheila and David Fuente Graduate Program in Cancer Biology, and
| | - Rawan Faramand
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - Kayla M Reid
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Meghan Menges
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | | | - Ling Cen
- Department of Biostatistics and Bioinformatics and
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics and
| | - Mohammad Hussaini
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Ola Landgren
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
| | - Marco L Davila
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Jonathan H Schatz
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
| | - Frederick L Locke
- Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Francesco Maura
- Division of Hematology, Department of Medicine
- Sylvester Comprehensive Cancer Center
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46
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Rasche L, Schinke C, Maura F, Bauer MA, Ashby C, Deshpande S, Poos AM, Zangari M, Thanendrarajan S, Davies FE, Walker BA, Barlogie B, Landgren O, Morgan GJ, van Rhee F, Weinhold N. The spatio-temporal evolution of multiple myeloma from baseline to relapse-refractory states. Nat Commun 2022; 13:4517. [PMID: 35922426 PMCID: PMC9349320 DOI: 10.1038/s41467-022-32145-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Deciphering Multiple Myeloma evolution in the whole bone marrow is key to inform curative strategies. Here, we perform spatial-longitudinal whole-exome sequencing, including 140 samples collected from 24 Multiple Myeloma patients during up to 14 years. Applying imaging-guided sampling we observe three evolutionary patterns, including relapse driven by a single-cell expansion, competing/co-existing sub-clones, and unique sub-clones at distinct locations. While we do not find the unique relapse sub-clone in the baseline focal lesion(s), we show a close phylogenetic relationship between baseline focal lesions and relapse disease, highlighting focal lesions as hotspots of tumor evolution. In patients with ≥3 focal lesions on positron-emission-tomography at diagnosis, relapse is driven by multiple distinct sub-clones, whereas in other patients, a single-cell expansion is typically seen (p < 0.01). Notably, we observe resistant sub-clones that can be hidden over years, suggesting that a prerequisite for curative therapies would be to overcome not only tumor heterogeneity but also dormancy.
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Affiliation(s)
- Leo Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center (MSNZ), University Hospital of Würzburg, Würzburg, Germany
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Francesco Maura
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Michael A Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Alexandra M Poos
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Faith E Davies
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Bart Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ola Landgren
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Niels Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany.
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47
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Solimando AG, Da Vià MC, Bolli N, Steinbrunn T. The Route of the Malignant Plasma Cell in Its Survival Niche: Exploring “Multiple Myelomas”. Cancers (Basel) 2022; 14:cancers14133271. [PMID: 35805041 PMCID: PMC9265748 DOI: 10.3390/cancers14133271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Growing evidence points to multiple myeloma (MM) and its stromal microenvironment using several mechanisms to subvert effective immune and anti-tumor responses. Recent advances have uncovered the tumor-stromal cell influence in regulating the immune-microenvironment and have envisioned targeting these suppressive pathways to improve therapeutic outcomes. Nevertheless, some subgroups of patients include those with particularly unfavorable prognoses. Biological stratification can be used to categorize patient-, disease- or therapy-related factors, or alternatively, these biological determinants can be included in a dynamic model that customizes a given treatment to a specific patient. Genetic heterogeneity and current knowledge enforce a systematic and comprehensive bench-to-bedside approach. Given the increasing role of cancer stem cells (CSCs) in better characterizing the pathogenesis of solid and hematological malignancies, disease relapse, and drug resistance, identifying and describing CSCs is of paramount importance in the management of MM. Even though the function of CSCs is well-known in other cancer types, their role in MM remains elusive. With this review, we aim to provide an update on MM homing and resilience in the bone marrow micro milieu. These data are particularly interesting for clinicians facing unmet medical needs while designing novel treatment approaches for MM.
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Affiliation(s)
- Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine ‘G. Baccelli’, University of Bari Medical School, 70124 Bari, Italy
- Department of Medicine II, University Hospital of Würzburg, 97080 Würzburg, Germany
- Correspondence: (A.G.S.); (T.S.); Tel.: +39-3395626475 (A.G.S.)
| | - Matteo Claudio Da Vià
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.C.D.V.); (N.B.)
| | - Niccolò Bolli
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.C.D.V.); (N.B.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Torsten Steinbrunn
- Department of Medicine II, University Hospital of Würzburg, 97080 Würzburg, Germany
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Correspondence: (A.G.S.); (T.S.); Tel.: +39-3395626475 (A.G.S.)
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48
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Sousos N, Ní Leathlobhair M, Simoglou Karali C, Louka E, Bienz N, Royston D, Clark SA, Hamblin A, Howard K, Mathews V, George B, Roy A, Psaila B, Wedge DC, Mead AJ. In utero origin of myelofibrosis presenting in adult monozygotic twins. Nat Med 2022; 28:1207-1211. [PMID: 35637336 PMCID: PMC9205768 DOI: 10.1038/s41591-022-01793-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/22/2022] [Indexed: 12/11/2022]
Abstract
The latency between acquisition of an initiating somatic driver mutation by a single-cell and clinical presentation with cancer is largely unknown. We describe a remarkable case of monozygotic twins presenting with CALR mutation-positive myeloproliferative neoplasms (MPNs) (aged 37 and 38 years), with a clinical phenotype of primary myelofibrosis. The CALR mutation was absent in T cells and dermal fibroblasts, confirming somatic acquisition. Whole-genome sequencing lineage tracing revealed a common clonal origin of the CALR-mutant MPN clone, which occurred in utero followed by twin-to-twin transplacental transmission and subsequent similar disease latency. Index sorting and single-colony genotyping revealed phenotypic hematopoietic stem cells (HSCs) as the likely MPN-propagating cell. Furthermore, neonatal blood spot analysis confirmed in utero origin of the JAK2V617F mutation in a patient presenting with polycythemia vera (aged 34 years). These findings provide a unique window into the prolonged evolutionary dynamics of MPNs and fitness advantage exerted by MPN-associated driver mutations in HSCs.
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Affiliation(s)
- Nikolaos Sousos
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Christina Simoglou Karali
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Eleni Louka
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicola Bienz
- Haematology Service, Wexham Park Hospital, Frimley Health NHS Foundation Trust, Slough, UK
| | - Daniel Royston
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angela Hamblin
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Kieran Howard
- National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, India
| | - Anindita Roy
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Paediatrics, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bethan Psaila
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David C Wedge
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK.
| | - Adam J Mead
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK.
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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49
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Wiedmeier-Nutor JE, Bergsagel PL. Review of Multiple Myeloma Genetics including Effects on Prognosis, Response to Treatment, and Diagnostic Workup. Life (Basel) 2022; 12:life12060812. [PMID: 35743843 PMCID: PMC9225019 DOI: 10.3390/life12060812] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/10/2022] [Accepted: 05/20/2022] [Indexed: 12/03/2022] Open
Abstract
Multiple myeloma is a disorder of the monoclonal plasma cells and is the second most common hematologic malignancy. Despite improvements in survival with newer treatment regimens, multiple myeloma remains an incurable disease and most patients experience multiple relapses. Multiple myeloma disease initiation and progression are highly dependent on complex genetic aberrations. This review will summarize the current knowledge of these genetic aberrations, how they affect prognosis and the response to treatment, and review sensitive molecular techniques for multiple myeloma workup, with the ultimate goal of detecting myeloma progression early, allowing for timely treatment initiation.
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50
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Clonal evolution after treatment pressure in multiple myeloma: heterogenous genomic aberrations and transcriptomic convergence. Leukemia 2022; 36:1887-1897. [PMID: 35643867 PMCID: PMC9252918 DOI: 10.1038/s41375-022-01597-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/27/2022] [Accepted: 05/09/2022] [Indexed: 11/27/2022]
Abstract
We investigated genomic and transcriptomic changes in paired tumor samples of 29 in-house multiple myeloma (MM) patients and 28 patients from the MMRF CoMMpass study before and after treatment. A change in clonal composition was found in 46/57 (82%) of patients, and single-nucleotide variants (SNVs) increased from median 67 to 86. The highest increase in prevalence of genetic aberrations was found in RAS genes (60% to 72%), amp1q21 (18% to 35%), and TP53 (9% to 18%). The SBS-MM1 mutation signature was detected both in patients receiving high and low dose melphalan. A total of 2589 genes were differentially expressed between early and late samples (FDR < 0.05). Gene set enrichment analysis (GSEA) showed increased expression of E2F, MYC, and glycolysis pathways and a decreased expression in TNF-NFkB and TGFbeta pathways in late compared to early stage. Single sample GSEA (ssGSEA) scores of differentially expressed pathways revealed that these changes were most evident in end-stage disease. Increased expression of several potentially targetable genes was found at late disease stages, including cancer-testis antigens, XPO1 and ABC transporters. Our study demonstrates a transcriptomic convergence of pathways supporting increased proliferation and metabolism during disease progression in MM.
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