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Testa U, Pelosi E, Castelli G, Leone G. Recent Advances in The Definition of the Molecular Alterations Occurring in Multiple Myeloma. Mediterr J Hematol Infect Dis 2024; 16:e2024062. [PMID: 38984097 PMCID: PMC11232684 DOI: 10.4084/mjhid.2024.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024] Open
Abstract
Multiple myeloma (MM) is a disorder of the monoclonal plasma cells and is the second most common hematologic malignancy. MM initiation and progression are dependent upon complex genomic abnormalities. The current pathogenic model of MM includes two types of primary events, represented by chromosome translocations or chromosome number alterations resulting in hyperdiploidy. These primary molecular events are observed both in MM and in monoclonal gammopathy, its premalignant precursor. Subsequent genetic events allow the progression of monoclonal gammopathy to MM and, together with primary events, contribute to the genetic complexity and heterogeneity of MM. Newer therapies have considerably improved patient outcomes; however, MM remains an incurable disease and most patients experience multiple relapses. The dramatic progresses achieved in the analysis of the heterogeneous molecular features of different MM patients allowed a comprehensive molecular classification of MM and the definition of an individualized prognostic model to predict an individual MM patient's response to different therapeutic options. Despite these progresses, prognostic models fail to identify a significant proportion of patients destined to early relapse. Treatment strategies are increasingly. Based on disease biology, trials are enriched for high-risk MMs, whose careful definition and categorization requires DNA sequencing studies.
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Affiliation(s)
- Ugo Testa
- Istituto Superiore di Sanità, Roma, Italy
| | | | | | - Giuseppe Leone
- Department of Radiological and Hematological Sciences, Catholic University, Rome, Italy
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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [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: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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3
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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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Clarke SE, Fuller KA, Erber WN. Chromosomal defects in multiple myeloma. Blood Rev 2024; 64:101168. [PMID: 38212176 DOI: 10.1016/j.blre.2024.101168] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
Multiple myeloma is a plasma cell neoplasm driven by primary (e.g. hyperdiploidy; IGH translocations) and secondary (e.g. 1q21 gains/amplifications; del(17p); MYC translocations) chromosomal events. These are important to detect as they influence prognosis, therapeutic response and disease survival. Currently, cytogenetic testing is most commonly performed by interphase fluorescence in situ hybridisation (FISH) on aspirated bone marrow samples. A number of variations to FISH methodology are available, including prior plasma cell enrichment and incorporation of immunophenotypic plasma cell identification. Other molecular methods are increasingly being utilised to provide a genome-wide view at high resolution (e.g. single nucleotide polymorphism (SNP) microarray analysis) and these can detect abnormalities in most cases. Despite their wide application at diagnostic assessment, both FISH and SNP-array have relatively low sensitivity, limiting their use for identification of prognostically significant low-level sub-clones or for disease monitoring. Next-generation sequencing is increasingly being used to detect mutations and new FISH techniques such as by flow cytometry are in development and may address some of the current test limitations. Here we review the primary and secondary cytogenetic aberrations in myeloma and discuss the range of techniques available for their assessment.
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Affiliation(s)
- Sarah E Clarke
- School of Biomedical Sciences, The University of Western Australia (M504), Crawley, WA 6009, Australia; Department of Haematology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, WA 6150, Australia.
| | - Kathryn A Fuller
- School of Biomedical Sciences, The University of Western Australia (M504), Crawley, WA 6009, Australia.
| | - Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia (M504), Crawley, WA 6009, Australia; PathWest Laboratory Medicine WA, Royal Perth Hospital, Perth, WA 6000, Australia.
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5
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Tonon G. Myeloma and DNA damage. Blood 2024; 143:488-495. [PMID: 37992215 DOI: 10.1182/blood.2023021384] [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: 09/07/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/24/2023] Open
Abstract
ABSTRACT DNA-damaging agents have represented the first effective treatment for the blood cancer multiple myeloma, and after 65 years since their introduction to the clinic, they remain one of the mainstay therapies for this disease. Myeloma is a cancer of plasma cells. Despite exceedingly slow proliferation, myeloma cells present extended genomic rearrangements and intense genomic instability, starting at the premalignant stage of the disease. Where does such DNA damage stem from? A reliable model argues that the powerful oncogenes activated in myeloma as well the phenotypic peculiarities of cancer plasma cells, including the dependency on the proteasome for survival and the constant presence of oxidative stress, all converge on modulating DNA damage and repair. Beleaguered by these contraposing forces, myeloma cells survive in a precarious balance, in which the robust engagement of DNA repair mechanisms to guarantee cell survival is continuously challenged by rampant genomic instability, essential for cancer cells to withstand hostile selective pressures. Shattering this delicate equilibrium has been the goal of the extensive use of DNA-damaging agents since their introduction in the clinic, now enriched by novel approaches that leverage upon synthetic lethality paradigms. Exploiting the impairment of homologous recombination caused by myeloma genetic lesions or treatments, it is now possible to design therapeutic combinations that could target myeloma cells more effectively. Furthermore, DNA-damaging agents, as demonstrated in solid tumors, may sensitize cells to immune therapies. In all, targeting DNA damage and repair remains as central as ever in myeloma, even for the foreseeable future.
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Affiliation(s)
- Giovanni Tonon
- Università Vita-Salute San Raffaele, Milan, Italy
- Division of Experimental Oncology and Center for Omics Sciences, Functional Genomics of Cancer Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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6
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Chojnacka M, Diamond B, Ziccheddu B, Rustad E, Maclachlan K, Papadimitriou M, Boyle EM, Blaney P, Usmani S, Morgan G, Landgren O, Maura F. Impact of Rare Structural Variant Events in Newly Diagnosed Multiple Myeloma. Clin Cancer Res 2024; 30:575-585. [PMID: 37939148 PMCID: PMC10841766 DOI: 10.1158/1078-0432.ccr-23-1045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/19/2023] [Accepted: 11/07/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE Whole-genome sequencing (WGS) of patients with newly diagnosed multiple myeloma (NDMM) has shown recurrent structural variant (SV) involvement in distinct regions of the genome (i.e., hotspots) and causing recurrent copy-number alterations. Together with canonical immunoglobulin translocations, these SVs are recognized as "recurrent SVs." More than half of SVs were not involved in recurrent events. The significance of these "rare SVs" has not been previously examined. EXPERIMENTAL DESIGN In this study, we utilize 752 WGS and 591 RNA sequencing data from patients with NDMM to determine the role of rare SVs in myeloma pathogenesis. RESULTS Ninety-four percent of patients harbored at least one rare SV event. Rare SVs showed an SV class-specific enrichment within genes and superenhancers associated with outlier gene expression. Furthermore, known myeloma driver genes recurrently impacted by point mutations were dysregulated by rare SVs. CONCLUSIONS Overall, we demonstrate the association of rare SVs with aberrant gene expression supporting a potential driver role in myeloma pathogenesis.
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Affiliation(s)
- Monika Chojnacka
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Benjamin Diamond
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Bachisio Ziccheddu
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Even Rustad
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marios Papadimitriou
- 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
| | - Patrick Blaney
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Saad Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gareth 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
| | - Francesco Maura
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
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Simhal AK, Maclachlan KH, Elkin R, Zhu J, Norton L, Deasy JO, Oh JH, Usmani SZ, Tannenbaum A. Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival. Blood Cancer J 2023; 13:175. [PMID: 38030619 PMCID: PMC10687027 DOI: 10.1038/s41408-023-00935-2] [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: 04/05/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
The plasma cell cancer multiple myeloma (MM) varies significantly in genomic characteristics, response to therapy, and long-term prognosis. To investigate global interactions in MM, we combined a known protein interaction network with a large clinically annotated MM dataset. We hypothesized that an unbiased network analysis method based on large-scale similarities in gene expression, copy number aberration, and protein interactions may provide novel biological insights. Applying a novel measure of network robustness, Ollivier-Ricci Curvature, we examined patterns in the RNA-Seq gene expression and CNA data and how they relate to clinical outcomes. Hierarchical clustering using ORC differentiated high-risk subtypes with low progression free survival. Differential gene expression analysis defined 118 genes with significantly aberrant expression. These genes, while not previously associated with MM, were associated with DNA repair, apoptosis, and the immune system. Univariate analysis identified 8/118 to be prognostic genes; all associated with the immune system. A network topology analysis identified both hub and bridge genes which connect known genes of biological significance of MM. Taken together, gene interaction network analysis in MM uses a novel method of global assessment to demonstrate complex immune dysregulation associated with shorter survival.
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Affiliation(s)
- Anish K Simhal
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kylee H Maclachlan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Rena Elkin
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiening Zhu
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph O Deasy
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jung Hun Oh
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saad Z Usmani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allen Tannenbaum
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Departments of Computer Science and Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY, USA.
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8
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Daudignon A, Cuccuini W, Bracquemart C, Godon C, Quilichini B, Penther D. Cytogenetics in the management of multiple Myeloma: The guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103427. [PMID: 38035476 DOI: 10.1016/j.retram.2023.103427] [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: 07/07/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023]
Abstract
Multiple myeloma (MM) is characterized by the accumulation of malignant plasma cells (PCs) in the bone marrow. Despite considerable advances in the treatment, MM is considered an incurable chronic disease with a very heterogeneous prognosis, mostly depending on genomic alterations whose complexity evolves over time. The cytogenetic analysis of MM is performed on CD138+ sorted PCs, in order to detect the following high risk cytogenetic abnormalities: t(4;14), 17p/TP53 deletion, 1q21 gain/amplification, 1p32 deletion, as well as t(11;14) because of its therapeutic implication. This minimal panel can be enlarged to detect other recurrent abnormalities, according to the prognostic score chosen by the laboratory. Although the knowledge of the genetic landscape of MM is evolving rapidly with improved molecular technologies, risk scores remain to be refined as they require more time for consensual validation. The GFCH present here the overview of genomics alterations identified in MM and related PCs diseases associated with their prognostic factor, when available, and recommendations from an expert group for identification and characterization of those alterations. This work is the update of previous 2016 recommendations.
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Affiliation(s)
- Agnès Daudignon
- Institut de Génétique Médicale - Hôpital Jeanne de Flandre - CHU de Lille, Lille, France
| | - Wendy Cuccuini
- Laboratoire d'hématologie, Hôpital Saint-Louis -Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Claire Bracquemart
- Normandie Univ, UNICAEN, CHU de Caen Normandie, Structure Fédérative d'Oncogénétique cyto-moléculaire (MOCAE), Caen, France
| | - Catherine Godon
- Laboratoire d'Hématologie Biologique, CHU Nantes, Nantes, France
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9
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Giguère A, Raymond-Bouchard I, Collin V, Claveau JS, Hébert J, LeBlanc R. Optical Genome Mapping Reveals the Complex Genetic Landscape of Myeloma. Cancers (Basel) 2023; 15:4687. [PMID: 37835381 PMCID: PMC10571866 DOI: 10.3390/cancers15194687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 10/15/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) on enriched CD138 plasma cells is the standard method for identification of clinically relevant genetic abnormalities in multiple myeloma. However, FISH is a targeted analysis that can be challenging due to the genetic complexity of myeloma. The aim of this study was to evaluate the potential of optical genome mapping (OGM) to detect clinically significant cytogenetic abnormalities in myeloma and to provide larger pangenomic information. OGM and FISH analyses were performed on CD138-purified cells of 20 myeloma patients. OGM successfully detected structural variants (SVs) (IGH and MYC rearrangements), copy number variants (CNVs) (17p/TP53 deletion, 1p deletion and 1q gain/amplification) and aneuploidy (gains of odd-numbered chromosomes, monosomy 13) classically expected with myeloma and led to a 30% increase in prognosis yield at our institution when compared to FISH. Despite challenges in the interpretation of OGM calls for CNV and aneuploidy losses in non-diploid genomes, OGM has the potential to replace FISH as the standard of care analysis in clinical settings and to efficiently change how we identify prognostic and predictive markers for therapies in the future. To our knowledge, this is the first study highlighting the feasibility and clinical utility of OGM in myeloma.
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Affiliation(s)
- Amélie Giguère
- Cytogenetics Laboratory, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada; (I.R.-B.); (V.C.); (J.H.)
| | - Isabelle Raymond-Bouchard
- Cytogenetics Laboratory, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada; (I.R.-B.); (V.C.); (J.H.)
| | - Vanessa Collin
- Cytogenetics Laboratory, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada; (I.R.-B.); (V.C.); (J.H.)
| | - Jean-Sébastien Claveau
- Division of Hematology, Oncology and Transplantation, Department of Medicine, Maisonneuve-Rosemont Hospital, Université de Montréal, Montreal, QC H1T 2M4, Canada; (J.-S.C.); (R.L.)
| | - Josée Hébert
- Cytogenetics Laboratory, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada; (I.R.-B.); (V.C.); (J.H.)
- Division of Hematology, Oncology and Transplantation, Department of Medicine, Maisonneuve-Rosemont Hospital, Université de Montréal, Montreal, QC H1T 2M4, Canada; (J.-S.C.); (R.L.)
| | - Richard LeBlanc
- Division of Hematology, Oncology and Transplantation, Department of Medicine, Maisonneuve-Rosemont Hospital, Université de Montréal, Montreal, QC H1T 2M4, Canada; (J.-S.C.); (R.L.)
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10
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Yu J, Chen N, Zheng Z, Gao M, Liang N, Wong KC. Chromothripsis detection with multiple myeloma patients based on deep graph learning. Bioinformatics 2023; 39:btad422. [PMID: 37399092 PMCID: PMC10343948 DOI: 10.1093/bioinformatics/btad422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023] Open
Abstract
MOTIVATION Chromothripsis, associated with poor clinical outcomes, is prognostically vital in multiple myeloma. The catastrophic event is reported to be detectable prior to the progression of multiple myeloma. As a result, chromothripsis detection can contribute to risk estimation and early treatment guidelines for multiple myeloma patients. However, manual diagnosis remains the gold standard approach to detect chromothripsis events with the whole-genome sequencing technology to retrieve both copy number variation (CNV) and structural variation data. Meanwhile, CNV data are much easier to obtain than structural variation data. Hence, in order to reduce the reliance on human experts' efforts and structural variation data extraction, it is necessary to establish a reliable and accurate chromothripsis detection method based on CNV data. RESULTS To address those issues, we propose a method to detect chromothripsis solely based on CNV data. With the help of structure learning, the intrinsic relationship-directed acyclic graph of CNV features is inferred to derive a CNV embedding graph (i.e. CNV-DAG). Subsequently, a neural network based on Graph Transformer, local feature extraction, and non-linear feature interaction, is proposed with the embedding graph as the input to distinguish whether the chromothripsis event occurs. Ablation experiments, clustering, and feature importance analysis are also conducted to enable the proposed model to be explained by capturing mechanistic insights. AVAILABILITY AND IMPLEMENTATION The source code and data are freely available at https://github.com/luvyfdawnYu/CNV_chromothripsis.
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Affiliation(s)
- Jixiang Yu
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Nanjun Chen
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Zetian Zheng
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Ming Gao
- School of Management Science and Engineering, Dongbei University of Finance and Economics, Dalian 116025, China
| | - Ning Liang
- University of Michigan, Ann Arbor, MI 48105, United States
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Hong Kong Institute for Data Science, City University of Hong Kong, Kowloon, 999077, Hong Kong
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11
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Coccaro N, Anelli L, Zagaria A, Tarantini F, Cumbo C, Tota G, Minervini CF, Minervini A, Conserva MR, Redavid I, Parciante E, Macchia MG, Specchia G, Musto P, Albano F. Feasibility of Optical Genome Mapping in Cytogenetic Diagnostics of Hematological Neoplasms: A New Way to Look at DNA. Diagnostics (Basel) 2023; 13:diagnostics13111841. [PMID: 37296693 DOI: 10.3390/diagnostics13111841] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Optical genome mapping (OGM) is a new genome-wide technology that can reveal both structural genomic variations (SVs) and copy number variations (CNVs) in a single assay. OGM was initially employed to perform genome assembly and genome research, but it is now more widely used to study chromosome aberrations in genetic disorders and in human cancer. One of the most useful OGM applications is in hematological malignancies, where chromosomal rearrangements are frequent and conventional cytogenetic analysis alone is insufficient, necessitating further confirmation using ancillary techniques such as fluorescence in situ hybridization, chromosomal microarrays, or multiple ligation-dependent probe amplification. The first studies tested OGM efficiency and sensitivity for SV and CNV detection, comparing heterogeneous groups of lymphoid and myeloid hematological sample data with those obtained using standard cytogenetic diagnostic tests. Most of the work based on this innovative technology was focused on myelodysplastic syndromes (MDSs), acute myeloid leukemia (AML), and acute lymphoblastic leukemia (ALL), whereas little attention was paid to chronic lymphocytic leukemia (CLL) or multiple myeloma (MM), and none was paid to lymphomas. The studies showed that OGM can now be considered as a highly reliable method, concordant with standard cytogenetic techniques but able to detect novel clinically significant SVs, thus allowing better patient classification, prognostic stratification, and therapeutic choices in hematological malignancies.
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Affiliation(s)
- Nicoletta Coccaro
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luisa Anelli
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Antonella Zagaria
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Tarantini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Cosimo Cumbo
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giuseppina Tota
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Crescenzio Francesco Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Angela Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Maria Rosa Conserva
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Immacolata Redavid
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Elisa Parciante
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Maria Giovanna Macchia
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giorgina Specchia
- School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Albano
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
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12
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Kadam Amare P, Nikalje Khasnis S, Hande P, Lele H, Wable N, Kaskar S, Nikam Gujar N, Gardi N, Prabhudesai A, Todi K, Waghole R, Roy P. Cytogenetic Abnormalities in Multiple Myeloma: Incidence, Prognostic Significance, and Geographic Heterogeneity in Indian and Western Populations. Cytogenet Genome Res 2023; 162:529-540. [PMID: 36780889 PMCID: PMC10534967 DOI: 10.1159/000529191] [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: 10/28/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
Multiple myeloma (MM) is a genetically complex and heterogeneous neoplasm in which cytogenetics is a major factor playing an important role in the risk stratification of disease. High-risk MM based upon cytogenetic classification includes primary IGH translocations t(4;14), t(14;16), t(14;20), and secondary progressive aberrations such as gain/amp(1q), 1p deletion, del(17p), and hypodiploidy. Several studies have proved that interphase FISH can detect primary as well as secondary cryptic aberrations very efficiently in lowest 5-10% abnormal plasma cell population. The present large-scale study was undertaken to evaluate the incidence of cytogenetic abnormalities, to analyse the correlation of conventional karyotyping with FISH, and to seek the geographic heterogeneity in the incidence of primary as well as secondary aberrations in our Indian versus Western populations. We conducted prospective studies of 1,104 patients consecutively referred from the primary, secondary, and tertiary oncology centres from all over India. Interphase FISH was performed on isolated plasma cells. Karyotype analysis was done as per ISCN 2016 and 2020. FISH could detect cytogenetic abnormalities in 67.6% of the cases with an incidence of 59% non-hyperdiploidy. The incidence of IGH translocation was 26% versus literature frequency of 40-50% which was mainly due to a low incidence (6%) of t(11;14) in contrast to 15-20% in other series. Additionally, the association of secondary progressive aberrations in the hyperdiploid group rather than the non-hyperdiploid group in our patients is not a common finding. A biallelic inactivation of TP53 as an ultra-high risk factor was detected in old-aged patients. These observations disclose the novel findings and strongly indicate the racial disparity which leads to geographic heterogeneity. In contrast to FISH, conventional karyotyping could detect MM-related aberrations in 50% of cases, of which 44% revealed highly complex karyotypes with common aberrations of chromosome 1q. Overall, FISH was found to be a novel, easy approach with high success rate and capability of detection of all cytogenetic abnormalities that add valid information for the risk stratification of disease. This, in future, in combination with mutation profile and gene expression profile will help in further refinement of disease and identification of actionable targets.
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Affiliation(s)
- Pratibha Kadam Amare
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | | | - Pranita Hande
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Hrushikesh Lele
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Nishigandha Wable
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Snehal Kaskar
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Nikita Nikam Gujar
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Nilesh Gardi
- ACTREC, Tata Memorial Center, Navi Mumbai, India
| | - Aniket Prabhudesai
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Karishma Todi
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Rohit Waghole
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Pritha Roy
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
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13
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Chojnacka M, Diamond B, Ziccheddu B, Rustad E, Maclachlan K, Papadimitriou M, Boyle EM, Blaney P, Usmani S, Morgan G, Landgren O, Maura F. Impact of rare structural variant events in newly diagnosed multiple myeloma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522573. [PMID: 36711679 PMCID: PMC9881878 DOI: 10.1101/2023.01.03.522573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Whole genome sequencing (WGS) of newly diagnosed multiple myeloma patients (NDMM) has shown recurrent structural variant (SV) involvement in distinct regions of the genome (i.e. hotspots) and causing recurrent copy number alterations. Together with canonical immunoglobulin translocations, these SVs are recognized as "recurrent SVs". More than half SVs were not involved in recurrent events. The significance of these "rare SVs" has not been previously examined. In this study, we utilize 752 WGS and 591 RNA-seq data from NDMM patients to determine the role of rare SVs in myeloma pathogenesis. 94% of patients harbored at least one rare SV event. Rare SVs showed an SV-class specific enrichment within genes and superenhancers associated with outlier gene expression. Furthermore, known myeloma driver genes recurrently impacted by point mutations were dysregulated by rare SVs. Overall, we demonstrate the association of rare SVs with aberrant gene expression supporting a driver role in myeloma pathogenesis. SIGNIFICANCE Characterization of multiple myeloma genome revealed that more than half structural variants are not involved in recurrent events. Here, we demonstrate that these rare SVs hold potential for myeloma pathogenesis through their gene expression impact. Rare SVs contribute to MM heterogeneity and have implications for development of individualized treatment.
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14
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de Groot D, Spanjaard A, Hogenbirk MA, Jacobs H. Chromosomal Rearrangements and Chromothripsis: The Alternative End Generation Model. Int J Mol Sci 2023; 24:ijms24010794. [PMID: 36614236 PMCID: PMC9821053 DOI: 10.3390/ijms24010794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
Chromothripsis defines a genetic phenomenon where up to hundreds of clustered chromosomal rearrangements can arise in a single catastrophic event. The phenomenon is associated with cancer and congenital diseases. Most current models on the origin of chromothripsis suggest that prior to chromatin reshuffling numerous DNA double-strand breaks (DSBs) have to exist, i.e., chromosomal shattering precedes rearrangements. However, the preference of a DNA end to rearrange in a proximal accessible region led us to propose chromothripsis as the reaction product of successive chromatin rearrangements. We previously coined this process Alternative End Generation (AEG), where a single DSB with a repair-blocking end initiates a domino effect of rearrangements. Accordingly, chromothripsis is the end product of this domino reaction taking place in a single catastrophic event.
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Affiliation(s)
- Daniel de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marc A. Hogenbirk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Agendia NV, Radarweg 60, 1043 NT Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Correspondence: ; Tel.: +31-20-512-2065
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15
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Aarabi M, Yoest JM, Farah R, Rajkovic A, Swerdlow SH, Yatsenko SA. A Novel Integrated Approach for Cytogenomic Evaluation of Plasma Cell Neoplasms. J Mol Diagn 2022; 24:1067-1078. [PMID: 35940519 DOI: 10.1016/j.jmoldx.2022.07.002] [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: 03/26/2022] [Revised: 06/24/2022] [Accepted: 07/19/2022] [Indexed: 12/29/2022] Open
Abstract
Plasma cell neoplasm (PCN) is associated with characteristic chromosomal aberrations of diagnostic and prognostic significance. The presence of a small percentage of neoplastic cells is a drawback in the application of karyotyping and fluorescence in situ hybridization for the evaluation of bone marrow aspirate. The analysis of samples enriched for CD138+ cells has improved the detection rate. However, fluorescence in situ hybridization requires several probes and may not be completed due to a limited number of isolated cells. To address the issues experienced with the conventional approach, a novel integrated protocol that consists of whole-genome amplification of DNA isolated from CD138+ cells, followed by microarray as well as one fluorescence in situ hybridization assay for balanced IGH gene rearrangements, has been developed. In the present study in a cohort of 56 patients with clinical suspicion for PCN, compared to conventional cytogenetic analysis, this approach provided higher yield in the detection of PCN-related abnormalities, irrespective of the initial percentage of plasma cells. Whole-genome profiling uncovered recurrent chromosomal abnormalities of prognostic value, including unbalanced alterations within the MYC locus, 16q loss, and hypodiploidy, that were not otherwise detectable by conventional methods. The proposed approach is cost-efficient and provides a superior detection rate, required for proper risk stratification and differential diagnosis of PCN regardless of initial plasma cell percentage.
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Affiliation(s)
- Mahmoud Aarabi
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jennifer M Yoest
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rafic Farah
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Aleksandar Rajkovic
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, University of California-San Francisco, San Francisco, California; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California-San Francisco, San Francisco, California; Institute of Human Genetics, University of California-San Francisco, San Francisco, California
| | - Steven H Swerdlow
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Svetlana A Yatsenko
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania.
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16
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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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17
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Holstein SA, Asimakopoulos F, Azab AK, Bianchi G, Bhutani M, Crews LA, Cupedo T, Giles H, Gooding S, Hillengass J, John L, Kaiser S, Lee L, Maclachlan K, Pasquini MC, Pichiorri F, Shah N, Shokeen M, Shy BR, Smith EL, Verona R, Usmani SZ, McCarthy PL. Proceedings from the Blood and Marrow Transplant Clinical Trials Network Myeloma Intergroup Workshop on Immune and Cellular Therapy in Multiple Myeloma. Transplant Cell Ther 2022; 28:446-454. [PMID: 35605882 PMCID: PMC9357156 DOI: 10.1016/j.jtct.2022.05.019] [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: 04/19/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/30/2022]
Abstract
The Blood and Marrow Transplant Clinical Trials Network (BMT CTN) Myeloma Intergroup conducted a workshop on Immune and Cellular Therapy in Multiple Myeloma on January 7, 2022. This workshop included presentations by basic, translational, and clinical researchers with expertise in plasma cell dyscrasias. Four main topics were discussed: platforms for myeloma disease evaluation, insights into pathophysiology, therapeutic target and resistance mechanisms, and cellular therapy for multiple myeloma. Here we provide a comprehensive summary of these workshop presentations.
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Affiliation(s)
| | - Fotis Asimakopoulos
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | | | - Giada Bianchi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Leslie A Crews
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Tom Cupedo
- ErasmusMC Cancer Institute Rotterdam, Rotterdam, The Netherlands
| | - Hannah Giles
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Sarah Gooding
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Lukas John
- University Hospital Heidelberg, Heidelberg, Germany
| | | | - Lydia Lee
- University College London, London, United Kingdom
| | | | | | - Flavia Pichiorri
- Judy and Bernard Briskin Center for Multiple Myeloma Research, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California; Department of Hematologic Malignancies Translational Science, Beckman Research Institute, City of Hope, Duarte, California
| | - Nina Shah
- University of California San Francisco, San Francisco, California
| | - Monica Shokeen
- Washington University School of Medicine, St. Louis, Missouri
| | - Brian R Shy
- University of California San Francisco, San Francisco, California
| | - Eric L Smith
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Raluca Verona
- Janssen Research & Development, Spring House, Pennsylvania
| | - Saad Z Usmani
- Memorial Sloan Kettering Cancer Center, New York, New York
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18
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Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults. Leukemia 2022; 36:2577-2585. [PMID: 35974102 PMCID: PMC9613476 DOI: 10.1038/s41375-022-01671-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/08/2022]
Abstract
Chromothripsis is a mitotic catastrophe that arises from multiple double strand breaks and incorrect re-joining of one or a few chromosomes. We report on incidence, distribution, and features of chromothriptic events in T-cell acute lymphoblastic leukemias (T-ALL). SNP array was performed in 103 T-ALL (39 ETP/near ETP, 59 non-ETP, and 5 with unknown stage of differentiation), including 38 children and 65 adults. Chromothripsis was detected in 11.6% of all T-ALL and occurred only in adult cases with an immature phenotype (12/39 cases; 30%). It affected 1 to 4 chromosomes, and recurrently involved chromosomes 1, 6, 7, and 17. Abnormalities of genes typically associated with T-ALL were found at breakpoints of chromothripsis. In addition, it gave rise to new/rare alterations, such as, the SFPQ::ZFP36L2 fusion, reported in pediatric T-ALL, deletions of putative suppressors, such as IKZF2 and CSMD1, and amplification of the BCL2 gene. Compared to negative cases, chromothripsis positive T-ALL had a significantly higher level of MYCN expression, and a significant downregulation of RGCC, which is typically induced by TP53 in response to DNA damage. Furthermore we identified mutations and/or deletions of DNA repair/genome stability genes in all cases, and an association with NUP214 rearrangements in 33% of cases.
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19
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Crasta K. Chromothripsis: A shattered chromosome in the spotlight. Semin Cell Dev Biol 2021; 123:88-89. [PMID: 34840079 DOI: 10.1016/j.semcdb.2021.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Karen Crasta
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; A(⁎)STAR Institute of Molecular and Cell Biology, Singapore.
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