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Elbahoty MH, Papineni B, Samant RS. Multiple myeloma: clinical characteristics, current therapies and emerging innovative treatments targeting ribosome biogenesis dynamics. Clin Exp Metastasis 2024:10.1007/s10585-024-10305-2. [PMID: 39162964 DOI: 10.1007/s10585-024-10305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/01/2024] [Indexed: 08/21/2024]
Abstract
Multiple myeloma (MM) is a clinical disorder characterized by aberrant plasma cell growth in the bone marrow microenvironment. Globally, the prevalence of MM has been steadily increasing at an alarming rate. In the United States, more than 30,000 cases will be diagnosed in 2024 and it accounts for about 2% of cancer diagnoses and more than 2% of cancer deaths, more than double the worldwide figure. Both symptomatic and active MM are distinguished by uncontrolled plasma cell growth, which results in severe renal impairment, anemia, hypercalcemia, and bone loss. Multiple drugs have been approved by the FDA and are now widely used in clinical practice for MM. Although triplet and quadruplet induction regimens, autologous stem cell transplantation (ASCT), and maintenance treatment are used, MM continues to be an incurable illness characterized by relapses that may occur at various phases of its progression. MM patients with frailty, extramedullary disease, plasma cell leukemia, central nervous system recurrence, functional high risk, and the elderly are among those with the greatest current unmet needs. The high cost of care is an additional challenge. MM cells are highly protein secretary cells and thus are dependent on the activation of certain translation pathways. MM also has a high chance of altering ribosomal protein-encoding genes like MYC mutation. In this article we discuss the importance of ribosome biogenesis in promoting MM and RNA polymerase I inhibition as an upcoming treatment with potential promise for MM patients.
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Affiliation(s)
- Mohamed H Elbahoty
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- Hematology Unit, Department of Internal Medicine, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Bhavyasree Papineni
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rajeev S Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Birmingham VA Medical Center, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
- , WTI 320E, 1824 6th Ave South, Birmingham, AL, 35294, USA.
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2
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Lind J, Aksoy O, Prchal-Murphy M, Fan F, Fulciniti M, Stoiber D, Bakiri L, Wagner EF, Zwickl-Traxler E, Sattler M, Kollmann K, Vallet S, Podar K. Dual therapeutic targeting of MYC and JUNB transcriptional programs for enhanced anti-myeloma activity. Blood Cancer J 2024; 14:138. [PMID: 39160158 PMCID: PMC11333473 DOI: 10.1038/s41408-024-01117-4] [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: 04/13/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/21/2024] Open
Abstract
Deregulation of transcription factors (TFs) leading to uncontrolled proliferation of tumor cells within the microenvironment represents a hallmark of cancer. However, the biological and clinical impact of transcriptional interference, particularly in multiple myeloma (MM) cells, remains poorly understood. The present study shows for the first time that MYC and JUNB, two crucial TFs implicated in MM pathogenesis, orchestrate distinct transcriptional programs. Specifically, our data revealed that expression levels of MYC, JUNB, and their respective downstream targets do not correlate and that their global chromatin-binding patterns are not significantly overlapping. Mechanistically, MYC expression was not affected by JUNB knockdown, and conversely, JUNB expression and transcriptional activity were not affected by MYC knockdown. Moreover, suppression of MYC levels in MM cells via targeting the master regulator BRD4 by either siRNA-mediated knockdown or treatment with the novel proteolysis targeting chimera (PROTAC) MZ-1 overcame bone marrow (BM) stroma cell/IL-6-induced MYC- but not MEK-dependent JUNB-upregulation and transcriptional activity. Consequently, targeting of the two non-overlapping MYC- and JUNB-transcriptoms by MZ-1 in combination with genetic or pharmacological JUNB-targeting approaches synergistically enhanced MM cell death, both in 2D and our novel dynamic 3D models of the BM milieu as well as in murine xenografts. In summary, our data emphasize the opportunity to employ MYC and JUNB dual-targeting treatment strategies in MM as another exciting approach to further improve patient outcomes.
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Affiliation(s)
- Judith Lind
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Osman Aksoy
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Michaela Prchal-Murphy
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mariateresa Fulciniti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Dagmar Stoiber
- Division of Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Latifa Bakiri
- Genes & Disease Group, Department of Laboratory Medicine, Medical University of Vienna (MUW), Vienna, Austria
| | - Erwin F Wagner
- Genes & Disease Group, Department of Laboratory Medicine, Medical University of Vienna (MUW), Vienna, Austria
- Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria
| | | | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Karoline Kollmann
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Sonia Vallet
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Division of Internal Medicine 2, University Hospital Krems, Krems/ Donau, Austria
| | - Klaus Podar
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.
- Division of Internal Medicine 2, University Hospital Krems, Krems/ Donau, Austria.
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3
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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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Xiong S, Zhou J, Tan TK, Chung TH, Tan TZ, Toh SHM, Tang NXN, Jia Y, See YX, Fullwood MJ, Sanda T, Chng WJ. Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma. Nat Commun 2024; 15:6810. [PMID: 39122682 PMCID: PMC11316114 DOI: 10.1038/s41467-024-50910-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Multiple myeloma is a hematological malignancy arising from immunoglobulin-secreting plasma cells. It remains poorly understood how chromatin rewiring of regulatory elements contributes to tumorigenesis and therapy resistance in myeloma. Here we generate a high-resolution contact map of myeloma-associated super-enhancers by integrating H3K27ac ChIP-seq and HiChIP from myeloma cell lines, patient-derived myeloma cells and normal plasma cells. Our comprehensive transcriptomic and phenomic analyses prioritize candidate genes with biological and clinical implications in myeloma. We show that myeloma cells frequently acquire SE that transcriptionally activate an oncogene PPP1R15B, which encodes a regulatory subunit of the holophosphatase complex that dephosphorylates translation initiation factor eIF2α. Epigenetic silencing or knockdown of PPP1R15B activates pro-apoptotic eIF2α-ATF4-CHOP pathway, while inhibiting protein synthesis and immunoglobulin production. Pharmacological inhibition of PPP1R15B using Raphin1 potentiates the anti-myeloma effect of bortezomib. Our study reveals that myeloma cells are vulnerable to perturbation of PPP1R15B-dependent protein homeostasis, highlighting a promising therapeutic strategy.
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Affiliation(s)
- Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nicole Xin Ning Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yunlu Jia
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yi Xiang See
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Takaomi Sanda
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), Singapore, Singapore.
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5
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Bolomsky A, Ceribelli M, Scheich S, Rinaldi K, Huang DW, Chakraborty P, Pham L, Wright GW, Hsiao T, Morris V, Choi J, Phelan JD, Holewinski RJ, Andresson T, Wisniewski J, Riley D, Pittaluga S, Hill E, Thomas CJ, Muppidi J, Young RM. IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma. Cancer Cell 2024; 42:1185-1201.e14. [PMID: 38906156 PMCID: PMC11233249 DOI: 10.1016/j.ccell.2024.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/03/2024] [Accepted: 05/30/2024] [Indexed: 06/23/2024]
Abstract
Multiple myeloma (MM) is an incurable plasma cell malignancy that exploits transcriptional networks driven by IRF4. We employ a multi-omics approach to discover IRF4 vulnerabilities, integrating functional genomics screening, spatial proteomics, and global chromatin mapping. ARID1A, a member of the SWI/SNF chromatin remodeling complex, is required for IRF4 expression and functionally associates with IRF4 protein on chromatin. Deleting Arid1a in activated murine B cells disrupts IRF4-dependent transcriptional networks and blocks plasma cell differentiation. Targeting SWI/SNF activity leads to rapid loss of IRF4-target gene expression and quenches global amplification of oncogenic gene expression by MYC, resulting in profound toxicity to MM cells. Notably, MM patients with aggressive disease bear the signature of SWI/SNF activity, and SMARCA2/4 inhibitors remain effective in immunomodulatory drug (IMiD)-resistant MM cells. Moreover, combinations of SWI/SNF and MEK inhibitors demonstrate synergistic toxicity to MM cells, providing a promising strategy for relapsed/refractory disease.
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Affiliation(s)
- Arnold Bolomsky
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michele Ceribelli
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20892, USA
| | - Sebastian Scheich
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kristina Rinaldi
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Papiya Chakraborty
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisette Pham
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - George W Wright
- Biometric Research Branch, DCTD, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tony Hsiao
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivian Morris
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jaewoo Choi
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James D Phelan
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald J Holewinski
- Protein Mass Spectrometry Group, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Mass Spectrometry Group, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Jan Wisniewski
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deanna Riley
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth Hill
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Craig J Thomas
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20892, USA
| | - Jagan Muppidi
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan M Young
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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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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7
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Patel-Tupper D, Kelikian A, Leipertz A, Maryn N, Tjahjadi M, Karavolias NG, Cho MJ, Niyogi KK. Multiplexed CRISPR-Cas9 mutagenesis of rice PSBS1 noncoding sequences for transgene-free overexpression. SCIENCE ADVANCES 2024; 10:eadm7452. [PMID: 38848363 PMCID: PMC11160471 DOI: 10.1126/sciadv.adm7452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Understanding CRISPR-Cas9's capacity to produce native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR-Cas9 mutagenesis of noncoding sequences upstream of the rice PSBS1 gene. We isolated 120 gene-edited alleles with varying non-photochemical quenching (NPQ) capacity in vivo-from knockout to overexpression-using a high-throughput screening pipeline. Overexpression increased OsPsbS1 protein abundance two- to threefold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced NPQ capacity and water-use efficiency. Across our resolved genetic variation, we identify the role of 5'UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252-kb duplication/inversion generated here, evidence the potential of CRISPR-Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have advanced the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.
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Affiliation(s)
- Dhruv Patel-Tupper
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Armen Kelikian
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Anna Leipertz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Nina Maryn
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Michelle Tjahjadi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Nicholas G. Karavolias
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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8
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Jin X, Li H, Zhang D, Liu S, Song Y, Zhang F, Li Z, Zhuang J. Myc rearrangement redefines the stratification of high-risk multiple myeloma. Cancer Med 2024; 13:e7194. [PMID: 38845529 PMCID: PMC11157166 DOI: 10.1002/cam4.7194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Myc rearrangement (Myc-R) is a controversial factor linked to adverse outcomes in newly diagnosed multiple myeloma (NDMM). AIMS This study aimed to evaluate the impact of Myc-R on the prognosis of NDMM patients and its role in risk stratification compared with traditional high-risk cytogenetic abnormalities (HRCAs). MATERIALS & METHODS A total of 417 NDMM patients enrolled from May 2009 to September 2022 were included. Fluorescence in situ hybridization (FISH) was used to detect Myc-R and other Myc abnormalities (Myc-OA). Median progression-free survival (PFS) and overall survival (OS) were analyzed using Kaplan-Meier methods and log-rank tests. Multivariate Cox regression analysis was used to identify independent risk factors. RESULTS Myc-R was identified in 13.7% of patients, while 14.6% had Myc-OA. Patients with Myc-R had significantly shorter median PFS (15.9 months) and OS (25.1 months) compared with those with Myc-OA (24.5 months PFS; 29.8 months OS) and Myc-negative (Myc-N) status (29.8 months PFS, 29.8 months OS). Myc-R was independently associated with worse PFS and OS compared to Myc-OA. Patients with Myc-R alone had inferior median PFS (15.9 months vs. 28.1 months, p = 0.032) and OS (25.1 months vs. 61.2 months, p = 0.04) compared to those with traditional single HRCA. DISCUSSION The study suggests that traditional single HRCA may not significantly impact survival in NDMM patients. However, incorporating Myc rearrangement or traditional double/triple-hit HRCAs into the risk stratification model improves its predictive value, highlighting the importance of Myc rearrangement in risk assessment. CONCLUSION Myc rearrangement is an independent adverse prognostic factor in NDMM. The incorporation of Myc rearrangement or multiple HRCAs into risk stratification models improves their prognostic value, providing a novel perspective on high-risk factors in NDMM.
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Affiliation(s)
- Xianghong Jin
- Department of Hematology, Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
- Department of Rare DiseasesPeking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijingChina
| | - Hui Li
- Department of Hematology, Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
| | - Dingding Zhang
- Medical Research Center, State Key laboratory of Complex Severe and Rare Diseases, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Shuangjiao Liu
- Department of Hematology, Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
| | - Yuhang Song
- Department of Hematology, Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
| | - Fujing Zhang
- Department of Hematology, Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
| | - Ziping Li
- Department of Hematology, Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
| | - Junling Zhuang
- Department of Hematology, Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijingChina
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9
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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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10
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Lai G, De Grossi F, Catusi I, Pesce E, Manfrini N. Dissecting the Puzzling Roles of FAM46C: A Multifaceted Pan-Cancer Tumour Suppressor with Increasing Clinical Relevance. Cancers (Basel) 2024; 16:1706. [PMID: 38730656 PMCID: PMC11083040 DOI: 10.3390/cancers16091706] [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: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
FAM46C is a well-established tumour suppressor with a role that is not completely defined or universally accepted. Although FAM46C expression is down-modulated in several tumours, significant mutations in the FAM46C gene are only found in multiple myeloma (MM). Consequently, its tumour suppressor activity has primarily been studied in the MM context. However, emerging evidence suggests that FAM46C is involved also in other cancer types, namely colorectal, prostate and gastric cancer and squamous cell and hepatocellular carcinoma, where FAM46C expression was found to be significantly reduced in tumoural versus non-tumoural tissues and where FAM46C was shown to possess anti-proliferative properties. Accordingly, FAM46C was recently proposed to function as a pan-cancer prognostic marker, bringing FAM46C under the spotlight and attracting growing interest from the scientific community in the pathways modulated by FAM46C and in its mechanistic activity. Here, we will provide the first comprehensive review regarding FAM46C by covering (1) the intracellular pathways regulated by FAM46C, namely the MAPK/ERK, PI3K/AKT, β-catenin and TGF-β/SMAD pathways; (2) the models regarding its mode of action, specifically the poly(A) polymerase, intracellular trafficking modulator and inhibitor of centriole duplication models, focusing on connections and interdependencies; (3) the regulation of FAM46C expression in different environments by interferons, IL-4, TLR engagement or transcriptional modulators; and, lastly, (4) how FAM46C expression levels associate with increased/decreased tumour cell sensitivity to anticancer agents, such as bortezomib, dexamethasone, lenalidomide, pomalidomide, doxorubicin, melphalan, SK1-I, docetaxel and norcantharidin.
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Affiliation(s)
- Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Federica De Grossi
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Ilaria Catusi
- SC Clinical Pathology, SS Medical Genetics Laboratory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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11
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Hasan Bou Issa L, Fléchon L, Laine W, Ouelkdite A, Gaggero S, Cozzani A, Tilmont R, Chauvet P, Gower N, Sklavenitis-Pistofidis R, Brinster C, Thuru X, Touil Y, Quesnel B, Mitra S, Ghobrial IM, Kluza J, Manier S. MYC dependency in GLS1 and NAMPT is a therapeutic vulnerability in multiple myeloma. iScience 2024; 27:109417. [PMID: 38510131 PMCID: PMC10952034 DOI: 10.1016/j.isci.2024.109417] [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: 09/25/2023] [Revised: 12/26/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
Multiple myeloma (MM) is an incurable hematological malignancy in which MYC alterations contribute to the malignant phenotype. Nevertheless, MYC lacks therapeutic druggability. Here, we leveraged large-scale loss-of-function screens and conducted a small molecule screen to identify genes and pathways with enhanced essentiality correlated with MYC expression. We reported a specific gene dependency in glutaminase (GLS1), essential for the viability and proliferation of MYC overexpressing cells. Conversely, the analysis of isogenic models, as well as cell lines dataset (CCLE) and patient datasets, revealed GLS1 as a non-oncogenic dependency in MYC-driven cells. We functionally delineated the differential modulation of glutamine to maintain mitochondrial function and cellular biosynthesis in MYC overexpressing cells. Furthermore, we observed that pharmaceutical inhibition of NAMPT selectively affects MYC upregulated cells. We demonstrate the effectiveness of combining GLS1 and NAMPT inhibitors, suggesting that targeting glutaminolysis and NAD synthesis may be a promising strategy to target MYC-driven MM.
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Affiliation(s)
- Lama Hasan Bou Issa
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Léa Fléchon
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - William Laine
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Aicha Ouelkdite
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Silvia Gaggero
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Adeline Cozzani
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Remi Tilmont
- Department of Hematology, CHU Lille, 59000 Lille, France
| | - Paul Chauvet
- Department of Hematology, CHU Lille, 59000 Lille, France
| | - Nicolas Gower
- Department of Hematology, CHU Lille, 59000 Lille, France
| | | | - Carine Brinster
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Xavier Thuru
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Yasmine Touil
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Bruno Quesnel
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
- Department of Hematology, CHU Lille, 59000 Lille, France
| | - Suman Mitra
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Irene M. Ghobrial
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jérôme Kluza
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
| | - Salomon Manier
- Canther, INSERM UMR-S1277 and CNRS UMR9020, Lille University, 59000 Lille, France
- Department of Hematology, CHU Lille, 59000 Lille, France
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12
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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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13
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Prutsch N, He S, Berezovskaya A, Durbin AD, Dharia NV, Maher KA, Matthews JD, Hare L, Turner SD, Stegmaier K, Kenner L, Merkel O, Look AT, Abraham BJ, Zimmerman MW. STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma. Cell Rep Med 2024; 5:101472. [PMID: 38508140 PMCID: PMC10983107 DOI: 10.1016/j.xcrm.2024.101472] [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: 09/25/2022] [Revised: 12/01/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Anaplastic large cell lymphoma (ALCL) is an aggressive, CD30+ T cell lymphoma of children and adults. ALK fusion transcripts or mutations in the JAK-STAT pathway are observed in most ALCL tumors, but the mechanisms underlying tumorigenesis are not fully understood. Here, we show that dysregulated STAT3 in ALCL cooccupies enhancers with master transcription factors BATF3, IRF4, and IKZF1 to form a core regulatory circuit that establishes and maintains the malignant cell state in ALCL. Critical downstream targets of this network in ALCL cells include the protooncogene MYC, which requires active STAT3 to facilitate high levels of MYC transcription. The core autoregulatory transcriptional circuitry activity is reinforced by MYC binding to the enhancer regions associated with STAT3 and each of the core regulatory transcription factors. Thus, activation of STAT3 provides the crucial link between aberrant tyrosine kinase signaling and the core transcriptional machinery that drives tumorigenesis and creates therapeutic vulnerabilities in ALCL.
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Affiliation(s)
- Nicole Prutsch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Alla Berezovskaya
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Adam D Durbin
- Division of Molecular Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Kelsey A Maher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jamie D Matthews
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Lucy Hare
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Department of Pediatric Oncology and Hematology, Addenbrooke's Hospital, Cambridge, UK
| | - Suzanne D Turner
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Lukas Kenner
- Department of Pathology, Unit of Experimental and Laboratory Animal Pathology, Medical University of Vienna, Vienna, Austria
| | - Olaf Merkel
- Department of Pathology, Unit of Experimental and Laboratory Animal Pathology, Medical University of Vienna, Vienna, Austria
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA.
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA.
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14
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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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15
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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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16
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Neri P, Barwick BG, Jung D, Patton JC, Maity R, Tagoug I, Stein CK, Tilmont R, Leblay N, Ahn S, Lee H, Welsh SJ, Riggs DL, Stong N, Flynt E, Thakurta A, Keats JJ, Lonial S, Bergsagel PL, Boise LH, Bahlis NJ. ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma. Blood Cancer Discov 2024; 5:56-73. [PMID: 37934799 PMCID: PMC10772538 DOI: 10.1158/2643-3230.bcd-23-0061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/01/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
Immunomodulatory drugs (IMiD) are a backbone therapy for multiple myeloma (MM). Despite their efficacy, most patients develop resistance, and the mechanisms are not fully defined. Here, we show that IMiD responses are directed by IMiD-dependent degradation of IKZF1 and IKZF3 that bind to enhancers necessary to sustain the expression of MYC and other myeloma oncogenes. IMiD treatment universally depleted chromatin-bound IKZF1, but eviction of P300 and BRD4 coactivators only occurred in IMiD-sensitive cells. IKZF1-bound enhancers overlapped other transcription factor binding motifs, including ETV4. Chromatin immunoprecipitation sequencing showed that ETV4 bound to the same enhancers as IKZF1, and ETV4 CRISPR/Cas9-mediated ablation resulted in sensitization of IMiD-resistant MM. ETV4 expression is associated with IMiD resistance in cell lines, poor prognosis in patients, and is upregulated at relapse. These data indicate that ETV4 alleviates IKZF1 and IKZF3 dependency in MM by maintaining oncogenic enhancer activity and identify transcriptional plasticity as a previously unrecognized mechanism of IMiD resistance. SIGNIFICANCE We show that IKZF1-bound enhancers are critical for IMiD efficacy and that the factor ETV4 can bind the same enhancers and substitute for IKZF1 and mediate IMiD resistance by maintaining MYC and other oncogenes. These data implicate transcription factor redundancy as a previously unrecognized mode of IMiD resistance in MM. See related article by Welsh, Barwick, et al., p. 34. See related commentary by Yun and Cleveland, p. 5. This article is featured in Selected Articles from This Issue, p. 4.
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Affiliation(s)
- Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - David Jung
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Jonathan C. Patton
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Ranjan Maity
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Ines Tagoug
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Caleb K. Stein
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Remi Tilmont
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Noemie Leblay
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Sungwoo Ahn
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Holly Lee
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Seth J. Welsh
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Daniel L. Riggs
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nicholas Stong
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Erin Flynt
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey
| | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | | | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - P. Leif Bergsagel
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Nizar J. Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
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17
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Welsh SJ, Barwick BG, Meermeier EW, Riggs DL, Shi CX, Zhu YX, Sharik ME, Du MT, Abrego Rocha LD, Garbitt VM, Stein CK, Petit JL, Meurice N, Tafoya Alvarado Y, Fonseca R, Todd KT, Brown S, Hammond ZJ, Cuc NH, Wittenberg C, Herzog C, Roschke AV, Demchenko YN, Chen WDD, Li P, Liao W, Leonard WJ, Lonial S, Bahlis NJ, Neri P, Boise LH, Chesi M, Bergsagel PL. Transcriptional Heterogeneity Overcomes Super-Enhancer Disrupting Drug Combinations in Multiple Myeloma. Blood Cancer Discov 2024; 5:34-55. [PMID: 37767768 PMCID: PMC10772542 DOI: 10.1158/2643-3230.bcd-23-0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Multiple myeloma (MM) is a malignancy that is often driven by MYC and that is sustained by IRF4, which are upregulated by super-enhancers. IKZF1 and IKZF3 bind to super-enhancers and can be degraded using immunomodulatory imide drugs (IMiD). Successful IMiD responses downregulate MYC and IRF4; however, this fails in IMiD-resistant cells. MYC and IRF4 downregulation can also be achieved in IMiD-resistant tumors using inhibitors of BET and EP300 transcriptional coactivator proteins; however, in vivo these drugs have a narrow therapeutic window. By combining IMiDs with EP300 inhibition, we demonstrate greater downregulation of MYC and IRF4, synergistic killing of myeloma in vitro and in vivo, and an increased therapeutic window. Interestingly, this potent combination failed where MYC and IRF4 expression was maintained by high levels of the AP-1 factor BATF. Our results identify an effective drug combination and a previously unrecognized mechanism of IMiD resistance. SIGNIFICANCE These results highlight the dependence of MM on IKZF1-bound super-enhancers, which can be effectively targeted by a potent therapeutic combination pairing IMiD-mediated degradation of IKZF1 and IKZF3 with EP300 inhibition. They also identify AP-1 factors as an unrecognized mechanism of IMiD resistance in MM. See related article by Neri, Barwick, et al., p. 56. See related commentary by Yun and Cleveland, p. 5. This article is featured in Selected Articles from This Issue, p. 4.
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Affiliation(s)
- Seth J. Welsh
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Erin W. Meermeier
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Daniel L. Riggs
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Chang-Xin Shi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Yuan Xiao Zhu
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Meaghen E. Sharik
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Megan T. Du
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Leslie D. Abrego Rocha
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Victoria M. Garbitt
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Caleb K. Stein
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Joachim L. Petit
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nathalie Meurice
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Yuliza Tafoya Alvarado
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Rodrigo Fonseca
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Kennedi T. Todd
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Sochilt Brown
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Zachery J. Hammond
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nicklus H. Cuc
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Courtney Wittenberg
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Camille Herzog
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Anna V. Roschke
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | | | - Wei-dong D. Chen
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Wei Liao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Warren J. Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Nizar J. Bahlis
- Department of Medical Oncology and Hematology, Tom Baker Cancer Center, Calgary, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada
| | - Paola Neri
- Department of Medical Oncology and Hematology, Tom Baker Cancer Center, Calgary, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Marta Chesi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - P. Leif Bergsagel
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
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Yun S, Cleveland JL. Transcriptional Plasticity Drives IMiD and p300 Inhibitor Resistance in Multiple Myeloma. Blood Cancer Discov 2024; 5:5-7. [PMID: 38085608 PMCID: PMC10772544 DOI: 10.1158/2643-3230.bcd-23-0223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
SUMMARY In this issue of Blood Cancer Discovery, Neri, Barwick, and colleagues and Welsh, Barwick, and colleagues performed RNA sequencing, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin using sequencing, and genetic studies to characterize the underlying mechanisms of immunomodulatory drug (IMiD) resistance in multiple myeloma. They demonstrated that IMiD resistance is driven by sustained expression of MYC and IRF4 via transcriptional plasticity that involves induction of ETV4 and BATF proteins, the binding of these proteins to their super-enhancers, and the recruitment of BRD4 and p300. Finally, these studies suggest IMiD and p300 inhibitor combination as a promising therapeutic strategy in multiple myeloma. See related article by Neri, Barwick, et al., p. 56 (9). See related article by Welsh, Barwick, et al., p. 34 (10).
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Affiliation(s)
- Seongseok Yun
- Department of Malignant Hematology, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John L. Cleveland
- Department of Tumor Microenvironment & Metastasis, Moffitt Cancer Center & Research Institute, Tampa, Florida
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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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Abstract
The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.
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Affiliation(s)
- Theophilus T Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA.
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21
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Petrilla C, Galloway J, Kudalkar R, Ismael A, Cottini F. Understanding DNA Damage Response and DNA Repair in Multiple Myeloma. Cancers (Basel) 2023; 15:4155. [PMID: 37627183 PMCID: PMC10453069 DOI: 10.3390/cancers15164155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Multiple myeloma (MM) is a plasma cell malignancy characterized by several genetic abnormalities, including chromosomal translocations, genomic deletions and gains, and point mutations. DNA damage response (DDR) and DNA repair mechanisms are altered in MM to allow for tumor development, progression, and resistance to therapies. Damaged DNA rarely induces an apoptotic response, given the presence of ataxia-telangiectasia mutated (ATM) loss-of-function or mutations, as well as deletions, mutations, or downregulation of tumor protein p53 (TP53) and tumor protein p73 (TP73). Moreover, DNA repair mechanisms are either hyperactive or defective to allow for rapid correction of the damage or permissive survival. Medications used to treat patients with MM can induce DNA damage, by either direct effects (mono-adducts induced by melphalan), or as a result of reactive oxygen species (ROS) production by proteasome inhibitors such as bortezomib. In this review, we will describe the mechanisms of DDR and DNA repair in normal tissues, the contribution of these pathways to MM disease progression and other phenotypes, and the potential therapeutic opportunities for patients with MM.
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Affiliation(s)
| | | | | | | | - Francesca Cottini
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
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22
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Boulos JC, Chatterjee M, Shan L, Efferth T. In Silico, In Vitro, and In Vivo Investigations on Adapalene as Repurposed Third Generation Retinoid against Multiple Myeloma and Leukemia. Cancers (Basel) 2023; 15:4136. [PMID: 37627164 PMCID: PMC10452460 DOI: 10.3390/cancers15164136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
The majority of hematopoietic cancers in adults are incurable and exhibit unpredictable remitting-relapsing patterns in response to various therapies. The proto-oncogene c-MYC has been associated with tumorigenesis, especially in hematological neoplasms. Therefore, targeting c-MYC is crucial to find effective, novel treatments for blood malignancies. To date, there are no clinically approved c-MYC inhibitors. In this study, we virtually screened 1578 Food and Drug Administration (FDA)-approved drugs from the ZINC15 database against c-MYC. The top 117 compounds from PyRx-based screening with the best binding affinities to c-MYC were subjected to molecular docking studies with AutoDock 4.2.6. Retinoids consist of synthetic and natural vitamin A derivatives. All-trans-retinoic acid (ATRA) were highly effective in hematological malignancies. In this study, adapalene, a third-generation retinoid usually used to treat acne vulgaris, was selected as a potent c-MYC inhibitor as it robustly bound to c-MYC with a lowest binding energy (LBE) of -7.27 kcal/mol, a predicted inhibition constant (pKi) of 4.69 µM, and a dissociation constant (Kd value) of 3.05 µM. Thus, we examined its impact on multiple myeloma (MM) cells in vitro and evaluated its efficiency in vivo using a xenograft tumor zebrafish model. We demonstrated that adapalene exerted substantial cytotoxicity against a panel of nine MM and two leukemic cell lines, with AMO1 cells being the most susceptible one (IC50 = 1.76 ± 0.39 µM) and, hence, the focus of this work. Adapalene (0.5 × IC50, 1 × IC50, 2 × IC50) decreased c-MYC expression and transcriptional activity in AMO1 cells in a dose-dependent manner. An examination of the cell cycle revealed that adapalene halted the cells in the G2/M phase and increased the portion of cells in the sub-G0/G1 phase after 48 and 72 h, indicating that cells failed to initiate mitosis, and consequently, cell death was triggered. Adapalene also increased the number of p-H3(Ser10) positive AMO1 cells, which is a further proof of its ability to prevent mitotic exit. Confocal imaging demonstrated that adapalene destroyed the tubulin network of U2OS cells stably transfected with a cDNA coding for α-tubulin-GFP, refraining the migration of malignant cells. Furthermore, adapalene induced DNA damage in AMO1 cells. It also induced apoptosis and autophagy, as demonstrated by flow cytometry and western blotting. Finally, adapalene impeded tumor growth in a xenograft tumor zebrafish model. In summary, the discovery of the vitamin A derivative adapalene as a c-MYC inhibitor reveals its potential as an avant-garde treatment for MM.
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Affiliation(s)
- Joelle C. Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
| | - Manik Chatterjee
- Translational Oncology, Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany;
| | - Letian Shan
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou 310053, China;
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
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23
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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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24
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Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science 2023; 380:eabm1696. [PMID: 37104607 PMCID: PMC10999243 DOI: 10.1126/science.abm1696] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2023] [Indexed: 04/29/2023]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.
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Affiliation(s)
- Kathleen C Keough
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Tyler Fair
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Hane Ryu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Alex Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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25
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Kravchuk EV, Ashniev GA, Gladkova MG, Orlov AV, Vasileva AV, Boldyreva AV, Burenin AG, Skirda AM, Nikitin PI, Orlova NN. Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. Cells 2023; 12:cells12081191. [PMID: 37190100 DOI: 10.3390/cells12081191] [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: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Super-enhancers (SEs) are cis-regulatory elements of the human genome that have been widely discussed since the discovery and origin of the term. Super-enhancers have been shown to be strongly associated with the expression of genes crucial for cell differentiation, cell stability maintenance, and tumorigenesis. Our goal was to systematize research studies dedicated to the investigation of structure and functions of super-enhancers as well as to define further perspectives of the field in various applications, such as drug development and clinical use. We overviewed the fundamental studies which provided experimental data on various pathologies and their associations with particular super-enhancers. The analysis of mainstream approaches for SE search and prediction allowed us to accumulate existing data and propose directions for further algorithmic improvements of SEs' reliability levels and efficiency. Thus, here we provide the description of the most robust algorithms such as ROSE, imPROSE, and DEEPSEN and suggest their further use for various research and development tasks. The most promising research direction, which is based on topic and number of published studies, are cancer-associated super-enhancers and prospective SE-targeted therapy strategies, most of which are discussed in this review.
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Affiliation(s)
- Ekaterina V Kravchuk
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
| | - German A Ashniev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Marina G Gladkova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Alexey V Orlov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anastasiia V Vasileva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anna V Boldyreva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Alexandr G Burenin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Artemiy M Skirda
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Petr I Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Natalia N Orlova
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
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26
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Di Giorgio E, Benetti R, Kerschbamer E, Xodo L, Brancolini C. Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:97-148. [PMID: 37657861 DOI: 10.1016/bs.ircmb.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Super-enhancers evolve as elements at the top of the hierarchical control of gene expression. They are important end-gatherers of signaling pathways that control stemness, differentiation or adaptive responses. Many epigenetic regulations focus on these regions, and not surprisingly, during the process of tumorigenesis, various alterations can account for their dysfunction. Super-enhancers are emerging as key drivers of the aberrant gene expression landscape that sustain the aggressiveness of cancer cells. In this review, we will describe and discuss about the structure of super-enhancers, their epigenetic regulation, and the major changes affecting their functionality in cancer.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Roberta Benetti
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Emanuela Kerschbamer
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Luigi Xodo
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy.
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27
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Jakubikova J, Cholujova D, Beke G, Hideshima T, Klucar L, Leiba M, Jamroziak K, Richardson PG, Kastritis E, Dorfman DM, Anderson KC. Heterogeneity of B cell lymphopoiesis in patients with premalignant and active myeloma. JCI Insight 2023; 8:159924. [PMID: 36752202 PMCID: PMC9977435 DOI: 10.1172/jci.insight.159924] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/15/2022] [Indexed: 02/09/2023] Open
Abstract
To better characterize the heterogeneity of multiple myeloma (MM), we profiled plasma cells (PCs) and their B cell lymphopoiesis in the BM samples from patients with monoclonal gammopathy of undetermined significance, smoldering MM, and active MM by mass cytometry (CyTOF) analysis. Characterization of intra- and interneoplastic heterogeneity of malignant plasmablasts and PCs revealed overexpression of the MM SET domain (MMSET), Notch-1, and CD47. Variations in upregulation of B cell signaling regulators (IFN regulatory factor 4 [IRF-4], CXCR4, B cell lymphoma 6 [Bcl-6], c-Myc, myeloid differentiation primary response protein 88 [MYD88], and spliced X box-binding protein 1 [sXBP-1]) and aberrant markers (CD319, CD269, CD200, CD117, CD56, and CD28) were associated with different clinical outcomes in clonal PC subsets. In addition, prognosis was related to heterogeneity in subclonal expression of stemness markers, including neuroepithelial stem cell protein (Nestin), SRY-box transcription factor 2 (Sox2), Krüppel-like factor 4 (KLF-4), and Nanog. Furthermore, we have defined significantly elevated levels of MMSET, MYD88, c-Myc, CD243, Notch-1, and CD47 from hematopoietic stem cells to PCs in myeloma B cell lymphopoiesis, noted even in premalignant conditions, with variably modulated expression of B cell development regulators, including IRF-4, Bcl-2, Bcl-6, and sXBP-1; aberrant PC markers (such as CD52, CD44, CD200, CD81, CD269, CD117, and CXCR4); and stemness-controlling regulators, including Nanog, KLF-4, octamer-binding transcription factor 3/4 (Oct3/4), Sox2, and retinoic acid receptor α2 (RARα2). This study provides the rationale for precise molecular profiling of patients with MM by CyTOF technology to define disease heterogeneity and prognosis.
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Affiliation(s)
- Jana Jakubikova
- Dana-Farber Cancer Institute, Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Department of Tumor Immunology, Cancer Research Institute, Biomedical Research Center,,Centre for Advanced Materials Application, and
| | - Danka Cholujova
- Department of Tumor Immunology, Cancer Research Institute, Biomedical Research Center,,Centre for Advanced Materials Application, and
| | - Gabor Beke
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Teru Hideshima
- Dana-Farber Cancer Institute, Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Lubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Merav Leiba
- Department of Hematology, Samson Assuta Ashdod University Hospital, Ashdod, Israel.,Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Paul G. Richardson
- Dana-Farber Cancer Institute, Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - David M. Dorfman
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Kenneth C. Anderson
- Dana-Farber Cancer Institute, Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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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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29
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Chow S, Kis O, Mulder DT, Danesh A, Bruce J, Wang TT, Reece D, Bhalis N, Neri P, Sabatini PJ, Keats J, Trudel S, Pugh TJ. Myeloma immunoglobulin rearrangement and translocation detection through targeted capture sequencing. Life Sci Alliance 2023; 6:e202201543. [PMID: 36328595 PMCID: PMC9644417 DOI: 10.26508/lsa.202201543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Multiple myeloma is a plasma cell neoplasm characterized by clonal immunoglobulin V(D)J signatures and oncogenic immunoglobulin gene translocations. Additional subclonal genomic changes are acquired with myeloma progression and therapeutic selection. PCR-based methods to detect V(D)J rearrangements can have biases introduced by highly multiplexed reactions and primers undermined by somatic hypermutation, and are not readily extended to include mutation detection. Here, we report a hybrid-capture approach (CapIG-seq) targeting the 3' and 5' ends of the V and J segments of all immunoglobulin loci that enable the efficient detection of V(D)J rearrangements. We also included baits for oncogenic translocations and mutation detection. We demonstrate complete concordance with matched whole-genome sequencing and/or PCR clonotyping of 24 cell lines and report the clonal sequences for 41 uncharacterized cell lines. We also demonstrate the application to patient specimens, including 29 bone marrow and 39 cell-free DNA samples. CapIG-seq shows concordance between bone marrow and cfDNA blood samples (both contemporaneous and follow-up) with regard to the somatic variant, V(D)J, and translocation detection. CapIG-seq is a novel, efficient approach to examining genomic alterations in myeloma.
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Affiliation(s)
- Signy Chow
- University Health Network, Toronto, Canada
- Sunnybrook Health Sciences Centre, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Olena Kis
- University Health Network, Toronto, Canada
| | | | | | - Jeff Bruce
- University Health Network, Toronto, Canada
| | - Ting Ting Wang
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Donna Reece
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | | | | | - Peter Jb Sabatini
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Jonathan Keats
- Translational Genomics Research Institute, City of Hope, AZ, USA
| | - Suzanne Trudel
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Trevor J Pugh
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
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30
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Maneix L, Iakova P, Moree SE, Hsu JI, Mistry RM, Stossi F, Lulla P, Sun Z, Sahin E, Yellapragada SV, Catic A. Proteasome Inhibitors Silence Oncogenes in Multiple Myeloma through Localized Histone Deacetylase 3 (HDAC3) Stabilization and Chromatin Condensation. CANCER RESEARCH COMMUNICATIONS 2022; 2:1693-1710. [PMID: 36846090 PMCID: PMC9949381 DOI: 10.1158/2767-9764.crc-22-0255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Proteasome inhibitors have become the standard of care for multiple myeloma (MM). Blocking protein degradation particularly perturbs the homeostasis of short-lived polypeptides such as transcription factors and epigenetic regulators. To determine how proteasome inhibitors directly impact gene regulation, we performed an integrative genomics study in MM cells. We discovered that proteasome inhibitors reduce the turnover of DNA-associated proteins and repress genes necessary for proliferation through epigenetic silencing. Specifically, proteasome inhibition results in the localized accumulation of histone deacetylase 3 (HDAC3) at defined genomic sites, which reduces H3K27 acetylation and increases chromatin condensation. The loss of active chromatin at super-enhancers critical for MM, including the super-enhancer controlling the proto-oncogene c-MYC, reduces metabolic activity and cancer cell growth. Epigenetic silencing is attenuated by HDAC3 depletion, suggesting a tumor-suppressive element of this deacetylase in the context of proteasome inhibition. In the absence of treatment, HDAC3 is continuously removed from DNA by the ubiquitin ligase SIAH2. Overexpression of SIAH2 increases H3K27 acetylation at c-MYC-controlled genes, increases metabolic output, and accelerates cancer cell proliferation. Our studies indicate a novel therapeutic function of proteasome inhibitors in MM by reshaping the epigenetic landscape in an HDAC3-dependent manner. As a result, blocking the proteasome effectively antagonizes c-MYC and the genes controlled by this proto-oncogene.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Polina Iakova
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Shannon E. Moree
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Joanne I. Hsu
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ragini M. Mistry
- Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - Premal Lulla
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Zheng Sun
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
| | - Sarvari V. Yellapragada
- Department of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
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31
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Zuo X, Liu D. Mechanism of immunomodulatory drug resistance and novel therapeutic strategies in multiple myeloma. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:1110-1121. [PMID: 36121114 DOI: 10.1080/16078454.2022.2124694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The mechanism of immunomodulatory drugs (IMiDs) resistance to multiple myeloma (MM) cells has been gradually demonstrated by recently studies, and some potential novel strategies have been confirmed to have antimyeloma activity and be associated with IMiD activity in MM. METHODS This article searched the Pubmed library, reviewed some recently studies related to IMiD resistance to MM cells and summarized some potent agents to improve IMiD resistance to MM cells. RESULTS Studies have confirmed that cereblon is a primary direct protein target of IMiDs. IRF4 not only is affected by the IKZF protein but also can directly inhibit the expression of BMF and BIM, thereby promoting the survival of MM cells. Additionally, the expression of IRF4 and MYC also plays an important role in three important signaling pathways (Wnt, STAT3 and MAPK/ERK) related to IMiD resistance. Notably, MYC, a downstream factor of IRF4, may be upregulated by BRD4, and upregulation of MYC promotes cell proliferation in MM and disease progression. Recently, some novel therapeutic agents targeting BRD4, a histone modification-related 'reader' of epigenetic marks, or other important factors (e.g. TAK1) in relevant signaling pathways have been developed and they may provide new options for relapse/refractory MM therapy, such as BET inhibitors, CBP/EP300 inhibitors, dual-target BET-CBP/EP300 inhibitors, TAK1 inhibitors, and they may provide new options for relapsed/refractory MM therapy. CONCLUSIONS Accumulated studies have revealed that some key factors associated with the mechanism of IMiD resistance to MM cells. Some agents represent promising new therapeutics of MM to regulate the IRF4/MYC axis by inhibiting BRD4 expression or signaling pathway activation.
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Affiliation(s)
- Xiaojia Zuo
- Department of Hematology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai, People's Republic of China.,Department of Oncology and Hematology, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, People's Republic of China.,Guizhou Medical University, Guiyang, People's Republic of China
| | - Dingsheng Liu
- Department of Hematology, Shanghai Gongli Hospital, The Second Military Medical University, Shanghai, People's Republic of China
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32
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Chen LY, Gooding S. Tumor and microenvironmental mechanisms of resistance to immunomodulatory drugs in multiple myeloma. Front Oncol 2022; 12:1038329. [PMID: 36439455 PMCID: PMC9682014 DOI: 10.3389/fonc.2022.1038329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/04/2022] [Indexed: 10/07/2023] Open
Abstract
Resistance to immunomodulatory drugs (IMiDs®) is a major cause of treatment failure, disease relapse and ultimately poorer outcomes in multiple myeloma (MM). In order to optimally deploy IMiDs and their newer derivates CRBN E3 ligase modulators (CELMoDs®) into future myeloma therapeutic regimens, it is imperative to understand the mechanisms behind the inevitable emergence of IMiD resistance. IMiDs bind and modulate Cereblon (CRBN), the substrate receptor of the CUL4CRBN E3 ubiquitin ligase, to target novel substrate proteins for ubiquitination and degradation. Most important of these are IKZF1 and IKZF3, key MM survival transcription factors which sustain the expression of myeloma oncogenes IRF4 and MYC. IMiDs directly target MM cell proliferation, but also stimulate T/NK cell activation by their CRBN-mediated effects, and therefore enhance anti-MM immunity. Thus, their benefits in myeloma are directed against tumor and immune microenvironment - and in considering the mechanisms by which IMiD resistance emerges, both these effects must be appraised. CRBN-dependent mechanisms of IMiD resistance, including CRBN genetic aberrations, CRBN protein loss and CRBN-substrate binding defects, are beginning to be understood. However, only a proportion of IMiD-resistant cases are related to CRBN and therefore additional mechanisms, which are currently less well described, need to be sought. These include resistance within the immune microenvironment. Here we review the existing evidence on both tumor and immune microenvironment mechanisms of resistance to IMiDs, pose important questions for future study, and consider how knowledge regarding resistance mechanism may be utilized to guide treatment decision making in the clinic.
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Affiliation(s)
- Lucia Y. Chen
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Sarah Gooding
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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33
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Cholujova D, Koklesova L, Lukacova Bujnakova Z, Dutkova E, Valuskova Z, Beblava P, Matisova A, Sedlak J, Jakubikova J. In vitro and ex vivo anti-myeloma effects of nanocomposite As 4S 4/ZnS/Fe 3O 4. Sci Rep 2022; 12:17961. [PMID: 36289430 PMCID: PMC9606304 DOI: 10.1038/s41598-022-22672-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/18/2022] [Indexed: 02/06/2023] Open
Abstract
Nanoparticles in medicine can integrate actively targeted imaging agents and drug delivery vehicles, and combining multiple types of therapeutics in a single particle has numerous advantages, especially in multiple myeloma. MM is an incurable hematological disorder characterized by clonal proliferation of plasma cells in the bone marrow. In this study, we evaluated the anti-myeloma activity of 3 nanocomposites (3NPs): As4S4/ZnS/Fe3O4 (1:4:1), As4S4/ZnS/Fe3O4 with folic acid (FA), and As4S4/ZnS/Fe3O4 with FA and albumin with reduced survival MM cell lines and primary MM samples by each of 3NP. Cytotoxic effects of 3NPs were associated with caspase- and mitochondria-dependent apoptosis induction and reduced c-Myc expression. Modulation of cell cycle regulators, such as p-ATM/ATM and p-ATR/ATR, and increases in p-Chk2, cyclin B1, and histones were accompanied by G2/M arrest triggered by 3NPs. In addition, 3NPs activated several myeloma-related signaling, including JNK1/2/3, ERK1/2 and mTOR. To overcome BM microenvironment-mediated drug resistance, nanocomposites retained its anti-MM activity in the presence of stroma. 3NPs significantly decreased the stem cell-like side population in MM cells, even in the context of stroma. We observed strong synergistic effects of 3NPs combined with lenalidomide, pomalidomide, or melphalan, suggesting the potential of these combinations for future clinical studies.
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Affiliation(s)
- Danka Cholujova
- grid.420087.90000 0001 2106 1943Department of Tumor Immunology, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84505 Slovakia ,grid.419303.c0000 0001 2180 9405Centre for Advanced Materials Application, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84511 Slovakia
| | - Lenka Koklesova
- grid.420087.90000 0001 2106 1943Department of Tumor Immunology, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84505 Slovakia ,grid.7634.60000000109409708Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, 03601 Slovakia
| | - Zdenka Lukacova Bujnakova
- grid.419303.c0000 0001 2180 9405Department of Mechanochemistry, Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, Košice, 04001 Slovakia
| | - Erika Dutkova
- grid.419303.c0000 0001 2180 9405Department of Mechanochemistry, Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, Košice, 04001 Slovakia
| | - Zuzana Valuskova
- grid.420087.90000 0001 2106 1943Department of Tumor Immunology, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84505 Slovakia
| | - Patricia Beblava
- grid.420087.90000 0001 2106 1943Department of Tumor Immunology, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84505 Slovakia
| | - Anna Matisova
- grid.420087.90000 0001 2106 1943Department of Tumor Immunology, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84505 Slovakia
| | - Jan Sedlak
- grid.420087.90000 0001 2106 1943Department of Tumor Immunology, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84505 Slovakia
| | - Jana Jakubikova
- grid.420087.90000 0001 2106 1943Department of Tumor Immunology, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84505 Slovakia ,grid.419303.c0000 0001 2180 9405Centre for Advanced Materials Application, Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava, 84511 Slovakia
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34
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Liquid-liquid phase separation in tumor biology. Signal Transduct Target Ther 2022; 7:221. [PMID: 35803926 PMCID: PMC9270353 DOI: 10.1038/s41392-022-01076-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a novel principle for explaining the precise spatial and temporal regulation in living cells. LLPS compartmentalizes proteins and nucleic acids into micron-scale, liquid-like, membraneless bodies with specific functions, which were recently termed biomolecular condensates. Biomolecular condensates are executors underlying the intracellular spatiotemporal coordination of various biological activities, including chromatin organization, genomic stability, DNA damage response and repair, transcription, and signal transduction. Dysregulation of these cellular processes is a key event in the initiation and/or evolution of cancer, and emerging evidence has linked the formation and regulation of LLPS to malignant transformations in tumor biology. In this review, we comprehensively summarize the detailed mechanisms of biomolecular condensate formation and biophysical function and review the recent major advances toward elucidating the multiple mechanisms involved in cancer cell pathology driven by aberrant LLPS. In addition, we discuss the therapeutic perspectives of LLPS in cancer research and the most recently developed drug candidates targeting LLPS modulation that can be used to combat tumorigenesis.
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35
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Mikulasova A, Kent D, Trevisan-Herraz M, Karataraki N, Fung KTM, Ashby C, Cieslak A, Yaccoby S, van Rhee F, Zangari M, Thanendrarajan S, Schinke C, Morgan GJ, Asnafi V, Spicuglia S, Brackley CA, Corcoran AE, Hambleton S, Walker BA, Rico D, Russell LJ. Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers. Genome Res 2022; 32:1343-1354. [PMID: 34933939 PMCID: PMC9341503 DOI: 10.1101/gr.276042.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with enhancers, often called enhancer hijacking We analyzed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus (IGH) and proto-oncogene CCND1 that are common in B cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterized the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the IGH locus of healthy B cells that was absent in samples with IGH-CCND1 translocations. The appearance of H3K4me3-BD over CCND1 in the latter was associated with overexpression and extensive chromatin accessibility of its gene body. We observed similar cancer-specific H3K4me3-BDs associated with hijacking of super-enhancers of other common oncogenes in B cell (MAF, MYC, and FGFR3/NSD2) and T cell malignancies (LMO2, TLX3, and TAL1). Our analysis suggests that H3K4me3-BDs can be created by super-enhancers and supports the new concept of epigenomic translocation, in which the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers.
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Affiliation(s)
- Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Kent
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Marco Trevisan-Herraz
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nefeli Karataraki
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Kent T M Fung
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Shmuel Yaccoby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | | | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Gareth J Morgan
- NYU Langone Medical Center, Perlmutter Cancer Center, NYU Langone Health, New York, New York 10016, USA
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Chris A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Anne E Corcoran
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, United Kingdom
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana 46202, USA
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lisa J Russell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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36
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Hagen P, Sellin M, Berg S, Zhang J. Increasing genomic discovery in newly diagnosed multiple myeloma: defining disease biology and its correlation to risk. Ann Hematol 2022; 101:1407-1420. [PMID: 35585246 PMCID: PMC9756633 DOI: 10.1007/s00277-022-04856-1] [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: 01/21/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023]
Abstract
Our understanding of MM genomics has expanded rapidly in the past 5-10 years as a consequence of cytogenetic analyses obtained in routine clinical practice as well as the ability to perform whole-exome/genome sequencing and gene expression profiling on large patient data sets. This knowledge has offered new insights into disease biology and is increasingly defining high-risk genomic patterns. In this manuscript, we present a thorough review of our current knowledge of MM genomics. The epidemiology and biology of chromosomal abnormalities including both copy number abnormalities and chromosomal translocation are described in full with a focus on those most clinically impactful such as 1q amplification and del(17p) as well as certain chromosome 14 translocations. A review of our ever-expanding knowledge of genetic mutations derived from recent whole-genome/exome data sets is then reviewed including those that drive disease pathogenesis from precursor states as well as those that may impact clinical outcomes. We then transition and attempt to elucidate how both chromosomal abnormalities and gene mutations are evolving our understanding of disease risk. We conclude by offering our perspectives moving forward as to how we might apply whole-genome/exome-level data in addition to routine cytogenetic analyses to improve patient outcomes as well as further knowledge gaps that must be addressed.
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Affiliation(s)
- Patrick Hagen
- Department of Hematology/Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Mark Sellin
- Department of Hematology/Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Stephanie Berg
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA,Department of Pathology and Department of Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA
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Histone H3K36me2 demethylase KDM2A promotes bladder cancer progression through epigenetically silencing RARRES3. Cell Death Dis 2022; 13:547. [PMID: 35697678 PMCID: PMC9192503 DOI: 10.1038/s41419-022-04983-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 01/21/2023]
Abstract
Epigenetic dysregulation contributes to bladder cancer tumorigenesis. H3K36me2 demethylase KDM2A functions as an important epigenetic regulator of cell fate in many types of tumors. However, its role in bladder cancer remains unknown. Here, we revealed a positive correlation between KDM2A gene copy number gain and upregulation of KDM2A mRNA expression in bladder cancer. Moreover, a super-enhancer (SE) driving KDM2A transcription was found in high-grade bladder cancer, resulting in a significantly higher expression of KDM2A mRNA compared to that in low-grade bladder tumors. KDM2A knockdown (KD) decreased the proliferation, invasion, and spheroid formation of high-grade bladder cancer cells and inhibited tumor growth in mouse xenograft models. Furthermore, we identified RARRES3 as a key KDM2A target gene. KDM2A suppresses RARRES3 expression via demethylation of H3K36me2 in the RARRES3 promoter. Intriguingly, RARRES3 KD attenuated the inhibitory effects of KDM2A depletion on the malignant phenotypes of high-grade bladder cancer cells. The combination of the KDM2A inhibitor IOX1 and the RARRES3 agonist all-trans retinoic acid (ATRA) synergistically inhibited the proliferation of high-grade bladder cancer cells, suggesting that the KDM2A/RARRES3 axis may be a promising therapeutic target for the treatment of high-grade bladder cancer.
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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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LaFave LM, Savage RE, Buenrostro JD. Single-Cell Epigenomics Reveals Mechanisms of Cancer Progression. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer initiation is driven by the cooperation between genetic and epigenetic aberrations that disrupt gene regulatory programs critical to maintaining specialized cellular functions. After initiation, cells acquire additional genetic and epigenetic alterations influenced by tumor-intrinsic and -extrinsic mechanisms, which increase intratumoral heterogeneity, reshape the cell's underlying gene regulatory networks and promote cancer evolution. Furthermore, environmental or therapeutic insults drive the selection of heterogeneous cell states, with implications for cancer initiation, maintenance, and drug resistance. The advancement of single-cell genomics has begun to uncover the full repertoire of chromatin and gene expression states (cell states) that exist within individual tumors. These single-cell analyses suggest that cells diversify in their regulatory states upon transformation by co-opting damage-induced and nonlineage regulatory programs that can lead to epigenomic plasticity. Here, we review these recent studies related to regulatory state changes in cancer progression and highlight the growing single-cell epigenomics toolkit poised to address unresolved questions in the field.
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Affiliation(s)
- Lindsay M. LaFave
- Department of Cell Biology and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Montefiore Health System, Bronx, NY, USA
| | - Rachel E. Savage
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jason D. Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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40
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Roosen M, Odé Z, Bunt J, Kool M. The oncogenic fusion landscape in pediatric CNS neoplasms. Acta Neuropathol 2022; 143:427-451. [PMID: 35169893 PMCID: PMC8960661 DOI: 10.1007/s00401-022-02405-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 01/09/2023]
Abstract
Pediatric neoplasms in the central nervous system (CNS) are the leading cause of cancer-related deaths in children. Recent developments in molecular analyses have greatly contributed to a more accurate diagnosis and risk stratification of CNS tumors. Additionally, sequencing studies have identified various, often entity specific, tumor-driving events. In contrast to adult tumors, which often harbor multiple mutated oncogenic drivers, the number of mutated genes in pediatric cancers is much lower and many tumors can have a single oncogenic driver. Moreover, in children, much more than in adults, fusion proteins play an important role in driving tumorigenesis, and many different fusions have been identified as potential driver events in pediatric CNS neoplasms. However, a comprehensive overview of all the different reported oncogenic fusion proteins in pediatric CNS neoplasms is still lacking. A better understanding of the fusion proteins detected in these tumors and of the molecular mechanisms how these proteins drive tumorigenesis, could improve diagnosis and further benefit translational research into targeted therapies necessary to treat these distinct entities. In this review, we discuss the different oncogenic fusions reported in pediatric CNS neoplasms and their structure to create an overview of the variety of oncogenic fusion proteins to date, the tumor entities they occur in and their proposed mode of action.
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Affiliation(s)
- Mieke Roosen
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Zelda Odé
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Jens Bunt
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands.
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany.
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41
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Super enhancers as master gene regulators in the pathogenesis of hematologic malignancies. Biochim Biophys Acta Rev Cancer 2022; 1877:188697. [PMID: 35150791 DOI: 10.1016/j.bbcan.2022.188697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/20/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
Transcriptional deregulation of multiple oncogenes, tumor suppressors and survival pathways is a cancer cell hallmark. Super enhancers (SE) are long stretches of active enhancers in close linear proximity that ensure extraordinarily high expression levels of key genes associated with cell lineage, function and survival. SE landscape is intrinsically prone to changes and reorganization during the course of normal cell differentiation. This functional plasticity is typically utilized by cancer cells, which remodel their SE landscapes to ensure oncogenic transcriptional reprogramming. Multiple recent studies highlighted structural genetic mechanisms in non-coding regions that create new SE or hijack already existing ones. In addition, alterations in abundance/activity of certain SE-associated proteins or certain viral infections can elicit new super enhancers and trigger SE-driven transcriptional changes. For these reasons, SE profiling emerged as a powerful tool for discovering the core transcriptional regulatory circuits in tumor cells. This, in turn, provides new insights into cancer cell biology, and identifies main nodes of key cellular pathways to be potentially targeted. Since SEs are susceptible to inhibition, their disruption results in exponentially amassing 'butterfly' effect on gene expression and cell function. Moreover, many of SE elements are druggable, opening new therapeutic opportunities. Indeed, SE targeting drugs have been studied preclinically in various hematologic malignancies with promising effects. Herein, we review the unique features of SEs, present different cis- and trans-acting mechanisms through which hematologic tumor cells acquire SEs, and finally, discuss the potential of SE targeting in the therapy of hematologic malignancies.
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42
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See YX, Chen K, Fullwood MJ. MYC overexpression leads to increased chromatin interactions at superenhancers and MYC binding sites. Genome Res 2022; 32:629-642. [PMID: 35115371 PMCID: PMC8997345 DOI: 10.1101/gr.276313.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/28/2022] [Indexed: 12/02/2022]
Abstract
The MYC oncogene encodes for the MYC protein and is frequently dysregulated across multiple cancer cell types, making it an attractive target for cancer therapy. MYC overexpression leads to MYC binding at active enhancers, resulting in a global transcriptional amplification of active genes. Because super-enhancers are frequently dysregulated in cancer, we hypothesized that MYC preferentially invades into super-enhancers and alters the cancer genome organization. To that end, we performed ChIP-seq, RNA-seq, circular chromosome conformation capture (4C-seq), and Spike-in Quantitative Hi-C (SIQHiC) on the U2OS osteosarcoma cell line with tetracycline-inducible MYC. MYC overexpression in U2OS cells modulated histone acetylation and increased MYC binding at super-enhancers. SIQHiC analysis revealed increased global chromatin contact frequency, particularly at chromatin interactions connecting MYC binding sites at promoters and enhancers. Immunofluorescence staining showed that MYC molecules formed punctate foci at these transcriptionally active domains after MYC overexpression. These results demonstrate the accumulation of overexpressed MYC at promoter–enhancer hubs and suggest that MYC invades into enhancers through spatial proximity. At the same time, the increased protein–protein interactions may strengthen these chromatin interactions to increase chromatin contact frequency. CTCF siRNA knockdown in MYC-overexpressed U2OS cells demonstrated that removal of architectural proteins can disperse MYC and abrogate the increase in chromatin contacts. By elucidating the chromatin landscape of MYC-driven cancers, we can potentially target MYC-associated chromatin interactions for cancer therapy.
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Affiliation(s)
- Yi Xiang See
- Nanyang Technological University, Cancer Science Institute of Singapore, National University of Singapore
| | - Kaijing Chen
- Nanyang Technological University, Cancer Science Institute of Singapore, National University of Singapore
| | - Melissa J Fullwood
- Nanyang Technological University, Cancer Science Institute of Singapore, National University of Singapore, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR)
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43
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Belloucif Y, Lobry C. Super-Enhancers Dysregulations in Hematological Malignancies. Cells 2022; 11:196. [PMID: 35053311 PMCID: PMC8774084 DOI: 10.3390/cells11020196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/17/2021] [Accepted: 12/27/2021] [Indexed: 01/27/2023] Open
Abstract
Hematological malignancies affecting either the lymphoid or the myeloid lineages involve epigenetic mutations or dysregulation in the majority of cases. These epigenetic abnormalities can affect regulatory elements in the genome and, particularly, enhancers. Recently, large regulatory elements known as super-enhancers, initially identified for their critical roles in cell-type specific expression regulation of genes controlling cell identity, have been shown to also be involved in tumorigenesis in many cancer types and hematological malignancies via the regulation of numerous oncogenes, including MYC. In this review, we highlight the existing links between super-enhancers and hematological malignancies, with a particular focus on acute myeloid leukemia, a clonal hematopoietic neoplasm with dismal outcomes, resulting in an uncontrolled proliferation of myeloblasts, abnormally blocked during differentiation and accumulating within the patient's bone marrow. We report recent works, performed during the last few years, treating this subject and consider the possibility of targeting oncogenic regulatory elements, as well as the effectiveness and limitations reported so far for such strategies.
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Affiliation(s)
| | - Camille Lobry
- INSERM U944, CNRS UMR7212, Institut de Recherche Saint Louis, Université de Paris, 75010 Paris, France;
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44
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Vervoort SJ, Devlin JR, Kwiatkowski N, Teng M, Gray NS, Johnstone RW. Targeting transcription cycles in cancer. Nat Rev Cancer 2022; 22:5-24. [PMID: 34675395 DOI: 10.1038/s41568-021-00411-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Accurate control of gene expression is essential for normal development and dysregulation of transcription underpins cancer onset and progression. Similar to cell cycle regulation, RNA polymerase II-driven transcription can be considered as a unidirectional multistep cycle, with thousands of unique transcription cycles occurring in concert within each cell. Each transcription cycle comprises recruitment, initiation, pausing, elongation, termination and recycling stages that are tightly controlled by the coordinated action of transcriptional cyclin-dependent kinases and their cognate cyclins as well as the opposing activity of transcriptional phosphatases. Oncogenic dysregulation of transcription can entail defective control of gene expression, either at select loci or more globally, impacting a large proportion of the genome. The resultant dependency on the core-transcriptional machinery is believed to render 'transcriptionally addicted' cancers sensitive to perturbation of transcription. Based on these findings, small molecules targeting transcriptional cyclin-dependent kinases and associated proteins hold promise for the treatment of cancer. Here, we utilize the transcription cycles concept to explain how dysregulation of these finely tuned gene expression processes may drive tumorigenesis and how therapeutically beneficial responses may arise from global or selective transcriptional perturbation. This conceptual framework helps to explain tumour-selective transcriptional dependencies and facilitates the rational design of combination therapies.
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Affiliation(s)
- Stephin J Vervoort
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer R Devlin
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingxing Teng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA.
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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45
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Botrugno OA, Tonon G. Genomic Instability and Replicative Stress in Multiple Myeloma: The Final Curtain? Cancers (Basel) 2021; 14:cancers14010025. [PMID: 35008191 PMCID: PMC8750813 DOI: 10.3390/cancers14010025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Genomic instability is recognized as a driving force in most cancers as well as in the haematological cancer multiple myeloma and remains among the leading cause of drug resistance. Several evidences suggest that replicative stress exerts a fundamental role in fuelling genomic instability. Notably, cancer cells rely on a single protein, ATR, to cope with the ensuing DNA damage. In this perspective, we provide an overview depicting how replicative stress represents an Achilles heel for multiple myeloma, which could be therapeutically exploited either alone or in combinatorial regimens to preferentially ablate tumor cells. Abstract Multiple Myeloma (MM) is a genetically complex and heterogeneous hematological cancer that remains incurable despite the introduction of novel therapies in the clinic. Sadly, despite efforts spanning several decades, genomic analysis has failed to identify shared genetic aberrations that could be targeted in this disease. Seeking alternative strategies, various efforts have attempted to target and exploit non-oncogene addictions of MM cells, including, for example, proteasome inhibitors. The surprising finding that MM cells present rampant genomic instability has ignited concerted efforts to understand its origin and exploit it for therapeutic purposes. A credible hypothesis, supported by several lines of evidence, suggests that at the root of this phenotype there is intense replicative stress. Here, we review the current understanding of the role of replicative stress in eliciting genomic instability in MM and how MM cells rely on a single protein, Ataxia Telangiectasia-mutated and Rad3-related protein, ATR, to control and survive the ensuing, potentially fatal DNA damage. From this perspective, replicative stress per se represents not only an opportunity for MM cells to increase their evolutionary pool by increasing their genomic heterogeneity, but also a vulnerability that could be leveraged for therapeutic purposes to selectively target MM tumor cells.
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Affiliation(s)
- Oronza A. Botrugno
- Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Correspondence: (O.A.B.); (G.T.); Tel.: +39-02-2643-6661 (O.A.B.); +39-02-2643-5624 (G.T.); Fax: +39-02-2643-6352 (O.A.B. & G.T.)
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Correspondence: (O.A.B.); (G.T.); Tel.: +39-02-2643-6661 (O.A.B.); +39-02-2643-5624 (G.T.); Fax: +39-02-2643-6352 (O.A.B. & G.T.)
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46
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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47
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Croucher DC, Richards LM, Tsofack SP, Waller D, Li Z, Wei EN, Huang XF, Chesi M, Bergsagel PL, Sebag M, Pugh TJ, Trudel S. Longitudinal single-cell analysis of a myeloma mouse model identifies subclonal molecular programs associated with progression. Nat Commun 2021; 12:6322. [PMID: 34732728 PMCID: PMC8566524 DOI: 10.1038/s41467-021-26598-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/12/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular programs that underlie precursor progression in multiple myeloma are incompletely understood. Here, we report a disease spectrum-spanning, single-cell analysis of the Vκ*MYC myeloma mouse model. Using samples obtained from mice with serologically undetectable disease, we identify malignant cells as early as 30 weeks of age and show that these tumours contain subclonal copy number variations that persist throughout progression. We detect intratumoural heterogeneity driven by transcriptional variability during active disease and show that subclonal expression programs are enriched at different times throughout early disease. We then show how one subclonal program related to GCN2 stress response is progressively activated during progression in myeloma patients. Finally, we use chemical and genetic perturbation of GCN2 in vitro to support this pathway as a therapeutic target in myeloma. These findings therefore present a model of precursor progression in Vκ*MYC mice, nominate an adaptive mechanism important for myeloma survival, and highlight the need for single-cell analyses to understand the biological underpinnings of disease progression.
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Affiliation(s)
- Danielle C Croucher
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Laura M Richards
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Serges P Tsofack
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daniel Waller
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Zhihua Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ellen Nong Wei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Xian Fang Huang
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Marta Chesi
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - P Leif Bergsagel
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Michael Sebag
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
| | - Suzanne Trudel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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48
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Bergsagel PL, Kuehl WM. Promiscuous Structural Variants Drive Myeloma Initiation and Progression. Blood Cancer Discov 2021; 1:221-223. [PMID: 34661146 DOI: 10.1158/2643-3230.bcd-20-0170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A comprehensive genomic analysis of structural variants in multiple myeloma in this issue highlights the key role of these events, involving primarily the immunoglobulin heavy chain locus in disease initiation and the MYC locus in disease progression. However, the current study reveals the large number of genomic hotspots, oncogenes, tumor suppressor genes, and recombination mechanisms that contribute to multiple myeloma heterogeneity. See related article by Rustad et al., p. 258.
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Affiliation(s)
- P Leif Bergsagel
- Department of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona
| | - W Michael Kuehl
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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Sharma N, Smadbeck JB, Abdallah N, Zepeda-Mendoza C, Binder M, Pearce KE, Asmann YW, Peterson JF, Ketterling RP, Greipp PT, Leif Bergsagel P, Vincent Rajkumar S, Kumar SK, Baughn LB. The Prognostic Role of MYC Structural Variants Identified by NGS and FISH in Multiple Myeloma. Clin Cancer Res 2021; 27:5430-5439. [PMID: 34233962 PMCID: PMC8738776 DOI: 10.1158/1078-0432.ccr-21-0005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/16/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Structural variants (SV) of the MYC gene region are common in multiple myeloma and influence disease progression. However, the prognostic significance of different MYC SVs in multiple myeloma has not been clearly established. EXPERIMENTAL DESIGN We conducted a retrospective study of multiple myeloma comparing MYC SV subtypes identified by next-generation sequencing (NGS) and FISH to MYC expression and disease survival using 140 cases from Mayo Clinic and 658 cases from the MMRF CoMMpass study. RESULTS MYC SVs were found in 41% of cases and were classified into nine subtypes. A correlation between the presence of a MYC SV and increased MYC expression was identified. Among the nine MYC subtypes, the non-immunoglobulin (non-Ig) insertion subtype was independently associated with improved outcomes, while the Ig insertion subtype, specifically involving the IgL gene partner, was independently associated with poorer outcomes compared with other MYC SV subtypes. Although the FISH methodology failed to detect approximately 70% of all MYC SVs, those detected by FISH were associated with elevated MYC gene expression and poor outcomes suggesting a different pathogenic role for FISH-detected MYC subtypes compared with other MYC subtypes. CONCLUSIONS Understanding the impact of different MYC SVs on disease outcome is necessary for the reliable interpretation of MYC SVs in multiple myeloma. NGS approaches should be considered as a replacement technique for a more comprehensive evaluation of the multiple myeloma clone.
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Affiliation(s)
- Neeraj Sharma
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Nadine Abdallah
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | - Moritz Binder
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Kathryn E. Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Yan W. Asmann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL
| | - Jess F. Peterson
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rhett P. Ketterling
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Patricia T. Greipp
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - P. Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ
| | - S. Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Shaji K. Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Linda B. Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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50
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Feng G, Wang T, Xue F, Qi Y, Wang R, Yuan H. Identification of enhancer RNAs for the prognosis of head and neck squamous cell carcinoma. Head Neck 2021; 43:3820-3831. [PMID: 34569097 DOI: 10.1002/hed.26877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/10/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Enhancer RNAs (eRNAs) play an important role in carcinogenesis. The landscape of eRNAs in head and neck squamous cell carcinoma (HNSCC) remains largely unknown. METHODS The eRNA expression matrix was obtained from the enhancer RNA in the cancer database. Functional enrichment analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). Prognostic eRNAs were identified using Cox regression analysis, and a prognostic prediction model was constructed based on coefficients. RESULTS KEGG analysis showed that eRNA-related transcription factors were mainly enriched in herpes simplex virus 1 (HSV1) infection. The zinc finger (ZNF) family may play an essential role in HNSCC. ENSR00000188847, ENSR00000250663, ENSR00000313345, ENSR00000317887, and ENSR00000336429 were identified. The prediction model was robust. CONCLUSIONS We constructed a robust 5-eRNA prognostic prediction model, and these eRNAs are potential biomarkers for HNSCC prognosis.
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Affiliation(s)
- Guanying Feng
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Tianxiao Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Feifei Xue
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yibo Qi
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ruixia Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
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