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Cun HT, Bernard L, Lande KT, Lawson BC, Nesbakken AJ, Davidson B, Lindemann K, Fellman B, Sørlie T, Soliman PT, Eriksson AGZ. Comprehensive molecular characterization of early stage grade 3 endometrioid endometrial adenocarcinoma. Gynecol Oncol 2024; 189:138-145. [PMID: 39126895 DOI: 10.1016/j.ygyno.2024.07.677] [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: 04/11/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]
Abstract
OBJECTIVE The treatment for stage IB grade 3 endometrioid endometrial adenocarcinoma is challenging with variable practice. Molecular characterization may help identify adjuvant therapy strategies beyond stage. We aimed to better understand the molecular features of these tumors by characterizing them by ProMisE classification, mutational signature, and commonly mutated genes. METHODS Patients with stage IB grade 3 EEC at two institutions were included. Immunohistochemistry and whole exome sequencing were performed on archival FFPE tissue sections to determine ProMisE classification. Personal Cancer Genome Reporter was used for somatic variant annotation, and mutational signatures were generated based on COSMIC single base substitution mutational signatures. RESULTS 46 patients were included with variable adjuvant treatment. Nine patients recurred (19.6%), most with extra-abdominal disease (n = 5, or 55.6%). 10 had POLE mutations (21.7%), 18 were MMR deficient (39.1%), 6 had abnormal p53 (13.0%), and 12 were p53 wildtype (26.1%). There were no recurrences in the POLE subgroup. A dominant mutational signature was identified in 38 patients: 17 SBS5 signature (44.7%), 10 SBS15 or SBS44 signature (26.3%), 7 SBS10a or SBS10b signature (18.4%), 3 SBS14 signature (7.9%), and 1 SBS40 signature (2.6%). The six patients that recurred had a SBS5 signature. Frequently mutated genes included ARID1A (n = 30, 65%), PTEN (n = 28, 61%), MUC16 (n = 27, 59%), and PIK3CA (n = 25, 54%). CONCLUSIONS This comprehensive evaluation found a molecularly diverse cohort of tumors, despite the same histology, stage and grade. Mutational signature SBS5 correlated with a high risk of recurrence. Further refining of endometrial cancer classification may enable more precise patient stratification and personalized treatment approaches.
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Affiliation(s)
- Han T Cun
- Section of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Chicago, Chicago, USA.
| | - Laurence Bernard
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, McGill University Health Centre, Montreal, Canada
| | - Karin Teien Lande
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Barrett C Lawson
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Anne-Jorunn Nesbakken
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Ben Davidson
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kristina Lindemann
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gynecologic Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Bryan Fellman
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pamela T Soliman
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Ane Gerda Zahl Eriksson
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gynecologic Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.
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2
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Monchusi B, Dube P, Takundwa MM, Kenmogne VL, Thimiri Govinda Raj DB. Advances in CRISPR-Cas systems for blood cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 208:261-284. [PMID: 39266186 DOI: 10.1016/bs.pmbts.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
CRISPR-Cas systems have revolutionised precision medicine by enabling personalised treatments tailored to an individual's genetic profile. Various CRISPR technologies have been developed to target specific disease-causing genes in blood cancers, and some have advanced to clinical trials. Although some studies have explored the in vivo applications of CRISPR-Cas systems, several challenges continue to impede their widespread use. Furthermore, CRISPR-Cas technology has shown promise in improving the response of immunotherapies to blood cancers. The emergence of CAR-T cell therapy has shown considerable success in the targeting and correcting of disease-causing genes in blood cancers. Despite the promising potential of CRISPR-Cas in the treatment of blood cancers, issues related to safety, ethics, and regulatory approval remain significant hurdles. This comprehensive review highlights the transformative potential of CRISPR-Cas technology to revolutionise blood cancer therapy.
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Affiliation(s)
- Bernice Monchusi
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Phumuzile Dube
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Mutsa Monica Takundwa
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Vanelle Larissa Kenmogne
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa; Department of Surgery, University of the Witwatersrand, Johannesburg, South Africa
| | - Deepak Balaji Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa.
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3
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Malard F, Neri P, Bahlis NJ, Terpos E, Moukalled N, Hungria VTM, Manier S, Mohty M. Multiple myeloma. Nat Rev Dis Primers 2024; 10:45. [PMID: 38937492 DOI: 10.1038/s41572-024-00529-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 06/29/2024]
Abstract
Multiple myeloma (MM) is a haematological lymphoid malignancy involving tumoural plasma cells and is usually characterized by the presence of a monoclonal immunoglobulin protein. MM is the second most common haematological malignancy, with an increasing global incidence. It remains incurable because most patients relapse or become refractory to treatments. MM is a genetically complex disease with high heterogeneity that develops as a multistep process, involving acquisition of genetic alterations in the tumour cells and changes in the bone marrow microenvironment. Symptomatic MM is diagnosed using the International Myeloma Working Group criteria as a bone marrow infiltration of ≥10% clonal plasma cells, and the presence of at least one myeloma-defining event, either standard CRAB features (hypercalcaemia, renal failure, anaemia and/or lytic bone lesions) or biomarkers of imminent organ damage. Younger and fit patients are considered eligible for transplant. They receive an induction, followed by consolidation with high-dose melphalan and autologous haematopoietic cell transplantation, and maintenance therapy. In older adults (ineligible for transplant), the combination of daratumumab, lenalidomide and dexamethasone is the preferred option. If relapse occurs and requires further therapy, the choice of therapy will be based on previous treatment and response and now includes immunotherapies, such as bi-specific monoclonal antibodies and chimeric antigen receptor T cell therapy.
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Affiliation(s)
- Florent Malard
- Sorbonne Université, Centre de Recherche Saint-Antoine INSERM UMRs938, Service d'Hématologie Clinique et de Thérapie Cellulaire, Hôpital Saint Antoine, AP-HP, Paris, France.
| | - Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Nizar J Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Evangelos Terpos
- Department of Clinical Therapeutics, Alexandra General Hospital, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Nour Moukalled
- Bone Marrow Transplantation Program, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | | | - Salomon Manier
- Department of Hematology, Lille University Hospital and INSERM UMR-S1277 and CNRS UMR9020, Lille, France
| | - Mohamad Mohty
- Sorbonne Université, Centre de Recherche Saint-Antoine INSERM UMRs938, Service d'Hématologie Clinique et de Thérapie Cellulaire, Hôpital Saint Antoine, AP-HP, Paris, France.
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4
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Morè S, Corvatta L, Manieri VM, Morsia E, Offidani M. The Challenging Approach to Multiple Myeloma: From Disease Diagnosis and Monitoring to Complications Management. Cancers (Basel) 2024; 16:2263. [PMID: 38927968 PMCID: PMC11202048 DOI: 10.3390/cancers16122263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
The outcome of multiple myeloma (MM) has significantly improved in the last few decades due to several factors such as new biological discoveries allowing to better stratify disease risk, development of more effective therapies and better management of side effects related to them. However, handling all these aspects requires an interdisciplinary approach involving multiple knowledge and collaboration of different specialists. The hematologist, faced with a patient with MM, must not only choose a treatment according to patient and disease characteristics but must also know when therapy needs to be started and how to monitor it during and after treatment. Moreover, he must deal not only with organ issues related to MM such as bone disease, renal failure or neurological disease but also with adverse events, often very serious, related to novel therapies, particularly new generation immunotherapies such as CAR T cell therapy and bispecific antibodies. In this review, we provide an overview on the newer MM diagnostic and monitoring strategies and on the main side effects of MM therapies, focusing on adverse events occurring during treatment with CAR T cells and bispecific antibodies.
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Affiliation(s)
- Sonia Morè
- Clinica di Ematologia Azienda Ospedaliero, Universitaria delle Marche, 60126 Ancona, Italy; (S.M.); (V.M.M.); (E.M.)
| | - Laura Corvatta
- U.O.C. Medicina, Ospedale Profili, 60044 Fabriano, Italy;
| | - Valentina Maria Manieri
- Clinica di Ematologia Azienda Ospedaliero, Universitaria delle Marche, 60126 Ancona, Italy; (S.M.); (V.M.M.); (E.M.)
| | - Erika Morsia
- Clinica di Ematologia Azienda Ospedaliero, Universitaria delle Marche, 60126 Ancona, Italy; (S.M.); (V.M.M.); (E.M.)
| | - Massimo Offidani
- Clinica di Ematologia Azienda Ospedaliero, Universitaria delle Marche, 60126 Ancona, Italy; (S.M.); (V.M.M.); (E.M.)
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5
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Battuello P, Corti G, Bartolini A, Lorenzato A, Sogari A, Russo M, Di Nicolantonio F, Bardelli A, Crisafulli G. Mutational signatures of colorectal cancers according to distinct computational workflows. Brief Bioinform 2024; 25:bbae249. [PMID: 38783705 PMCID: PMC11116831 DOI: 10.1093/bib/bbae249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
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Affiliation(s)
- Paolo Battuello
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
| | - Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giovanni Crisafulli
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
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6
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Zhuk AS, Stepchenkova EI, Zotova IV, Belopolskaya OB, Pavlov YI, Kostroma II, Gritsaev SV, Aksenova AY. G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients. Int J Mol Sci 2024; 25:5269. [PMID: 38791307 PMCID: PMC11121618 DOI: 10.3390/ijms25105269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy, which remains incurable despite recent advances in treatment strategies. Like other forms of cancer, MM is characterized by genomic instability, caused by defects in DNA repair. Along with mutations in DNA repair genes and genotoxic drugs used to treat MM, non-canonical secondary DNA structures (four-stranded G-quadruplex structures) can affect accumulation of somatic mutations and chromosomal abnormalities in the tumor cells of MM patients. Here, we tested the hypothesis that G-quadruplex structures may influence the distribution of somatic mutations in the tumor cells of MM patients. We sequenced exomes of normal and tumor cells of 11 MM patients and analyzed the data for the presence of G4 context around points of somatic mutations. To identify molecular mechanisms that could affect mutational profile of tumors, we also analyzed mutational signatures in tumor cells as well as germline mutations for the presence of specific SNPs in DNA repair genes or in genes regulating G-quadruplex unwinding. In several patients, we found that sites of somatic mutations are frequently located in regions with G4 context. This pattern correlated with specific germline variants found in these patients. We discuss the possible implications of these variants for mutation accumulation and specificity in MM and propose that the extent of G4 context enrichment around somatic mutation sites may be a novel metric characterizing mutational processes in tumors.
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Affiliation(s)
- Anna S. Zhuk
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Institute of Applied Computer Science, ITMO University, 197101 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Irina V. Zotova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
| | - Olesya B. Belopolskaya
- Resource Center “Bio-Bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia;
- The Laboratory of Genogeography, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ivan I. Kostroma
- City Hospital No. 15, 198205 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | | | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
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7
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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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8
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Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJ. Accurate and sensitive mutational signature analysis with MuSiCal. Nat Genet 2024; 56:541-552. [PMID: 38361034 PMCID: PMC10937379 DOI: 10.1038/s41588-024-01659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
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Affiliation(s)
- Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedikt Geiger
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniel Ben-Isvy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - David Geng
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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9
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Bar N, Firestone RS, Usmani SZ. Aiming for the cure in myeloma: Putting our best foot forward. Blood Rev 2023; 62:101116. [PMID: 37596172 DOI: 10.1016/j.blre.2023.101116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/20/2023]
Abstract
Frontline therapy for multiple myeloma (MM) is evolving to include novel combinations that can achieve unprecedented deep response rates. Several treatment strategies exist, varying in induction regimen composition, use of transplant and or consolidation and maintenance. In this sea of different treatment permutations, the overarching theme is the powerful prognostic factors of disease risk and achievement of minimal residual disease (MRD) negativity. MM has significant inter-patient variability that requires treatment to be individualized. Risk-adapted and response-adapted strategies which are increasingly being explored to define the extent and duration of therapy, and eventually aim for functional curability. In addition, with T-cell redirection therapies rapidly revolutionizing myeloma treatments, the current standard of care for myeloma will change. This review analyzes the current relevant literature in upfront therapy for fit myeloma patients and provides suggestions for treatment approach while novel clinical trials are maturing.
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Affiliation(s)
- Noffar Bar
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine University, New Haven, CT, USA.
| | - Ross S Firestone
- Multiple Myeloma Service, Department of medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Saad Z Usmani
- Multiple Myeloma Service, Department of medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Dong F, Davies KD. Mutational Signatures in Cancer: Laboratory Considerations and Emerging Applications. J Mol Diagn 2023; 25:790-795. [PMID: 37633594 DOI: 10.1016/j.jmoldx.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/29/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Patterns of somatic mutations have emerged from the broad sequencing of human cancer genomes. These mutational signatures reflect mechanisms of mutagenesis and DNA repair defects and represent an emerging class of cancer biomarkers. The appropriate interpretation of mutational signatures from sequencing assays holds implications in the reporting of molecular diagnostic results for patients with cancer. This brief review describes the scientific principles, laboratory considerations, and emerging clinical applications of mutational signature analysis from clinical cancer genomes.
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Affiliation(s)
- Fei Dong
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
| | - Kurtis D Davies
- Emerging and Evolving Biomarker Content Committee, A Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
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11
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Tsukamoto T, Kinoshita M, Yamada K, Ito H, Yamaguchi T, Chinen Y, Mizutani S, Fujino T, Kobayashi T, Shimura Y, Inazawa J, Kuroda J. Imaging flow cytometry-based multiplex FISH for three IGH translocations in multiple myeloma. J Hum Genet 2023; 68:507-514. [PMID: 36882509 PMCID: PMC10290952 DOI: 10.1038/s10038-023-01136-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/28/2023] [Accepted: 02/14/2023] [Indexed: 03/09/2023]
Abstract
Three types of chromosomal translocations, t(4;14)(p16;q32), t(14;16)(q32;q23), and t(11;14)(q13;q32), are associated with prognosis and the decision making of therapeutic strategy for multiple myeloma (MM). In this study, we developed a new diagnostic modality of the multiplex FISH in immunophenotyped cells in suspension (Immunophenotyped-Suspension-Multiplex (ISM)-FISH). For the ISM-FISH, we first subject cells in suspension to the immunostaining by anti-CD138 antibody and, then, to the hybridization with four different FISH probes for genes of IGH, FGFR3, MAF, and CCND1 tagged by different fluorescence in suspension. Then, cells are analyzed by the imaging flow cytometry MI-1000 combined with the FISH spot counting tool. By this system of the ISM-FISH, we can simultaneously examine the three chromosomal translocations, i.e, t(4;14), t(14;16), and t(11;14), in CD138-positive tumor cells in more than 2.5 × 104 nucleated cells with the sensitivity at least up to 1%, possibly up to 0.1%. The experiments on bone marrow nucleated cells (BMNCs) from 70 patients with MM or monoclonal gammopathy of undetermined significance demonstrated the promising qualitative diagnostic ability in detecting t(11;14), t(4;14), and t(14;16) of our ISM-FISH, which was more sensitive compared with standard double-color (DC) FISH examining 200 interphase cells with its best sensitivity up to 1.0%. Moreover, the ISM-FISH showed a positive concordance of 96.6% and negative concordance of 98.8% with standard DC-FISH examining 1000 interphase cells. In conclusion, the ISM-FISH is a rapid and reliable diagnostic tool for the simultaneous examination of three critically important IGH translocations, which may promote risk-adapted individualized therapy in MM.
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Affiliation(s)
- Taku Tsukamoto
- Division of Hematology & Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | | | - Hodaka Ito
- General Laboratory, Bio Medical Laboratories, Inc., Tokyo, Japan
| | | | - Yoshiaki Chinen
- Division of Hematology & Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shinsuke Mizutani
- Division of Hematology & Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takahiro Fujino
- Division of Hematology & Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsutomu Kobayashi
- Division of Hematology & Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology & Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Blood Transfusion and Cell Therapy, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
- Research Core Center, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Junya Kuroda
- Division of Hematology & Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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12
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García-Sánchez D, González-González A, Alfonso-Fernández A, Del Dujo-Gutiérrez M, Pérez-Campo FM. Communication between bone marrow mesenchymal stem cells and multiple myeloma cells: Impact on disease progression. World J Stem Cells 2023; 15:421-437. [PMID: 37342223 PMCID: PMC10277973 DOI: 10.4252/wjsc.v15.i5.421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 05/26/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy characterized by the accumulation of immunoglobulin-secreting clonal plasma cells at the bone marrow (BM). The interaction between MM cells and the BM microenvironment, and specifically BM mesenchymal stem cells (BM-MSCs), has a key role in the pathophysiology of this disease. Multiple data support the idea that BM-MSCs not only enhance the proliferation and survival of MM cells but are also involved in the resistance of MM cells to certain drugs, aiding the progression of this hematological tumor. The relation of MM cells with the resident BM-MSCs is a two-way interaction. MM modulate the behavior of BM-MSCs altering their expression profile, proliferation rate, osteogenic potential, and expression of senescence markers. In turn, modified BM-MSCs can produce a set of cytokines that would modulate the BM microenvironment to favor disease progression. The interaction between MM cells and BM-MSCs can be mediated by the secretion of a variety of soluble factors and extracellular vesicles carrying microRNAs, long non-coding RNAs or other molecules. However, the communication between these two types of cells could also involve a direct physical interaction through adhesion molecules or tunneling nanotubes. Thus, understanding the way this communication works and developing strategies to interfere in the process, would preclude the expansion of the MM cells and might offer alternative treatments for this incurable disease.
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Affiliation(s)
- Daniel García-Sánchez
- Department of Molecular Biology_IDIVAL, Faculty of Medicine, University of Cantabria, Santander 39011, Cantabria, Spain
| | - Alberto González-González
- Department of Molecular Biology_IDIVAL, Faculty of Medicine, University of Cantabria, Santander 39011, Cantabria, Spain
| | - Ana Alfonso-Fernández
- Servicio de Traumatología y Cirugía Ortopédica, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Facultad de Medicina, Universidad de Cantabria, Santander 39008, Cantabria, Spain
| | - Mónica Del Dujo-Gutiérrez
- Department of Molecular Biology_IDIVAL, Faculty of Medicine, University of Cantabria, Santander 39011, Cantabria, Spain
| | - Flor M Pérez-Campo
- Department of Molecular Biology_IDIVAL, Faculty of Medicine, University of Cantabria, Santander 39011, Cantabria, Spain
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13
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Zhao A, Zhou H, Yang J, Li M, Niu T. Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Affiliation(s)
- Ailin Zhao
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Hui Zhou
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Jinrong Yang
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Meng Li
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China.
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14
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Neumeister P, Schulz E, Pansy K, Szmyra M, Deutsch AJA. Targeting the Microenvironment for Treating Multiple Myeloma. Int J Mol Sci 2022; 23:ijms23147627. [PMID: 35886976 PMCID: PMC9317002 DOI: 10.3390/ijms23147627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 12/23/2022] Open
Abstract
Multiple myeloma (MM) is a malignant, incurable disease characterized by the expansion of monoclonal terminally differentiated plasma cells in the bone marrow. MM is consistently preceded by an asymptomatic monoclonal gammopathy of undetermined significance, and in the absence of myeloma defining events followed by a stage termed smoldering multiple myeloma (SMM), which finally progresses to active myeloma if signs of organ damage are present. The reciprocal interaction between tumor cells and the tumor microenvironment plays a crucial role in the development of MM and the establishment of a tumor-promoting stroma facilitates tumor growth and myeloma progression. Since myeloma cells depend on signals from the bone marrow microenvironment (BMME) for their survival, therapeutic interventions targeting the BMME are a novel and successful strategy for myeloma care. Here, we describe the complex interplay between myeloma cells and the cellular components of the BMME that is essential for MM development and progression. Finally, we present BMME modifying treatment options such as anti-CD38 based therapies, immunomodulatory drugs (IMiDs), CAR T-cell therapies, bispecific antibodies, and antibody-drug conjugates which have significantly improved the long-term outcome of myeloma patients, and thus represent novel therapeutic standards.
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Affiliation(s)
- Peter Neumeister
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036 Graz, Austria; (E.S.); (K.P.); (M.S.); (A.J.D.)
- Correspondence:
| | - Eduard Schulz
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036 Graz, Austria; (E.S.); (K.P.); (M.S.); (A.J.D.)
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katrin Pansy
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036 Graz, Austria; (E.S.); (K.P.); (M.S.); (A.J.D.)
| | - Marta Szmyra
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036 Graz, Austria; (E.S.); (K.P.); (M.S.); (A.J.D.)
| | - Alexander JA Deutsch
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036 Graz, Austria; (E.S.); (K.P.); (M.S.); (A.J.D.)
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15
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Davies FE, Pawlyn C, Usmani SZ, San-Miguel JF, Einsele H, Boyle EM, Corre J, Auclair D, Cho HJ, Lonial S, Sonneveld P, Stewart AK, Bergsagel PL, Kaiser MF, Weisel K, Keats JJ, Mikhael JR, Morgan KE, Ghobrial IM, Orlowski RZ, Landgren CO, Gay F, Caers J, Chng WJ, Chari A, Walker BA, Kumar SK, Costa LJ, Anderson KC, Morgan GJ. Perspectives on the Risk-Stratified Treatment of Multiple Myeloma. Blood Cancer Discov 2022; 3:273-284. [PMID: 35653112 PMCID: PMC9894570 DOI: 10.1158/2643-3230.bcd-21-0205] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The multiple myeloma treatment landscape has changed dramatically. This change, paralleled by an increase in scientific knowledge, has resulted in significant improvement in survival. However, heterogeneity remains in clinical outcomes, with a proportion of patients not benefiting from current approaches and continuing to have a poor prognosis. A significant proportion of the variability in outcome can be predicted on the basis of clinical and biochemical parameters and tumor-acquired genetic variants, allowing for risk stratification and a more personalized approach to therapy. This article discusses the principles that can enable the rational and effective development of therapeutic approaches for high-risk multiple myeloma.
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Affiliation(s)
| | - Charlotte Pawlyn
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, Department of Haematology, London, United Kingdom
| | - Saad Z. Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | | | - Jill Corre
- Unité de Génomique du Myélome, Institut Universitaire du Cancer, Toulouse France. Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Daniel Auclair
- The Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Hearn Jay Cho
- The Multiple Myeloma Research Foundation, Norwalk, Connecticut
- Multiple Myeloma Center of Excellence, Icahn School of Medicine at Mt. Sinai, New York, New York
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Pieter Sonneveld
- Erasmus MC Cancer Institute, Department of Hematology, Rotterdam, the Netherlands
| | - A. Keith Stewart
- University Health Network and the Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Martin F. Kaiser
- The Royal Marsden Hospital, Department of Haematology, London, United Kingdom
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Katja Weisel
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonathan J. Keats
- Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Joseph R. Mikhael
- Translational Genomics Research Institute, City of Hope Cancer Center, Phoenix, Arizona
| | | | - Irene M. Ghobrial
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Robert Z. Orlowski
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - C. Ola Landgren
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Francesca Gay
- Division of Hematology, University of Torino, Torino, Italy
| | - Joseph Caers
- Department of Hematology, Centre Hospitalier Universitaire (CHU) de Liège, Liège, Belgium
| | - Wee Joo Chng
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana
- Department of Hematology, Mayo Clinic, Rochester, Minnesota
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ajai Chari
- Multiple Myeloma Center of Excellence, Icahn School of Medicine at Mt. Sinai, New York, New York
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana
| | - Shaji K. Kumar
- Department of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Luciano J. Costa
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kenneth C. Anderson
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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16
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Farswan A, Gupta A, Jena L, Ruhela V, Kaur G, Gupta R. Characterizing the mutational landscape of MM and its precursor MGUS. Am J Cancer Res 2022; 12:1919-1933. [PMID: 35530275 PMCID: PMC9077084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023] Open
Abstract
Mutational Signatures and Tumor mutational burden (TMB) have emerged as prognostic biomarkers in cancer genomics. However, the association of TMB with overall survival (OS) is still unknown in newly diagnosed multiple myeloma (NDMM) patients. Further, the change in the mutational spectrum involving both synonymous and non-synonymous mutations as MGUS progresses to MM is unexplored. This study addresses both these aspects via extensive evaluation of the mutations in MGUS and NDMM. WES data of 1018 NDMM patients and 61 MGUS patients collected from three different global regions were analyzed in this study. Single base substitutions, mutational signatures and TMB were inferred from the variants identified in MGUS and MM patients. The cutoff value for TMB was estimated to divide patients into low TMB and high TMB (hypermutators) groups. This study finds a change in the mutational spectrum with a statistically significant increase from MGUS to MM. There was a statistically significant increase in the frequency of all the three categories of variants, non-synonymous (NS), synonymous (SYN), and others (OTH), from MGUS to MM (P<0.05). However, there was a statistically significant rise in the TMB values for TMB_NS and TMB_SYN only. We also observed that 3' and 5'UTR mutations were more frequent in MM and might be responsible for driving MGUS to MM via regulatory binding sites. NDMM patients were also examined separately along with their survival outcomes. The frequency of hypermutators was low in MM with poor OS and PFS outcome. We observed a statistically significant rise in the frequency of C>A and C>T substitutions and a statistically significant decline in T>G substitutions in the MM patients with poor outcomes. Additionally, there was a statistically significant increase in the TMB of the patients with poor outcome compared to patients with a superior outcome. A statistically significant association between the APOBEC activity and poor overall survival in MM was discovered. These findings have potential clinical relevance and can assist in designing risk-adapted therapies to inhibit the progression of MGUS to MM and prolong the overall survival in high-risk MM patients.
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Affiliation(s)
- Akanksha Farswan
- SBILab, Department of ECE, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi)New Delhi 110020, India
| | - Anubha Gupta
- SBILab, Department of ECE, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi)New Delhi 110020, India
| | - Lingaraja Jena
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, AIIMSNew Delhi 110029, India
| | - Vivek Ruhela
- Department of Computational Biology, IIIT-DelhiNew Delhi 110020, India
| | - Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, AIIMSNew Delhi 110029, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, AIIMSNew Delhi 110029, India
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17
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Isa R, Horinaka M, Tsukamoto T, Mizuhara K, Fujibayashi Y, Taminishi-Katsuragawa Y, Okamoto H, Yasuda S, Kawaji-Kanayama Y, Matsumura-Kimoto Y, Mizutani S, Shimura Y, Taniwaki M, Sakai T, Kuroda J. The Rationale for the Dual-Targeting Therapy for RSK2 and AKT in Multiple Myeloma. Int J Mol Sci 2022; 23:ijms23062919. [PMID: 35328342 PMCID: PMC8949999 DOI: 10.3390/ijms23062919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Multiple myeloma (MM) is characterized by remarkable cytogenetic/molecular heterogeneity among patients and intraclonal diversity even in a single patient. We previously demonstrated that PDPK1, the master kinase of series of AGC kinases, is universally active in MM, and plays pivotal roles in cell proliferation and cell survival of myeloma cells regardless of the profiles of cytogenetic and genetic abnormalities. This study investigated the therapeutic efficacy and mechanism of action of dual blockade of two major PDPK1 substrates, RSK2 and AKT, in MM. The combinatory treatment of BI-D1870, an inhibitor for N-terminal kinase domain (NTKD) of RSK2, and ipatasertib, an inhibitor for AKT, showed the additive to synergistic anti-tumor effect on human MM-derived cell lines (HMCLs) with active RSK2-NTKD and AKT, by enhancing apoptotic induction with BIM and BID activation. Moreover, the dual blockade of RSK2 and AKT exerted robust molecular effects on critical gene sets associated with myeloma pathophysiologies, such as those with MYC, mTOR, STK33, ribosomal biogenesis, or cell-extrinsic stimuli of soluble factors, in HMCLs. These results provide the biological and molecular rationales for the dual-targeting strategy for RSK2 and AKT, which may overcome the therapeutic difficulty due to cytogenetic/molecular heterogeneity in MM.
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Affiliation(s)
- Reiko Isa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Mano Horinaka
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (M.H.); (S.Y.); (T.S.)
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Kentaro Mizuhara
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yoko Taminishi-Katsuragawa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Haruya Okamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Shusuke Yasuda
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (M.H.); (S.Y.); (T.S.)
| | - Yuka Kawaji-Kanayama
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Shinsuke Mizutani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Toshiyuki Sakai
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (M.H.); (S.Y.); (T.S.)
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
- Correspondence:
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18
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Oben B, Cosemans C, Geerdens E, Linsen L, Vanhees K, Maes B, Theunissen K, Cruys B, Lionetti M, Arijs I, Bolli N, Froyen G, Rummens JL. The Dynamics of Nucleotide Variants in the Progression from Low-Intermediate Myeloma Precursor Conditions to Multiple Myeloma: Studying Serial Samples with a Targeted Sequencing Approach. Cancers (Basel) 2022; 14:cancers14041035. [PMID: 35205782 PMCID: PMC8870380 DOI: 10.3390/cancers14041035] [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: 12/20/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Multiple myeloma (MM), characterized by the expansion of plasma cells in the bone marrow, is the second most common hematological malignancy. This incurable cancer is consistently preceded by non-malignant asymptomatic precursor conditions known as monoclonal gammopathy of undetermined significance (MGUS) and/or smoldering multiple myeloma (SMM). These pre-stages are relatively frequent, but only a select percentage of them will progress to MM. However, it is still not possible to individually predict when and which patients will develop MM. Therefore, this study aimed to investigate the mutational profile in the progression in serial bone marrow samples with a custom targeted sequencing panel, designed to detect variants in myeloma-related genes. Remarkably, almost all variants identified in the MM samples were also already present in the pre-stages, sometimes even many years before the progression. These results provide new important insights into the molecular mechanisms of the precursor conditions and progression to MM. Abstract Multiple myeloma (MM), or Kahler’s disease, is an incurable plasma cell (PC) cancer in the bone marrow (BM). This malignancy is preceded by one or more asymptomatic precursor conditions, monoclonal gammopathy of undetermined significance (MGUS) and/or smoldering multiple myeloma (SMM). The molecular mechanisms and exact cause of this progression are still not completely understood. In this study, the mutational profile underlying the progression from low–intermediate risk myeloma precursor conditions to MM was studied in serial BM smears. A custom capture-based sequencing platform was developed, including 81 myeloma-related genes. The clonal evolution of single nucleotide variants and short insertions and deletions was studied in serial BM smears from 21 progressed precursor patients with a median time of progression of six years. From the 21 patients, four patients had no variation in one of the 81 studied genes. Interestingly, in 16 of the 17 other patients, at least one variant present in MM was also detected in its precursor BM, even years before progression. Here, the variants were present in the pre-stage at a median of 62 months before progression to MM. Studying these paired BM samples contributes to the knowledge of the evolutionary genetic landscape and provides additional insight into the mutational behavior of mutant clones over time throughout progression.
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Affiliation(s)
- Bénedith Oben
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Correspondence:
| | - Charlotte Cosemans
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Ellen Geerdens
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Loes Linsen
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Activity Center Biobanking, University Hospitals Leuven, 3000 Leuven, Belgium
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
| | - Kimberly Vanhees
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
| | - Brigitte Maes
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Koen Theunissen
- Department Hematology, Jessa Hospital, 3500 Hasselt, Belgium;
| | - Bert Cruys
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Marta Lionetti
- Department Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (M.L.); (N.B.)
| | - Ingrid Arijs
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Laboratory for Translational Genetics, Department Human Genetics, University of Leuven, 3000 Leuven, Belgium
- Belgian Inflammatory Bowel Disease Research and Development (BIRD), 1930 Zaventem, Belgium
| | - Niccolò Bolli
- Department Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (M.L.); (N.B.)
- Unità Operativa Complessa di Ematologia, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Guy Froyen
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Jean-Luc Rummens
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
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19
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Deng J, Xiao W, Wang Z. FAM46C as a Potential Marker for Pan-Cancer Prognosis and Predicting Immunotherapeutic Efficacy. Front Genet 2022; 13:810252. [PMID: 35222533 PMCID: PMC8864238 DOI: 10.3389/fgene.2022.810252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/18/2022] [Indexed: 12/28/2022] Open
Abstract
Background:FAM46C is a common mutated gene in tumours. A comprehensive understanding of the relationship between FAM46C expression and pan-cancer can guide clinical prognosis and broaden the immunotherapeutic targets.Methods: Data from The Cancer Genome Atlas and Genotype-Tissue Expression (GTEx) databases were obtained, and gene expression of different tumour types and stages was analysed. Immunohistochemical analysis was performed to detect differences in the FAM46C protein levels in normal and cancerous tissues. The genetic variation of FAM46C was characterised using cBioPortal. The clinical prognostic value of FAM46C and the impact of FAM46C expression levels on the prognosis of patients with different types of cancer were assessed based on Kaplan–Meier and Cox regression analyses. Gene set enrichment analysis (GSEA) was used to analyse the pathways associated with FAM46C. Correlations between FAM46C expression levels and immune infiltration were assessed using the TIMER2 database and CIBERSORT algorithm, and correlations between FAM46C expression and the ESTIMATE, immune and stromal scores were analysed using the ESTIMATE algorithm. In addition, we also analysed the correlation between FAM46C expression and immune activation, suppression genes and immune chemokines.Results: The expression level of FAM46C was correlated with the prognosis of most tumours, and low expression levels often suggested a poor prognosis. FAM46C was positively correlated with the abundance of CD4+ T cells, CD8+ T cells and plasma B lymphocytes in the tumour microenvironment. FAM46C exhibited a strong correlation with immunomodulatory pathways, immunomodulatory factors and immune markers. In addition, high FAM46C expression correlated with tumour mutational burden in acute myeloid leukaemia and microsatellite instability in endometrial cancer.Conclusion: Our study suggests that FAM46C can be a potential prognostic marker for pan-cancer, is closely associated with immune regulation and may be an immune checkpoint to guide future clinical immunotherapy.
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Affiliation(s)
- Jiehua Deng
- Centre of Imaging Diagnosis, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Wei Xiao
- Department of Clinical Medicine, Medical College of Shihezi University, Shihezi, China
| | - Zheng Wang
- Centre of Imaging Diagnosis, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Zheng Wang,
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20
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Brady SW, Gout AM, Zhang J. Therapeutic and prognostic insights from the analysis of cancer mutational signatures. Trends Genet 2022; 38:194-208. [PMID: 34483003 PMCID: PMC8752466 DOI: 10.1016/j.tig.2021.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The somatic mutations in each cancer genome are caused by multiple mutational processes, each of which leaves a characteristic imprint (or 'signature'), potentially caused by specific etiologies or exposures. Deconvolution of these signatures offers a glimpse into the evolutionary history of individual tumors. Recent work has shown that mutational signatures may also yield therapeutic and prognostic insights, including the identification of cell-intrinsic signatures as biomarkers of drug response and prognosis. For example, mutational signatures indicating homologous recombination deficiency are associated with poly(ADP)-ribose polymerase (PARP) inhibitor sensitivity, whereas APOBEC-associated signatures are associated with ataxia telangiectasia and Rad3-related kinase (ATR) inhibitor sensitivity. Furthermore, therapy-induced mutational signatures implicated in cancer progression have also been uncovered, including the identification of thiopurine-induced TP53 mutations in leukemia. In this review, we explore the various ways mutational signatures can reveal new therapeutic and prognostic insights, thus extending their traditional role in identifying disease etiology.
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Affiliation(s)
- Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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21
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Pan D, Richter J. Where We Stand With Precision Therapeutics in Myeloma: Prosperity, Promises, and Pipedreams. Front Oncol 2022; 11:819127. [PMID: 35127532 PMCID: PMC8811139 DOI: 10.3389/fonc.2021.819127] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple myeloma remains an incurable disease despite numerous novel agents being approved in the last decade. Furthermore, disease behavior and susceptibility to current treatments often vary drastically from patient to patient. To date there are no approved therapies in myeloma that are targeted to specific patient populations based on genomic or immunologic findings. Precision medicine, using biomarkers descriptive of a specific tumor's biology and predictive of response to appropriate agents, may continue to push the field forward by expanding our treatment arsenal while refining our ability to expose patients to only those treatments likely to be efficacious. Extensive research efforts have been carried out in this endeavor including the use of agents targeting Bcl2 and the RAS/MAPK and PI3K/AKT/mTOR pathways. Thus far, clinical trials have yielded occasional successes intermixed with disappointments, reflecting significant hurdles which still remain including the complex crosstalk between oncogenic pathways and the nonlinear genetic development of myeloma, prone to cultivating sub-clones with distinctive mutations. In this review, we explore the landscape of precision therapeutics in multiple myeloma and underscore the degree to which research efforts have produced tangible clinical results.
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Affiliation(s)
- Darren Pan
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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22
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Ortiz-Estévez M, Towfic F, Flynt E, Stong N, Jang IS, Wang K, Trotter MWB, Thakurta A. Integrative multi-omics identifies high risk multiple myeloma subgroup associated with significant DNA loss and dysregulated DNA repair and cell cycle pathways. BMC Med Genomics 2021; 14:295. [PMID: 34922559 PMCID: PMC8684160 DOI: 10.1186/s12920-021-01140-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Background Despite significant therapeutic advances in improving lives of multiple myeloma (MM) patients, it remains mostly incurable, with patients ultimately becoming refractory to therapies. MM is a genetically heterogeneous disease and therapeutic resistance is driven by a complex interplay of disease pathobiology and mechanisms of drug resistance. We applied a multi-omics strategy using tumor-derived gene expression, single nucleotide variant, copy number variant, and structural variant profiles to investigate molecular subgroups in 514 newly diagnosed MM (NDMM) samples and identified 12 molecularly defined MM subgroups (MDMS1-12) with distinct genomic and transcriptomic features. Results Our integrative approach let us identify NDMM subgroups with transversal profiles to previously described ones, based on single data types, which shows the impact of this approach for disease stratification. One key novel subgroup is our MDMS8, associated with poor clinical outcome [median overall survival, 38 months (global log-rank p-value < 1 × 10−6)], which uniquely presents a broad genomic loss (> 9% of entire genome, t-test p value < 1e−5) driving dysregulation of various transcriptional programs affecting DNA repair and cell cycle/mitotic processes. This subgroup was validated on multiple independent datasets, and a master regulator analyses identified transcription factors controlling MDMS8 transcriptomic profile, including CKS1B and PRKDC among others, which are regulators of the DNA repair and cell cycle pathways. Conclusion Using multi-omics unsupervised clustering we were able to discover a new high-risk multiple myeloma patient segment. This high-risk group presents diverse previously known genetic markers, but also a new characteristic defined by accumulation of genomic loss which seems to drive transcriptional dysregulation of cell cycle, DNA repair and DNA damage. Finally, our work identified various master regulators, including E2F2 and CKS1B as the genes controlling these key biological pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01140-5.
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Affiliation(s)
- María Ortiz-Estévez
- BMS Center for Innovation and Translational Research Europe (CITRE), A Bristol Myers Squibb Company, Sevilla, Spain
| | | | - Erin Flynt
- Bristol Myers Squibb, 181 Passaic Ave, Summit, NJ, 07901, USA
| | - Nicholas Stong
- Bristol Myers Squibb, 181 Passaic Ave, Summit, NJ, 07901, USA
| | | | - Kai Wang
- Bristol Myers Squibb, San Diego, CA, USA
| | - Matthew W B Trotter
- BMS Center for Innovation and Translational Research Europe (CITRE), A Bristol Myers Squibb Company, Sevilla, Spain
| | - Anjan Thakurta
- Bristol Myers Squibb, 181 Passaic Ave, Summit, NJ, 07901, USA.
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23
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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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24
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Kos IA, Thurner L, Bittenbring JT, Christofyllakis K, Kaddu-Mulindwa D. Advances in Lymphoma Molecular Diagnostics. Diagnostics (Basel) 2021; 11:diagnostics11122174. [PMID: 34943410 PMCID: PMC8699850 DOI: 10.3390/diagnostics11122174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Lymphomas encompass a diverse group of malignant lymphoid neoplasms. Over recent years much scientific effort has been undertaken to identify and understand molecular changes in lymphomas, resulting in a wide range of genetic alterations that have been reported across all types of lymphomas. As many of these changes are now incorporated into the World Health Organization’s defined criteria for the diagnostic evaluation of patients with lymphoid neoplasms, their accurate identification is crucial. Even if many alterations are not routinely evaluated in daily clinical practice, they may still have implications in risk stratification, treatment, prognosis or disease monitoring. Moreover, some alterations can be used for targeted treatment. Therefore, these advances in lymphoma molecular diagnostics in some cases have led to changes in treatment algorithms. Here, we give an overview of and discuss advances in molecular techniques in current clinical practice, as well as highlight some of them in a clinical context.
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25
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Talluri S, Samur MK, Buon L, Kumar S, Potluri LB, Shi J, Prabhala RH, Shammas MA, Munshi NC. Dysregulated APOBEC3G causes DNA damage and promotes genomic instability in multiple myeloma. Blood Cancer J 2021; 11:166. [PMID: 34625538 PMCID: PMC8501035 DOI: 10.1038/s41408-021-00554-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/14/2021] [Accepted: 09/01/2021] [Indexed: 12/22/2022] Open
Abstract
Multiple myeloma (MM) is a heterogeneous disease characterized by significant genomic instability. Recently, a causal role for the AID/APOBEC deaminases in inducing somatic mutations in myeloma has been reported. We have identified APOBEC/AID as a prominent mutational signature at diagnosis with further increase at relapse in MM. In this study, we identified upregulation of several members of APOBEC3 family (A3A, A3B, A3C, and A3G) with A3G, as one of the most expressed APOBECs. We investigated the role of APOBEC3G in MM and observed that A3G expression and APOBEC deaminase activity is elevated in myeloma cell lines and patient samples. Loss-of and gain-of function studies demonstrated that APOBEC3G significantly contributes to increase in DNA damage (abasic sites and DNA breaks) in MM cells. Evaluation of the impact on genome stability, using SNP arrays and whole genome sequencing, indicated that elevated APOBEC3G contributes to ongoing acquisition of both the copy number and mutational changes in MM cells over time. Elevated APOBEC3G also contributed to increased homologous recombination activity, a mechanism that can utilize increased DNA breaks to mediate genomic rearrangements in cancer cells. These data identify APOBEC3G as a novel gene impacting genomic evolution and underlying mechanisms in MM.
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Affiliation(s)
- Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | | | - Leutz Buon
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
| | - Subodh Kumar
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Lakshmi B Potluri
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Jialan Shi
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Rao H Prabhala
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
- Harvard Medical School, Boston, MA, 02215, USA
| | - Masood A Shammas
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Nikhil C Munshi
- Dana Farber Cancer Institute, Boston, MA, 02115, USA.
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA.
- Harvard Medical School, Boston, MA, 02215, USA.
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26
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Maclachlan KH, Rustad EH, Derkach A, Zheng-Lin B, Yellapantula V, Diamond B, Hultcrantz M, Ziccheddu B, Boyle EM, Blaney P, Bolli N, Zhang Y, Dogan A, Lesokhin AM, Morgan GJ, Landgren O, Maura F. Copy number signatures predict chromothripsis and clinical outcomes in newly diagnosed multiple myeloma. Nat Commun 2021; 12:5172. [PMID: 34453055 PMCID: PMC8397708 DOI: 10.1038/s41467-021-25469-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/02/2021] [Indexed: 12/14/2022] Open
Abstract
Chromothripsis is detectable in 20–30% of newly diagnosed multiple myeloma (NDMM) patients and is emerging as a new independent adverse prognostic factor. In this study we interrogate 752 NDMM patients using whole genome sequencing (WGS) to investigate the relationship of copy number (CN) signatures to chromothripsis and show they are highly associated. CN signatures are highly predictive of the presence of chromothripsis (AUC = 0.90) and can be used identify its adverse prognostic impact. The ability of CN signatures to predict the presence of chromothripsis is confirmed in a validation series of WGS comprised of 235 hematological cancers (AUC = 0.97) and an independent series of 34 NDMM (AUC = 0.87). We show that CN signatures can also be derived from whole exome data (WES) and using 677 cases from the same series of NDMM, we are able to predict both the presence of chromothripsis (AUC = 0.82) and its adverse prognostic impact. CN signatures constitute a flexible tool to identify the presence of chromothripsis and is applicable to WES and WGS data. Chromothripsis is associated with unfavourable outcomes in multiple myeloma (MM), but its detection usually requires whole genome sequencing. Here the authors develop an approach to detect chromothripsis in MM based on copy-number signatures that also works with whole exome sequencing data.
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Affiliation(s)
- Kylee H Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Even H Rustad
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Andriy Derkach
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Binbin Zheng-Lin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Venkata Yellapantula
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Diamond
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Malin Hultcrantz
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bachisio Ziccheddu
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.,Department of Molecular Biotechnologies and Health Sciences, University of Turin, Turin, Italy
| | - 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
| | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander M Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Gareth J Morgan
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Ola Landgren
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Francesco Maura
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
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27
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Clonal Evolution of Multiple Myeloma-Clinical and Diagnostic Implications. Diagnostics (Basel) 2021; 11:diagnostics11091534. [PMID: 34573876 PMCID: PMC8469181 DOI: 10.3390/diagnostics11091534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022] Open
Abstract
Plasma cell dyscrasias are a heterogeneous group of diseases characterized by the expansion of bone marrow plasma cells. Malignant transformation of plasma cells depends on the continuity of events resulting in a sequence of well-defined disease stages, from monoclonal gammopathy of undetermined significance (MGUS) through smoldering myeloma (SMM) to symptomatic multiple myeloma (MM). Evolution of a pre-malignant cell into a malignant cell, as well as further tumor progression, dissemination, and relapse, require development of multiple driver lesions conferring selective advantage of the dominant clone and allowing subsequent evolution under selective pressure of microenvironment and treatment. This process of natural selection facilitates tumor plasticity leading to the formation of genetically complex and heterogenous tumors that are notoriously difficult to treat. Better understanding of the mechanisms underlying tumor evolution in MM and identification of lesions driving the evolution from the premalignant clone is therefore a key to development of effective treatment and long-term disease control. Here, we review recent advances in clonal evolution patterns and genomic landscape dynamics of MM, focusing on their clinical implications.
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28
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Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153755. [PMID: 34359660 PMCID: PMC8345052 DOI: 10.3390/cancers13153755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma. Abstract Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.
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29
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Taiana E, Gallo Cantafio ME, Favasuli VK, Bandini C, Viglietto G, Piva R, Neri A, Amodio N. Genomic Instability in Multiple Myeloma: A "Non-Coding RNA" Perspective. Cancers (Basel) 2021; 13:cancers13092127. [PMID: 33924959 PMCID: PMC8125142 DOI: 10.3390/cancers13092127] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Genomic instability (GI) plays an important role in the pathobiology of multiple myeloma (MM) by promoting the acquisition of several tumor hallmarks. Molecular determinants of GI in MM are continuously emerging and will be herein discussed, with specific regard to non-coding RNAs. Targeting non-coding RNA molecules known to be involved in GI indeed provides novel routes to dampen such oncogenic mechanisms in MM. Abstract Multiple myeloma (MM) is a complex hematological malignancy characterized by abnormal proliferation of malignant plasma cells (PCs) within a permissive bone marrow microenvironment. The pathogenesis of MM is unequivocally linked to the acquisition of genomic instability (GI), which indicates the tendency of tumor cells to accumulate a wide repertoire of genetic alterations. Such alterations can even be detected at the premalignant stages of monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM) and, overall, contribute to the acquisition of the malignant traits underlying disease progression. The molecular basis of GI remains unclear, with replication stress and deregulation of DNA damage repair pathways representing the most documented mechanisms. The discovery that non-coding RNA molecules are deeply dysregulated in MM and can target pivotal components of GI pathways has introduced a further layer of complexity to the GI scenario in this disease. In this review, we will summarize available information on the molecular determinants of GI in MM, focusing on the role of non-coding RNAs as novel means to tackle GI for therapeutic intervention.
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Affiliation(s)
- Elisa Taiana
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.T.); (V.K.F.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy
| | - Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.E.G.C.); (G.V.)
| | - Vanessa Katia Favasuli
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.T.); (V.K.F.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy
| | - Cecilia Bandini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (C.B.); (R.P.)
- Città Della Salute e della Scienza Hospital, 10126 Torino, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.E.G.C.); (G.V.)
| | - Roberto Piva
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (C.B.); (R.P.)
- Città Della Salute e della Scienza Hospital, 10126 Torino, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.T.); (V.K.F.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy
- Correspondence: (A.N.); (N.A.)
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.E.G.C.); (G.V.)
- Correspondence: (A.N.); (N.A.)
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Genomic Uracil and Aberrant Profile of Demethylation Intermediates in Epigenetics and Hematologic Malignancies. Int J Mol Sci 2021; 22:ijms22084212. [PMID: 33921666 PMCID: PMC8073381 DOI: 10.3390/ijms22084212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/30/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
DNA of all living cells undergoes continuous structural and chemical alterations resulting from fundamental cellular metabolic processes and reactivity of normal cellular metabolites and constituents. Examples include enzymatically oxidized bases, aberrantly methylated bases, and deaminated bases, the latter largely uracil from deaminated cytosine. In addition, the non-canonical DNA base uracil may result from misincorporated dUMP. Furthermore, uracil generated by deamination of cytosine in DNA is not always damage as it is also an intermediate in normal somatic hypermutation (SHM) and class shift recombination (CSR) at the Ig locus of B-cells in adaptive immunity. Many of the modifications alter base-pairing properties and may thus cause replicative and transcriptional mutagenesis. The best known and most studied epigenetic mark in DNA is 5-methylcytosine (5mC), generated by a methyltransferase that uses SAM as methyl donor, usually in CpG contexts. Oxidation products of 5mC are now thought to be intermediates in active demethylation as well as epigenetic marks in their own rights. The aim of this review is to describe the endogenous processes that surround the generation and removal of the most common types of DNA nucleobase modifications, namely, uracil and certain epigenetic modifications, together with their role in the development of hematological malignances. We also discuss what dictates whether the presence of an altered nucleobase is defined as damage or a natural modification.
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31
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mmsig: a fitting approach to accurately identify somatic mutational signatures in hematological malignancies. Commun Biol 2021; 4:424. [PMID: 33782531 PMCID: PMC8007623 DOI: 10.1038/s42003-021-01938-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
Mutational signatures have emerged as powerful biomarkers in cancer patients, with prognostic and therapeutic implications. Wider clinical utility requires access to reproducible algorithms, which allow characterization of mutational signatures in a given tumor sample. Here, we show how mutational signature fitting can be applied to hematological cancer genomes to identify biologically and clinically important mutational processes, highlighting the importance of careful interpretation in light of biological knowledge. Our newly released R package mmsig comes with a dynamic error-suppression procedure that improves specificity in important clinical and biological settings. In particular, mmsig allows accurate detection of mutational signatures with low abundance, such as those introduced by APOBEC cytidine deaminases. This is particularly important in the most recent mutational signature reference (COSMIC v3.1) where each signature is more clearly defined. Our mutational signature fitting algorithm mmsig is a robust tool that can be implemented immediately in the clinic. Rustad et al. present a software package for the R statistical environment for the accurately quantify of somatic mutational signatures in hematological malignancies
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32
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Metabolic Effects of Recurrent Genetic Aberrations in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13030396. [PMID: 33494394 PMCID: PMC7865460 DOI: 10.3390/cancers13030396] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
Oncogene activation and malignant transformation exerts energetic, biosynthetic and redox demands on cancer cells due to increased proliferation, cell growth and tumor microenvironment adaptation. As such, altered metabolism is a hallmark of cancer, which is characterized by the reprogramming of multiple metabolic pathways. Multiple myeloma (MM) is a genetically heterogeneous disease that arises from terminally differentiated B cells. MM is characterized by reciprocal chromosomal translocations that often involve the immunoglobulin loci and a restricted set of partner loci, and complex chromosomal rearrangements that are associated with disease progression. Recurrent chromosomal aberrations in MM result in the aberrant expression of MYC, cyclin D1, FGFR3/MMSET and MAF/MAFB. In recent years, the intricate mechanisms that drive cancer cell metabolism and the many metabolic functions of the aforementioned MM-associated oncogenes have been investigated. Here, we discuss the metabolic consequences of recurrent chromosomal translocations in MM and provide a framework for the identification of metabolic changes that characterize MM cells.
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33
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Maura F, Landgren O, Morgan GJ. Designing Evolutionary-based Interception Strategies to Block the Transition from Precursor Phases to Multiple Myeloma. Clin Cancer Res 2021; 27:15-23. [PMID: 32759358 PMCID: PMC7785564 DOI: 10.1158/1078-0432.ccr-20-1395] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/17/2020] [Accepted: 07/31/2020] [Indexed: 11/16/2022]
Abstract
The development of next-generation sequencing technology has dramatically improved our understanding of the genetic landscape of multiple myeloma. Several new drivers and recurrent events have been reported and linked to a potential driver role. This complex landscape is enhanced by intraclonal mutational heterogeneity and variability introduced through the dimensions of time and space. The evolutionary history of multiple myeloma is driven by both the accumulation of different genomic drivers and by the activity of different mutational processes active overtime. In this review, we describe how these new findings and sequencing technologies have been progressively allowed to understand and reshape our knowledge of the complexity of multiple myeloma at each of its developmental stages: premalignant, at diagnosis, and in relapsed/refractory states. We discuss how these evolutionary concepts can be utilized in the clinic to alter evolutionary trajectories providing a framework for therapeutic intervention at early-disease stages.
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Affiliation(s)
- Francesco Maura
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Ola Landgren
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Gareth J Morgan
- Perlmutter Cancer Center, New York University Langone Health, New York, New York.
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34
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Locher M, Jukic E, Bohn JP, Untergasser G, Steurer M, Cramer CA, Schwendinger S, Vogi V, Verdorfer I, Witsch-Baumgartner M, Nachbaur D, Gunsilius E, Wolf D, Zschocke J, Steiner N. Clonal dynamics in a composite chronic lymphocytic leukemia and hairy cell leukemia-variant. Genes Chromosomes Cancer 2020; 60:287-292. [PMID: 33277788 PMCID: PMC7984250 DOI: 10.1002/gcc.22925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/28/2022] Open
Abstract
Composite lymphoma is the rare simultaneous manifestation of two distinct lymphomas. Chronic lymphocytic leukemia (CLL) has a propensity for occurring in composite lymphomas, a phenomenon that remains to be elucidated. We applied cytogenetics, droplet digital polymerase chain reaction, and massively parallel sequencing to analyze longitudinally a patient with CLL, who 3 years later showed transformation to a hairy cell leukemia-variant (HCL-V). Outgrowth of the IGHV4-34-positive HCL-V clone at the expense of the initially dominant CLL clone with trisomy 12 and MED12 mutation started before CLL-guided treatment and was accompanied by a TP53 mutation, which was already detectable at diagnosis of CLL. Furthermore, deep sequencing of IGH showed a composite lymphoma with presence of both disease components at all analyzed timepoints (down to a minor clone: major clone ratio of ~1:1000). Overall, our analyses showed a disease course that resembled clonal dynamics reported for malignancies with intratumoral heterogeneity and illustrate the utility of deep sequencing of IGH to detect distinct clonal populations at diagnosis, monitor clonal response to therapy, and possibly improve clinical outcomes.
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Affiliation(s)
- Maurus Locher
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Emina Jukic
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Jan-Paul Bohn
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerold Untergasser
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Steurer
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Simon Schwendinger
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Verena Vogi
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Irmgard Verdorfer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | | | - David Nachbaur
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Eberhard Gunsilius
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria.,Medical Clinic III, Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Normann Steiner
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
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35
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Hoang PH, Cornish AJ, Sherborne AL, Chubb D, Kimber S, Jackson G, Morgan GJ, Cook G, Kinnersley B, Kaiser M, Houlston RS. An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics. Blood Cancer J 2020; 10:101. [PMID: 33057009 PMCID: PMC7560599 DOI: 10.1038/s41408-020-00367-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/15/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023] Open
Abstract
Most patients with multiple myeloma (MM) die from progressive disease after relapse. To advance our understanding of MM evolution mechanisms, we performed whole-genome sequencing of 80 IGH-translocated tumour-normal newly diagnosed pairs and 24 matched relapsed tumours from the Myeloma XI trial. We identify multiple events as potentially important for survival and therapy-resistance at relapse including driver point mutations (e.g., TET2), translocations (MAP3K14), lengthened telomeres, and increased genomic instability (e.g., 17p deletions). Despite heterogeneous mutational processes contributing to relapsed mutations across MM subtypes, increased AID/APOBEC activity is particularly associated with shorter progression time to relapse, and contributes to higher mutational burden at relapse. In addition, we identify three enhanced major clonal evolution patterns of MM relapse, independent of treatment strategies and molecular karyotypes, questioning the viability of "evolutionary herding" approach in treating drug-resistant MM. Our data show that MM relapse is associated with acquisition of new mutations and clonal selection, and suggest APOBEC enzymes among potential targets for therapy-resistant MM.
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Affiliation(s)
- Phuc H Hoang
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Amy L Sherborne
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Scott Kimber
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Graham Jackson
- Department of Haematology, University of Newcastle, Newcastle Upon Tyne, UK
| | | | - Gordon Cook
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK.
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK.
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36
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Samur MK, Aktas Samur A, Fulciniti M, Szalat R, Han T, Shammas M, Richardson P, Magrangeas F, Minvielle S, Corre J, Moreau P, Thakurta A, Anderson KC, Parmigiani G, Avet-Loiseau H, Munshi NC. Genome-Wide Somatic Alterations in Multiple Myeloma Reveal a Superior Outcome Group. J Clin Oncol 2020; 38:3107-3118. [PMID: 32687451 PMCID: PMC7499613 DOI: 10.1200/jco.20.00461] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Multiple myeloma (MM) is accompanied by heterogeneous somatic alterations. The overall goal of this study was to describe the genomic landscape of myeloma using deep whole-genome sequencing (WGS) and develop a model that identifies patients with long survival. METHODS We analyzed deep WGS data from 183 newly diagnosed patients with MM treated with lenalidomide, bortezomib, and dexamethasone (RVD) alone or RVD + autologous stem cell transplant (ASCT) in the IFM/DFCI 2009 study (ClinicalTrials.gov identifier: NCT01191060). We integrated genomic markers with clinical data. RESULTS We report significant variability in mutational load and processes within MM subgroups. The timeline of observed activation of mutational processes provides the basis for 2 distinct models of acquisition of mutational changes detected at the time of diagnosis of myeloma. Virtually all MM subgroups have activated DNA repair-associated signature as a prominent late mutational process, whereas APOBEC signature targeting C>G is activated in the intermediate phase of disease progression in high-risk MM. Importantly, we identify a genomically defined MM subgroup (17% of newly diagnosed patients) with low DNA damage (low genomic scar score with chromosome 9 gain) and a superior outcome (100% overall survival at 69 months), which was validated in a large independent cohort. This subgroup allowed us to distinguish patients with low- and high-risk hyperdiploid MM and identify patients with prolongation of progression-free survival. Genomic characteristics of this subgroup included lower mutational load with significant contribution from age-related mutations as well as frequent NRAS mutation. Surprisingly, their overall survival was independent of International Staging System and minimal residual disease status. CONCLUSION This is a comprehensive study identifying genomic markers of a good-risk group with prolonged survival. Identification of this patient subgroup will affect future therapeutic algorithms and research planning.
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Affiliation(s)
- Mehmet Kemal Samur
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Anil Aktas Samur
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Mariateresa Fulciniti
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Raphael Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tessa Han
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
| | - Masood Shammas
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Paul Richardson
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Florence Magrangeas
- Inserm UMR892, CNRS 6299, Université de Nantes, and Centre Hospitalier Universitaire de Nantes, Unité Mixte de Genomique du Cancer, Nantes, France
| | - Stephane Minvielle
- Inserm UMR892, CNRS 6299, Université de Nantes, and Centre Hospitalier Universitaire de Nantes, Unité Mixte de Genomique du Cancer, Nantes, France
| | - Jill Corre
- University Cancer Center of Toulouse Institut National de la Santé, Toulouse, France
| | - Philippe Moreau
- Inserm UMR892, CNRS 6299, Université de Nantes, and Centre Hospitalier Universitaire de Nantes, Unité Mixte de Genomique du Cancer, Nantes, France
| | | | - Kenneth C. Anderson
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Giovanni Parmigiani
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Hervé Avet-Loiseau
- University Cancer Center of Toulouse Institut National de la Santé, Toulouse, France
| | - Nikhil C. Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
- VA Boston Healthcare System, Boston, MA
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37
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Williams LS, Caro J, Razzo B, Boyle EM, Morgan GJ. Deep sequencing as an approach to understanding the complexity and improving the treatment of multiple myeloma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1792285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Louis S. Williams
- Department of Hematology & Medical Oncology, NYU Langone Medical Center, New York, NY, USA
| | - Jessica Caro
- Department of Hematology & Medical Oncology, NYU Langone Medical Center, New York, NY, USA
| | - Beatrice Razzo
- Department of Internal Medicine, NYU Langone Medical Center, New York, NY, USA
| | - Eileen M. Boyle
- Department of Hematology & Medical Oncology, Multiple Myeloma Research Program, NYU Langone Medical Center, New York, NY, USA
| | - Gareth J. Morgan
- Department of Hematology & Medical Oncology, Multiple Myeloma Research Program, NYU Langone Medical Center, New York, NY, USA
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38
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Alagpulinsa DA, Szalat RE, Poznansky MC, Shmookler Reis RJ. Genomic Instability in Multiple Myeloma. Trends Cancer 2020; 6:858-873. [PMID: 32487486 DOI: 10.1016/j.trecan.2020.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Genomic instability (GIN), an increased tendency to acquire genomic alterations, is a cancer hallmark. However, its frequency, underlying causes, and disease relevance vary across different cancers. Multiple myeloma (MM), a plasma cell malignancy, evolves through premalignant phases characterized by genomic abnormalities. Next-generation sequencing (NGS) methods are deconstructing the genomic landscape of MM across the continuum of its development, inextricably linking malignant transformation and disease progression with increasing acquisition of genomic alterations, and illuminating the mechanisms that generate these alterations. Although GIN drives disease evolution, it also creates vulnerabilities such as dependencies on 'superfluous' repair mechanisms and the induction of tumor-specific antigens that can be targeted. We review the mechanisms of GIN in MM, the associated vulnerabilities, and therapeutic targeting strategies.
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Affiliation(s)
- David A Alagpulinsa
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA.
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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39
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Impact of mitochondrial DNA mutations in multiple myeloma. Blood Cancer J 2020; 10:46. [PMID: 32358481 PMCID: PMC7195394 DOI: 10.1038/s41408-020-0315-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023] Open
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40
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Furukawa Y, Kikuchi J. Molecular basis of clonal evolution in multiple myeloma. Int J Hematol 2020; 111:496-511. [DOI: 10.1007/s12185-020-02829-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
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