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Ang DA, Carter JM, Deka K, Tan JHL, Zhou J, Chen Q, Chng WJ, Harmston N, Li Y. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma. Nat Commun 2024; 15:2513. [PMID: 38514625 PMCID: PMC10957915 DOI: 10.1038/s41467-024-46728-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro-proliferative mutations. Under these conditions, many cases eventually develop genetic abnormalities endowing them with constitutive NF-κB activation. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression.
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Affiliation(s)
- Daniel A Ang
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jean-Michel Carter
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Kamalakshi Deka
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Joel H L Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore
| | - Nathan Harmston
- Division of Science, Yale-NUS College, Singapore, 138527, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Molecular Biosciences Division, Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
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Song H, Shin U, Nam U, Lee Y. Exploring hematopoiesis in zebrafish using forward genetic screening. Exp Mol Med 2024; 56:51-58. [PMID: 38172599 PMCID: PMC10834449 DOI: 10.1038/s12276-023-01138-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 01/05/2024] Open
Abstract
Zebrafish have emerged as a powerful animal model for investigating the genetic basis of hematopoiesis. Owing to its close genetic and developmental similarities to humans, combined with its rapid reproduction and extensive genomic resources, zebrafish have become a versatile and efficient platform for genetic studies. In particular, the forward genetic screening approach has enabled the unbiased identification of novel genes and pathways related to blood development, from hematopoietic stem cell formation to terminal differentiation. Recent advances in mutant gene mapping have further expanded the scope of forward genetic screening, facilitating the identification of previously unknown genes and pathways relevant to hematopoiesis. In this review, we provide an overview of the zebrafish forward screening approach for hematopoietic gene discovery and highlight the key genes and pathways identified using this method. This review emphasizes the importance of zebrafish as a model system for understanding the genetic basis of hematopoiesis and its associated disorders.
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Affiliation(s)
- Hyemin Song
- Department of Biomedical Sciences, UC San Diego School of Medicine, La Jolla, CA, 92093, USA
- Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Uijeong Nam
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul, 05278, Republic of Korea
| | - Yoonsung Lee
- Clinical Research Institute, Kyung Hee University Hospital at Gangdong, School of Medicine, Kyung Hee University, Seoul, 05278, Republic of Korea.
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Raimondi V, Iannozzi NT, Burroughs-Garcìa J, Toscani D, Storti P, Giuliani N. A personalized molecular approach in multiple myeloma: the possible use of RAF/RAS/MEK/ERK and BCL-2 inhibitors. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:463-479. [PMID: 36071980 PMCID: PMC9446161 DOI: 10.37349/etat.2022.00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/08/2022] [Indexed: 11/19/2022] Open
Abstract
Multiple myeloma (MM) is a blood cancer that derives from plasma cells (PCs), which will accumulate in the bone marrow (BM). Over time, several drugs have been developed to treat this disease that is still uncurable. The therapies used to treat the disease target immune activity, inhibit proteasome activity, and involve the use of monoclonal antibodies. However, MM is a highly heterogeneous disease, in fact, there are several mutations in signaling pathways that are particularly important for MM cell biology and that are possible therapeutic targets. Indeed, some studies suggest that MM is driven by mutations within the rat sarcoma virus (RAS) signaling cascade, which regulates cell survival and proliferation. The RAS/proto-oncogene, serine/threonine kinase (RAF)/mitogen-activated extracellular signal-regulated kinase (ERK) kinase (MEK)/ERK signaling pathway is deregulated in several cancers, for which drugs have been developed to inhibit these pathways. In addition to the signaling pathways, the disease implements mechanisms to ensure the survival and consequently a high replicative capacity. This strategy consists in the deregulation of apoptosis. In particular, some cases of MM show overexpression of anti-apoptotic proteins belonging to the B cell lymphoma 2 (BCL-2) family that represent a possible druggable target. Venetoclax is an anti-BCL-2 molecule used in hematological malignancies that may be used in selected MM patients based on their molecular profile. We focused on the possible effects in MM of off-label drugs that are currently used for other cancers with the same molecular characteristics. Their use, combined with the current treatments, could be a good strategy against MM.
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Affiliation(s)
- Vincenzo Raimondi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | | | - Denise Toscani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Paola Storti
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Nicola Giuliani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy;Hematology, “Azienda Ospedaliero-Universitaria di Parma”, 43126 Parma, Italy
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4
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Bruno T, Corleone G, Catena V, Cortile C, De Nicola F, Fabretti F, Gumenyuk S, Pisani F, Mengarelli A, Passananti C, Fanciulli M. AATF/Che-1 localizes to paraspeckles and suppresses R-loops accumulation and interferon activation in Multiple Myeloma. EMBO J 2022; 41:e109711. [PMID: 35929179 PMCID: PMC9670196 DOI: 10.15252/embj.2021109711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 01/13/2023] Open
Abstract
Several kinds of stress promote the formation of three-stranded RNA:DNA hybrids called R-loops. Insufficient clearance of these structures promotes genomic instability and DNA damage, which ultimately contribute to the establishment of cancer phenotypes. Paraspeckle assemblies participate in R-loop resolution and preserve genome stability, however, the main determinants of this mechanism are still unknown. This study finds that in Multiple Myeloma (MM), AATF/Che-1 (Che-1), an RNA-binding protein fundamental to transcription regulation, interacts with paraspeckles via the lncRNA NEAT1_2 (NEAT1) and directly localizes on R-loops. We systematically show that depletion of Che-1 produces a marked accumulation of RNA:DNA hybrids. We provide evidence that such failure to resolve R-loops causes sustained activation of a systemic inflammatory response characterized by an interferon (IFN) gene expression signature. Furthermore, elevated levels of R-loops and of mRNA for paraspeckle genes in patient cells are linearly correlated with Multiple Myeloma progression. Moreover, increased interferon gene expression signature in patients is associated with markedly poor prognosis. Taken together, our study indicates that Che-1/NEAT1 cooperation prevents excessive inflammatory signaling in Multiple Myeloma by facilitating the clearance of R-loops. Further studies on different cancer types are needed to test if this mechanism is ubiquitously conserved and fundamental for cell homeostasis.
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Affiliation(s)
- Tiziana Bruno
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Giacomo Corleone
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Valeria Catena
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Clelia Cortile
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany,Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Svitlana Gumenyuk
- Hematology UnitIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Francesco Pisani
- Hematology UnitIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Andrea Mengarelli
- Hematology UnitIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Claudio Passananti
- Department of Molecular Medicine, CNR‐Institute of Molecular Biology and PathologySapienza University of RomeRomeItaly
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
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Diamantidis MD, Papadaki S, Hatjiharissi E. Exploring the current molecular landscape and management of multiple myeloma patients with the t(11;14) translocation. Front Oncol 2022; 12:934008. [PMID: 35982976 PMCID: PMC9379277 DOI: 10.3389/fonc.2022.934008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Multiple myeloma (MM) is a genetically complex disease. The key myeloma-initiating genetic events are hyperdiploidy and translocations involving the immunoglobulin heavy chain (IgH) enhancer on chromosome 14, which leads to the activation of oncogenes (e.g., CCND1, CCND3, MAF, and MMSET). The t(11;14) translocation is the most common in MM (15%–20%) and results in cyclin D1 (CCND1) upregulation, which leads to kinase activation and tumor cell proliferation. Notably, t(11;14) occurs at a higher rate in patients with plasma cell leukemia (40%) and light chain amyloidosis (50%). Patients with myeloma who harbor the t(11;14) translocation have high levels of the anti-apoptotic protein B-cell lymphoma 2 (BCL2). Multiple studies demonstrated that the presence of t(11;14) was predictive of BCL2 dependency, suggesting that BCL2 could be a target in this subtype of myeloma. Venetoclax, an oral BCL2 inhibitor, has shown remarkable activity in treating relapsed/refractory MM patients with t(11;14) and BCL2 overexpression, either as monotherapy or in combination with other anti-myeloma agents. In this review, we describe the molecular defects associated with the t(11;14), bring into question the standard cytogenetic risk of myeloma patients harboring t(11;14), summarize current efficacy and safety data of targeted venetoclax-based therapies, and discuss the future of individualized or precision medicine for this unique myeloma subgroup, which will guide optimal treatment.
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Affiliation(s)
- Michael D. Diamantidis
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, General Hospital of Larissa, Larissa, Greece
| | - Sofia Papadaki
- Division of Hematology, First Department of Internal Medicine, AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evdoxia Hatjiharissi
- Division of Hematology, First Department of Internal Medicine, AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
- *Correspondence: Evdoxia Hatjiharissi,
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6
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Dragoș ML, Ivanov IC, Mențel M, Văcărean-Trandafir IC, Sireteanu A, Titianu AA, Dăscălescu AS, Stache AB, Jitaru D, Gorgan DL. Prognostic Value of Association of Copy Number Alterations and Cell-Surface Expression Markers in Newly Diagnosed Multiple Myeloma Patients. Int J Mol Sci 2022; 23:ijms23147530. [PMID: 35886877 PMCID: PMC9318311 DOI: 10.3390/ijms23147530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Multiple myeloma results from the clonal proliferation of abnormal plasma cells (PCs) in the bone marrow (BM). In this study, the cell surface expression markers (CD) on atypical PCs (detected by multiparametric flow cytometry (MFC)) were correlated with copy number alterations (CNAs) in the genome (detected by multiplex ligation-dependent probe amplification (MLPA)) to assess their impact on prognosis in newly diagnosed MM patients. Statistically significant results were obtained when different stages of PC maturation (classified based on CD19 and CD81 expression) were associated with CD117 expression and identified CNAs. In the intermediately differentiated PC group (CD19(−) CD81(+)), patients who didn’t express CD117 had a lower median progression free survival (PFS) (p = 0.024). Moreover, within this group, patients with less than three adverse CNAs, which harbor CD117, had a better outcome with a PFS of more than 48 months compared with 19 months (p = 0.008). Considering all the results, our study suggested the need to integrate both the CD markers and copy number alterations to evaluate the prognosis of newly diagnosed multiple myeloma patients.
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Affiliation(s)
- Mihaiela L. Dragoș
- Biology Department, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, 700506 Iasi, Romania; (M.L.D.); (A.B.S.)
| | - Iuliu C. Ivanov
- Molecular Diagnosis Department, Regional Institute of Oncology, 700483 Iasi, Romania; (I.C.I.); (A.S.)
| | - Mihaela Mențel
- Center for Fundamental Research and Experimental Development in Translation Medicine—TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania; (M.M.); (I.C.V.-T.)
- Immunophenotyping Department, Regional Institute of Oncology, 700483 Iasi, Romania
| | - Irina C. Văcărean-Trandafir
- Center for Fundamental Research and Experimental Development in Translation Medicine—TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania; (M.M.); (I.C.V.-T.)
| | - Adriana Sireteanu
- Molecular Diagnosis Department, Regional Institute of Oncology, 700483 Iasi, Romania; (I.C.I.); (A.S.)
| | - Amalia A. Titianu
- Department of Hematology, Regional Institute of Oncology, 700483 Iasi, Romania; (A.A.T.); (A.S.D.)
- Department of Hematology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
| | - Angela S. Dăscălescu
- Department of Hematology, Regional Institute of Oncology, 700483 Iasi, Romania; (A.A.T.); (A.S.D.)
- Department of Hematology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
| | - Alexandru B. Stache
- Biology Department, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, 700506 Iasi, Romania; (M.L.D.); (A.B.S.)
- Molecular Diagnosis Department, Regional Institute of Oncology, 700483 Iasi, Romania; (I.C.I.); (A.S.)
| | - Daniela Jitaru
- Biology Department, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, 700506 Iasi, Romania; (M.L.D.); (A.B.S.)
- Correspondence: (D.J.); (D.L.G.); Tel.: +40-723-780-266 (D.J.); +40-0232-201-102 (ext. 1574) (D.L.G.)
| | - Dragoș L. Gorgan
- Biology Department, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, 700506 Iasi, Romania; (M.L.D.); (A.B.S.)
- Correspondence: (D.J.); (D.L.G.); Tel.: +40-723-780-266 (D.J.); +40-0232-201-102 (ext. 1574) (D.L.G.)
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7
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Sudha P, Ahsan A, Ashby C, Kausar T, Khera A, Kazeroun MH, Hsu CC, Wang L, Fitzsimons E, Salminen O, Blaney P, Czader M, Williams J, Abu Zaid MI, Ansari-Pour N, Yong KL, van Rhee F, Pierceall WE, Morgan GJ, Flynt E, Gooding S, Abonour R, Ramasamy K, Thakurta A, Walker BA. Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma. Clin Cancer Res 2022; 28:2854-2864. [PMID: 35522533 PMCID: PMC9250632 DOI: 10.1158/1078-0432.ccr-21-3695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/11/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE We designed a comprehensive multiple myeloma targeted sequencing panel to identify common genomic abnormalities in a single assay and validated it against known standards. EXPERIMENTAL DESIGN The panel comprised 228 genes/exons for mutations, 6 regions for translocations, and 56 regions for copy number abnormalities (CNA). Toward panel validation, targeted sequencing was conducted on 233 patient samples and further validated using clinical FISH (translocations), multiplex ligation probe analysis (MLPA; CNAs), whole-genome sequencing (WGS; CNAs, mutations, translocations), or droplet digital PCR (ddPCR) of known standards (mutations). RESULTS Canonical immunoglobulin heavy chain translocations were detected in 43.2% of patients by sequencing, and aligned with FISH except for 1 patient. CNAs determined by sequencing and MLPA for 22 regions were comparable in 103 samples and concordance between platforms was R2 = 0.969. Variant allele frequency (VAF) for 74 mutations were compared between sequencing and ddPCR with concordance of R2 = 0.9849. CONCLUSIONS In summary, we have developed a targeted sequencing panel that is as robust or superior to FISH and WGS. This molecular panel is cost-effective, comprehensive, clinically actionable, and can be routinely deployed to assist risk stratification at diagnosis or posttreatment to guide sequencing of therapies.
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Affiliation(s)
- Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Aarif Ahsan
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Cody Ashby
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Tasneem Kausar
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Akhil Khera
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad H. Kazeroun
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Chih-Chao Hsu
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Lin Wang
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | | | - Outi Salminen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Magdalena Czader
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Jonathan Williams
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad I. Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kwee L. Yong
- Cancer Institute, University College London, London, United Kingdom
| | - Frits van Rhee
- Myeloma Center, Winthrop P. Rockefeller Cancer institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Gareth J. Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Sarah Gooding
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Karthik Ramasamy
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Anjan Thakurta
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
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8
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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9
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Puła A, Robak P, Mikulski D, Robak T. The Significance of mRNA in the Biology of Multiple Myeloma and Its Clinical Implications. Int J Mol Sci 2021; 22:12070. [PMID: 34769503 PMCID: PMC8584466 DOI: 10.3390/ijms222112070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Multiple myeloma (MM) is a genetically complex disease that results from a multistep transformation of normal to malignant plasma cells in the bone marrow. However, the molecular mechanisms responsible for the initiation and heterogeneous evolution of MM remain largely unknown. A fundamental step needed to understand the oncogenesis of MM and its response to therapy is the identification of driver mutations. The introduction of gene expression profiling (GEP) in MM is an important step in elucidating the molecular heterogeneity of MM and its clinical relevance. Since some mutations in myeloma occur in non-coding regions, studies based on the analysis of mRNA provide more comprehensive information on the oncogenic pathways and mechanisms relevant to MM biology. In this review, we discuss the role of gene expression profiling in understanding the biology of multiple myeloma together with the clinical manifestation of the disease, as well as its impact on treatment decisions and future directions.
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Affiliation(s)
- Anna Puła
- Department of Hematology, Medical University of Lodz, 93-510 Lodz, Poland;
| | - Paweł Robak
- Department of Experimental Hematology, Medical University of Lodz, 93-510 Lodz, Poland;
| | - Damian Mikulski
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, 93-510 Lodz, Poland;
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10
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Goldman-Mazur S, Jurczyszyn A, Castillo JJ, Waszczuk-Gajda A, Grząśko N, Radocha J, Bittrich M, Kortüm KM, Gozzetti A, Usnarska-Zubkiewicz L, Valls JD, Jayabalan DS, Niesvizky R, Kelman J, Coriu D, Rosiñol L, Szukalski Ł, González-Calle V, Mateos MV, Jamroziak K, Hus I, Avivi I, Cohen Y, Mazur P, Suska A, Chappell A, Madduri D, Chhabra S, Kleman A, Hari P, Delforge M, Robak P, Gentile M, Kozłowska I, Goldberg SL, Czepiel J, Długosz-Danecka M, Silbermann R, Olszewski AJ, Barth P, Mikala G, Chim CS, Vesole DH. Different MAF translocations confer similar prognosis in newly diagnosed multiple myeloma patients. Leuk Lymphoma 2020; 61:1885-1893. [PMID: 32306794 DOI: 10.1080/10428194.2020.1749605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The MAF translocations, t(14;16) and t(14;20), are considered as adverse prognostic factors based on few studies with small sample sizes. We report on their prognostic impact in a large group of 254 patients - 223 (87.8%) with t(14;16) and 31 (12.2%) with t(14;20). There were no intergroup differences in survival estimates. Median progression-free survival was 16.6 months for t(14;16) and 24.9 months for t(14;20) (p = 0.28). Median overall survival (OS) was 54.0 months and 49.0 months, respectively (p = 0.62). Median OS in patients who underwent double autologous stem cell transplantation (ASCT) was 107.0 months versus 60.0 months in patients who received single ASCT (p < 0.001). ISS 3 was associated with shorter OS (HR = 1.89; 95% CI 1.24-3.19; p = 0.005) in Cox analysis. Our study suggests that t(14;20) should be considered as an adverse factor of equal prognostic implication to t(14;16).
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Affiliation(s)
- Sarah Goldman-Mazur
- Department of Hematology, Jagiellonian University Medical College, Cracow, Poland
| | - Artur Jurczyszyn
- Department of Hematology, Jagiellonian University Medical College, Cracow, Poland
| | - Jorge J Castillo
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Anna Waszczuk-Gajda
- Department of Hematology, Oncology and Internal Diseases, Warsaw Medical University, Warsaw, Poland
| | - Norbert Grząśko
- Department of Experimental Hematology, Medical University of Lublin, Lublin, Poland.,Department of Hematology, St. John's Cancer Center, Lublin, Poland
| | - Jakub Radocha
- 4th Department of Internal Medicine - Hematology, University Hospital, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Max Bittrich
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Klaus Martin Kortüm
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Alessandro Gozzetti
- Division of Hematology, Department of Medical Science, Surgery and Neuroscience, University of Siena, Siena, Italy
| | | | | | | | | | - Julia Kelman
- Weill Cornell Medical College, New York, NY, USA
| | - Daniel Coriu
- Department of Hematology, Fundeni Clinical Institute, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Laura Rosiñol
- Departments of Hematology, Amyloidosis and Myeloma Unit, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Łukasz Szukalski
- Department of Hematology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Veronica González-Calle
- Hospital Universitario de Salamanca/Instituto Biosanitario de Salamanca (IBSAL), Salamanca, Spain
| | - María-Victoria Mateos
- Hospital Universitario de Salamanca/Instituto Biosanitario de Salamanca (IBSAL), Salamanca, Spain
| | | | - Iwona Hus
- Department of Experimental Hematology, Medical University of Lublin, Lublin, Poland.,Department of Hematology, St. John's Cancer Center, Lublin, Poland.,Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Irit Avivi
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Cohen
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Piotr Mazur
- Institute of Cardiology, Jagiellonian University Medical College, Cracow, Poland
| | - Anna Suska
- Department of Hematology, Jagiellonian University Medical College, Cracow, Poland
| | - Aimee Chappell
- Department of Hematology/Oncology, Medstar Georgetown University Hospital, Washington, NW, USA
| | - Deepu Madduri
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY, USA
| | - Saurabh Chhabra
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ariel Kleman
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Parameswaran Hari
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Paweł Robak
- Department of Experimental Hematology, Medical University of Lodz, Lodz, Poland
| | | | | | - Stuart L Goldberg
- John Theurer Cancer Center, Hackensack UMC, Hackensack, NJ, USA.,Cota Inc, Boston, MA, USA
| | - Jacek Czepiel
- Department of Infectious and Tropical Diseases, Jagiellonian University Medical College, Cracow, Poland
| | | | - Rebecca Silbermann
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Adam J Olszewski
- Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Peter Barth
- Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Gabor Mikala
- Department of Hematology and Stem Cell Transplantation, South-Pest Central Hospital, National Institute of Hematology and Infectology, Budapest, Hungary
| | - Chor S Chim
- Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, Hong Kong
| | - David H Vesole
- John Theurer Cancer Center, Hackensack UMC, Hackensack, NJ, USA
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11
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Comprehensive detection of recurring genomic abnormalities: a targeted sequencing approach for multiple myeloma. Blood Cancer J 2019; 9:101. [PMID: 31827071 PMCID: PMC6906304 DOI: 10.1038/s41408-019-0264-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/31/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
Recent genomic research efforts in multiple myeloma have revealed clinically relevant molecular subgroups beyond conventional cytogenetic classifications. Implementing these advances in clinical trial design and in routine patient care requires a new generation of molecular diagnostic tools. Here, we present a custom capture next-generation sequencing (NGS) panel designed to identify rearrangements involving the IGH locus, arm level, and focal copy number aberrations, as well as frequently mutated genes in multiple myeloma in a single assay. We sequenced 154 patients with plasma cell disorders and performed a head-to-head comparison with the results from conventional clinical assays, i.e., fluorescent in situ hybridization (FISH) and single-nucleotide polymorphism (SNP) microarray. Our custom capture NGS panel had high sensitivity (>99%) and specificity (>99%) for detection of IGH translocations and relevant chromosomal gains and losses in multiple myeloma. In addition, the assay was able to capture novel genomic markers associated with poor outcome such as bi-allelic events involving TP53. In summary, we show that a multiple myeloma designed custom capture NGS panel can detect IGH translocations and CNAs with very high concordance in relation to FISH and SNP microarrays and importantly captures the most relevant and recurrent somatic mutations in multiple myeloma rendering this approach highly suitable for clinical application in the modern era.
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12
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Towards Molecular Profiling in Multiple Myeloma: A Literature Review and Early Indications of Its Efficacy for Informing Treatment Strategies. Int J Mol Sci 2018; 19:ijms19072087. [PMID: 30021955 PMCID: PMC6073692 DOI: 10.3390/ijms19072087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 12/26/2022] Open
Abstract
Multiple myeloma (MM), the second most common hematologic malignancy, is characterized by the clonal expansion of plasma cells. Despite dramatic improvements in patients′ survival over the past decade due to advances in therapy exploiting novel molecular targets (immunomodulatory drugs, proteasome inhibitors and monoclonal antibodies), the treatment of relapsed and refractory disease remains challenging. Recent studies confirmed complex, dynamic, and heterogeneous genomic alterations without unifying gene mutations in MM patients. In the current review, we survey recent therapeutic strategies, as well as molecular profiling data on MM, with emphasis on relapsed and refractory cases. A critical appraisal of novel findings and of their potential therapeutic implications will be discussed in detail, along with the author’s own experiences/views.
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13
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Saxe D, Seo EJ, Bergeron MB, Han JY. Recent advances in cytogenetic characterization of multiple myeloma. Int J Lab Hematol 2018; 41:5-14. [PMID: 29971938 DOI: 10.1111/ijlh.12882] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022]
Abstract
The detection of cytogenetic abnormalities in multiple myeloma (MM) has received more importance over last years for risk stratification and the new risk-adapted treatment strategies. Conventional G-banding analysis should be included in a routine procedure for the initial diagnostic workup for patients suspected of MM. However, the detection of chromosomal abnormalities in MM by conventional cytogenetics is limited owing to the low proliferative activity of malignant plasma cells as well as the low number of plasma cells in bone marrow specimens. Fluorescence in situ hybridization (FISH) or microarray-based technologies can overcome some of those drawbacks and detect specific target arrangements as well as chromosomal copy number changes. In this review, we will discuss different cytogenetic approaches and compare their strength and weakness to provide genetic information for risk stratification and prediction of outcome in MM patients.
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Affiliation(s)
- Debra Saxe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Eul-Ju Seo
- Department of Laboratory Medicine, College of Medicine and Asan Medical Center, University of Ulsan, Seoul, Korea
| | - Melanie Beaulieu Bergeron
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Jin-Yeong Han
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
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14
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Liu P, Jin Y, Sattar H, Liu H, Xie W, Zhou F. Natural killer cell immunotherapy against multiple myeloma: Progress and possibilities. J Leukoc Biol 2018; 103:821-828. [PMID: 29733502 DOI: 10.1002/jlb.2ru0517-176rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 01/06/2018] [Accepted: 01/07/2018] [Indexed: 12/29/2022] Open
Affiliation(s)
- Pan Liu
- Department of Hematology; Zhongnan Hospital; Wuhan University; Wuhan P.R. China
| | - Yanxia Jin
- Department of Hematology; Zhongnan Hospital; Wuhan University; Wuhan P.R. China
| | - Haseeb Sattar
- Department of Clinical Pharmacy; Wuhan Union Hospital; affiliated Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan P.R. China
| | - Hailing Liu
- Department of Clinical Hematology; Second Affiliated Hospital; Xi'an Jiao Tong University; Xi'an P.R. China
| | - Weiling Xie
- Department of Hematology; Zhongnan Hospital; Wuhan University; Wuhan P.R. China
| | - Fuling Zhou
- Department of Hematology; Zhongnan Hospital; Wuhan University; Wuhan P.R. China
- Hubei Key Laboratory of Tumor Biological Behavior; Wuhan P.R. China
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15
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Yang L, Wang YZ, Zhu HH, Chang Y, Li LD, Chen WM, Long LY, Zhang YH, Liu YR, Lu J, Qin YZ. PRAME Gene Copy Number Variation Is Related to Its Expression in Multiple Myeloma. DNA Cell Biol 2017; 36:1099-1107. [PMID: 28953414 DOI: 10.1089/dna.2017.3951] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multiple myeloma (MM) patients commonly present abnormal expression of cancer-testis antigens, which may serve as immunotherapeutic targets and prognostic factors. We previously reported that preferentially expressed antigen of melanoma (PRAME) overexpression in bone marrow mononuclear cells is related to progression in MM patients treated with non-bortezomib-containing regimens. The mechanism underlying variations in PRAME expression remains unknown. To investigate the impact of gene copy number variation (CNV) on PRAME expression, plasma cells were sorted from 50 newly diagnosed patients and 8 healthy volunteers to measure PRAME transcript levels and gene copy numbers by real-time quantitative polymerase chain reaction. A total of 14 (28.0%), 7 (14.0%), and 29 (58.0%) patients exhibited overexpression, expression within the normal range, and low expression, respectively. PRAME overexpression was significantly related to a lower 1-year progression-free survival rate compared with PRAME low expression (20.0% vs. 88.9%, p = 0.043). The mean PRAME gene copy number relative to albumin (ALB) in normal samples was ∼1.0, whereas 4.0%, 24.0%, 70.0%, and 2.0% of patients had PRAME gene relative copy numbers of approximately 0, 0.5, 1.0, and 2.0, respectively. Patients with PRAME gene deletion (relative copy number of 0 or 0.5) had significantly higher frequency of PRAME nonoverexpression and lambda light chain expression than those with no deletion (p = 0.011 and 0.003). Thus, PRAME gene CNV occurs in MM. Gene deletion may be one mechanism leading to PRAME nonoverexpression and related to immunoglobulin lambda light chain locus rearrangement. PRAME overexpression in plasma cells might be an adverse prognostic factor for progression in MM.
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Affiliation(s)
- Lu Yang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ya-Zhe Wang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Hong-Hu Zhu
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Yan Chang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ling-Di Li
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Wen-Min Chen
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ling-Yu Long
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Yan-Huan Zhang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Yan-Rong Liu
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Jin Lu
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
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