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Bong IPN, Esa E. Molecular genetic aberrations in the pathogenesis of multiple myeloma. ASIAN BIOMED 2023; 17:152-162. [PMID: 37860676 PMCID: PMC10584387 DOI: 10.2478/abm-2023-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Multiple myeloma (MM) is the second most common form of blood cancer characterized by clonal expansion of malignant plasma cells within the bone marrow. MM is a complex, progressive, and highly heterogeneous malignancy, which occurs via a multistep transformation process involving primary and secondary oncogenic events. Recent advances in molecular techniques have further expanded our understanding of the mutational landscape, clonal composition, and dynamic evolution patterns of MM. The first part of this review describes the key oncogenic events involved in the initiation and progression of MM, together with their prognostic impact. The latter part highlights the most prominent findings concerning genomic aberrations promoted by gene expression profiling (GEP) and next-generation sequencing (NGS) in MM. This review provides a concise understanding of the molecular pathogenesis of the MM genome and the importance of adopting emerging molecular technology in future clinical management of MM.
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Affiliation(s)
- Ivyna Pau Ni Bong
- Hematology Unit, Cancer Research Center, Institute for Medical Research, National Institute of Health, Ministry of Health, Malaysia
| | - Ezalia Esa
- Hematology Unit, Cancer Research Center, Institute for Medical Research, National Institute of Health, Ministry of Health, Malaysia
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2
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Saadoune C, Nouadi B, Hamdaoui H, Chegdani F, Bennis F. Multiple Myeloma: Bioinformatic Analysis for Identification of Key Genes and Pathways. Bioinform Biol Insights 2022; 16:11779322221115545. [PMID: 35958298 PMCID: PMC9358573 DOI: 10.1177/11779322221115545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/26/2022] [Indexed: 01/02/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy in which monoclonal plasma cells multiply in the bone marrow and monoclonal immunoglobulins are overproduced in older people. Several molecular and cytogenetic advances allow scientists to identify several genetic and chromosomal abnormalities that cause the disease. The comprehension of the pathophysiology of MM requires an understanding of the characteristics of malignant clones and the changes in the bone marrow microenvironment. This study aims to identify the central genes and to determine the key signaling pathways in MM by in silico approaches. A list of 114 differentially expressed genes (DEGs) is important in the prognosis of MM. The DEGs are collected from scientific publications and databases (https://www.ncbi.nlm.nih.gov/). These data are analyzed by Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) software (https://string-db.org/) through the construction of protein-protein interaction (PPI) networks and enrichment analysis of the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, by CytoHubba, AutoAnnotate, Bingo Apps plugins in Cytoscape software (https://cytoscape.org/) and by DAVID database (https://david.ncifcrf.gov/). The analysis of the results shows that there are 7 core genes, including TP53; MYC; CDND1; IL6; UBA52; EZH2, and MDM2. These top genes appear to play a role in the promotion and progression of MM. According to functional enrichment analysis, these genes are mainly involved in the following signaling pathways: Epstein-Barr virus infection, microRNA pathway, PI3K-Akt signaling pathway, and p53 signaling pathway. Several crucial genes, including TP53, MYC, CDND1, IL6, UBA52, EZH2, and MDM2, are significantly correlated with MM, which may exert their role in the onset and evolution of MM.
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Affiliation(s)
- Chaimaa Saadoune
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Badreddine Nouadi
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Hasna Hamdaoui
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco.,Laboratory of Medical Genetics, University Hospital Center Tangier-Tetouan-Al Hoceima, Tangier, Morocco
| | - Fatima Chegdani
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Faiza Bennis
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
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3
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CCND2 and CCND3 hijack immunoglobulin light-chain enhancers in cyclin D1 - mantle cell lymphoma. Blood 2018; 133:940-951. [PMID: 30538135 DOI: 10.1182/blood-2018-07-862151] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/01/2018] [Indexed: 12/15/2022] Open
Abstract
Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation resulting in overexpression of cyclin D1. However, a small subset of cyclin D1- MCL has been recognized, and approximately one-half of them harbor CCND2 translocations while the primary event in cyclin D1-/D2- MCL remains elusive. To identify other potential mechanisms driving MCL pathogenesis, we investigated 56 cyclin D1-/SOX11+ MCL by fluorescence in situ hybridization (FISH), whole-genome/exome sequencing, and gene-expression and copy-number arrays. FISH with break-apart probes identified CCND2 rearrangements in 39 cases (70%) but not CCND3 rearrangements. We analyzed 3 of these negative cases by whole-genome/exome sequencing and identified IGK (n = 2) and IGL (n = 1) enhancer hijackings near CCND3 that were associated with cyclin D3 overexpression. By specific FISH probes, including the IGK enhancer region, we detected 10 additional cryptic IGK juxtapositions to CCND3 (6 cases) and CCND2 (4 cases) in MCL that overexpressed, respectively, these cyclins. A minor subset of 4 cyclin D1- MCL cases lacked cyclin D rearrangements and showed upregulation of CCNE1 and CCNE2. These cases had blastoid morphology, high genomic complexity, and CDKN2A and RB1 deletions. Both genomic and gene-expression profiles of cyclin D1- MCL cases were indistinguishable from cyclin D1+ MCL. In conclusion, virtually all cyclin D1- MCLs carry CCND2/CCND3 rearrangements with immunoglobulin genes, including a novel IGK/L enhancer hijacking mechanism. A subset of cyclin D1-/D2-/D3- MCL with aggressive features has cyclin E dysregulation. Specific FISH probes may allow the molecular identification and diagnosis of cyclin D1- MCL.
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Sondka Z, Bamford S, Cole CG, Ward SA, Dunham I, Forbes SA. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat Rev Cancer 2018; 18:696-705. [PMID: 30293088 PMCID: PMC6450507 DOI: 10.1038/s41568-018-0060-1] [Citation(s) in RCA: 860] [Impact Index Per Article: 143.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Catalogue of Somatic Mutations in Cancer (COSMIC) Cancer Gene Census (CGC) is an expert-curated description of the genes driving human cancer that is used as a standard in cancer genetics across basic research, medical reporting and pharmaceutical development. After a major expansion and complete re-evaluation, the 2018 CGC describes in detail the effect of 719 cancer-driving genes. The recent expansion includes functional and mechanistic descriptions of how each gene contributes to disease generation in terms of the key cancer hallmarks and the impact of mutations on gene and protein function. These functional characteristics depict the extraordinary complexity of cancer biology and suggest multiple cancer-related functions for many genes, which are often highly tissue-dependent or tumour stage-dependent. The 2018 CGC encompasses a second tier, describing an expanding list of genes (currently 145) from more recent cancer studies that show supportive but less detailed indications of a role in cancer.
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Affiliation(s)
- Zbyslaw Sondka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sally Bamford
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Charlotte G Cole
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sari A Ward
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Simon A Forbes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Atrash S, Zhang Q, Papanikolaou X, Stein C, Abdallah AO, Barlogie B. Clinical Presentation and Gene Expression Profiling of Immunoglobulin M Multiple Myeloma Compared With Other Myeloma Subtypes and Waldenström Macroglobulinemia. J Glob Oncol 2018; 4:1-8. [PMID: 30241189 PMCID: PMC6180798 DOI: 10.1200/jgo.2016.008003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Multiple myeloma (MM) is a clonal bone marrow disease characterized by the neoplastic transformation of differentiated postgerminal B cells. It is a heterogeneous disease both at the genetic level and in terms of clinical outcome. Immunoglobulin M (IgM) MM is a rare subtype of myeloma. Similar to Waldenström macroglobulinemia (WM), patients with MM experience IgM monoclonal gammopathy; however, both diseases are distinct in terms of treatment and clinical behavior. MATERIALS AND METHODS To shed light on the presentation of IgM MM, its prognosis, and its gene expression profiling, we identified and characterized 21 patients with IgM MM from our database. RESULTS One of these patients presented with a rare IgM monoclonal gammopathy of undetermined significance that progressed to smoldering myeloma. The median survival of the 21 patients was 4.9 years, which was comparable to a matched group of patients with non-IgM MM with similar myeloma prognostic factors (age, gender, albumin, creatinine, anemia, lactate dehydrogenase, β2-microglobulin, cytogenetics abnormalities), but much less than the median survival reported for patients with WM (9 years). We identified a cluster of genes that differ in their expression profile between MM and WM and found that the patients with IgM MM displayed a gene expression profile most similar to patients with non-IgM MM, confirming that IgM MM is a subtype of MM that should be differentiated from WM. CONCLUSION Because the prognosis of IgM MM and WM differ significantly, an accurate diagnosis is essential. Our gene expression model can assist with the differential diagnosis in controversial cases.
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Affiliation(s)
- Shebli Atrash
- Shebli Atrash, Qing Zhang, Xenofon Papanikolaou, Caleb Stein, Al-Ola Abdallah, and Bart Barlogie, University of Arkansas for Medical Sciences, Little Rock, Arkansas; and Qing Zhang, Levine Cancer Institute, Charlotte, NC
| | - Qing Zhang
- Shebli Atrash, Qing Zhang, Xenofon Papanikolaou, Caleb Stein, Al-Ola Abdallah, and Bart Barlogie, University of Arkansas for Medical Sciences, Little Rock, Arkansas; and Qing Zhang, Levine Cancer Institute, Charlotte, NC
| | - Xenofon Papanikolaou
- Shebli Atrash, Qing Zhang, Xenofon Papanikolaou, Caleb Stein, Al-Ola Abdallah, and Bart Barlogie, University of Arkansas for Medical Sciences, Little Rock, Arkansas; and Qing Zhang, Levine Cancer Institute, Charlotte, NC
| | - Caleb Stein
- Shebli Atrash, Qing Zhang, Xenofon Papanikolaou, Caleb Stein, Al-Ola Abdallah, and Bart Barlogie, University of Arkansas for Medical Sciences, Little Rock, Arkansas; and Qing Zhang, Levine Cancer Institute, Charlotte, NC
| | - Al-Ola Abdallah
- Shebli Atrash, Qing Zhang, Xenofon Papanikolaou, Caleb Stein, Al-Ola Abdallah, and Bart Barlogie, University of Arkansas for Medical Sciences, Little Rock, Arkansas; and Qing Zhang, Levine Cancer Institute, Charlotte, NC
| | - Bart Barlogie
- Shebli Atrash, Qing Zhang, Xenofon Papanikolaou, Caleb Stein, Al-Ola Abdallah, and Bart Barlogie, University of Arkansas for Medical Sciences, Little Rock, Arkansas; and Qing Zhang, Levine Cancer Institute, Charlotte, NC
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Abstract
The application of fluorescence in situ hybridization (FISH) technology in diagnosis and molecular classification of cancer-risk has become an essential tool in the proceeding of personalized therapy. In multiple myeloma, the precise FISH detection of numerical and structural genetic aberrations can be carried out on metaphase chromosome spreads, interphase nuclei, and formalin fixed paraffin-embedded (FFPE) tissues. To dissect highly complex cancer genomes, a broad variety of novel DNA probes, which outpace supplies from commercial resources on the market, are also crucial to the advanced translational researches. Here, we provide the protocols for the creation of custom-made DNA probes and for conducting hybridizations on various targeting cells and tissues.
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Expressed fusion gene landscape and its impact in multiple myeloma. Nat Commun 2017; 8:1893. [PMID: 29196615 PMCID: PMC5711960 DOI: 10.1038/s41467-017-00638-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 07/17/2017] [Indexed: 02/07/2023] Open
Abstract
Multiple myeloma is a plasma cell malignancy characterized by recurrent IgH translocations and well described genomic heterogeneity. Although transcriptome profiles in multiple myeloma has been described, landscape of expressed fusion genes and their clinical impact remains unknown. To provide a comprehensive and detailed fusion gene cartography and suggest new mechanisms of tumorigenesis in multiple myeloma, we performed RNA sequencing in a cohort of 255 newly diagnosed and homogeneously treated multiple myeloma patients with long follow-up. Here, we report that patients have on average 5.5 expressed fusion genes. Kappa and lambda light chains and IgH genes are main partners in a third of all fusion genes. We also identify recurrent fusion genes that significantly impact both progression-free and overall survival and may act as drivers of the disease. Lastly, we find a correlation between the number of fusions, the age of patients and the clinical outcome, strongly suggesting that genomic instability drives prognosis of the disease. Multiple myeloma is a malignancy of plasma cells in the blood. Here, the authors establish the landscape of fusion genes within this disease, identifying novel recurrent fusion genes that impact survival and may drive disease progression.
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Vangsted AJ, Helm-Petersen S, Cowland JB, Jensen PB, Gimsing P, Barlogie B, Knudsen S. Drug response prediction in high-risk multiple myeloma. Gene 2017; 644:80-86. [PMID: 29122646 DOI: 10.1016/j.gene.2017.10.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/30/2017] [Accepted: 10/25/2017] [Indexed: 01/05/2023]
Abstract
A Drug Response Prediction (DRP) score was developed based on gene expression profiling (GEP) from cell lines and tumor samples. Twenty percent of high-risk patients by GEP70 treated in Total Therapy 2 and 3A have a progression-free survival (PFS) of more than 10years. We used available GEP data from high-risk patients by GEP70 at diagnosis from Total Therapy 2 and 3A to predict the response by the DRP score of drugs used in the treatment of myeloma patients. The DRP score stratified patients further. High-risk myeloma with a predicted sensitivity to melphalan by the DRP score had a prolonged PFS, HR=2.4 (1.2-4.9, P=0.014) and those with predicted sensitivity to bortezomib had a HR 5.7 (1.2-27, P=0.027). In case of predicted sensitivity to bortezomib, a better response to treatment was found (P=0.022). This method may provide us with a tool for identifying candidates for effective personalized medicine and spare potential non-responders from suffering toxicity.
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Affiliation(s)
- A J Vangsted
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
| | - S Helm-Petersen
- Granulocyte Research Laboratory, Copenhagen University Hospital, Copenhagen, Denmark
| | - J B Cowland
- Granulocyte Research Laboratory, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - P B Jensen
- Medical Prognosis Institute, Hørsholm, Hematology-Oncology, Denmark
| | - P Gimsing
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - S Knudsen
- Medical Prognosis Institute, Hørsholm, Hematology-Oncology, Denmark
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9
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Innao V, Allegra A, Russo S, Gerace D, Vaddinelli D, Alonci A, Allegra AG, Musolino C. Standardisation of minimal residual disease in multiple myeloma. Eur J Cancer Care (Engl) 2017; 26. [PMID: 28671297 DOI: 10.1111/ecc.12732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2017] [Indexed: 12/16/2022]
Abstract
The assessment of the effectiveness of chemotherapy in oncology cannot disregard the concept of minimal residual disease (MRD). In fact, the efforts of numerous scientific groups all over the world are currently focusing on this issue, with the sole purpose of defining sensitive, effective assessment criteria that are, above all, able to give acceptable, easily repeatable results worldwide. Regarding this issue, especially with the advent of new drugs, multiple myeloma is one of the haematologic malignancies for which a consensus has not yet been reached. In this review, we analyse various techniques that have been used to improve the sensitivity of response, aimed at reducing the cut-off values previously allowed, as well as serological values like serum-free light chain, or immunophenotypic tools on bone marrow or peripheral blood, like multi-parameter flow cytometry, or molecular ones such as allele-specific oligonucleotide (ASO)-qPCR and next-generation/high-throughput sequencing technologies (NGS). Moreover, our discussion makes a brief reference to promising techniques, such as mass spectrometry for identifying Ig light chain (LC) in peripheral blood, and the assessment of gene expression profile not only in defining prognostic risk at the diagnosis but also as a tool for evaluation of response.
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Affiliation(s)
- V Innao
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
| | - A Allegra
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
| | - S Russo
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
| | - D Gerace
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
| | - D Vaddinelli
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
| | - A Alonci
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
| | - A G Allegra
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
| | - C Musolino
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età Evolutiva, Policlinico G Martino, University of Messina, Messina, Italy
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Cheng X, Hao Y, Shu W, Zhao M, Zhao C, Wu Y, Peng X, Yao P, Xiao D, Qing G, Pan Z, Yin L, Hu D, Du HN. Cell cycle-dependent degradation of the methyltransferase SETD3 attenuates cell proliferation and liver tumorigenesis. J Biol Chem 2017; 292:9022-9033. [PMID: 28442573 DOI: 10.1074/jbc.m117.778001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/23/2017] [Indexed: 01/22/2023] Open
Abstract
Histone modifications, including lysine methylation, are epigenetic marks that influence many biological pathways. Accordingly, many methyltransferases have critical roles in various biological processes, and their dysregulation is often associated with cancer. However, the biological functions and regulation of many methyltransferases are unclear. Here, we report that a human homolog of the methyltransferase SET (SU(var), enhancer of zeste, and trithorax) domain containing 3 (SETD3) is cell cycle-regulated; SETD3 protein levels peaked in S phase and were lowest in M phase. We found that the β-isoform of the tumor suppressor F-box and WD repeat domain containing 7 (FBXW7β) specifically mediates SETD3 degradation. Aligning the SETD3 sequence with those of well known FBXW7 substrates, we identified six potential non-canonical Cdc4 phosphodegrons (CPDs), and one of them, CPD1, is primarily phosphorylated by the kinase glycogen synthase kinase 3 (GSK3β), which is required for FBXW7β-mediated recognition and degradation. Moreover, depletion or inhibition of GSK3β or FBXW7β resulted in elevated SETD3 levels. Mutations of the phosphorylated residues in CPD1 of SETD3 abolished the interaction between FBXW7β and SETD3 and prevented SETD3 degradation. Our data further indicated that SETD3 levels positively correlated with cell proliferation of liver cancer cells and liver tumorigenesis in a xenograft mouse model, and that overexpression of FBXW7β counteracts the SETD3's tumorigenic role. We also show that SETD3 levels correlate with cancer malignancy, indicated by SETD3 levels that the 54 liver tumors are 2-fold higher than those in the relevant adjacent tissues. Collectively, these data elucidated that a GSK3β-FBXW7β-dependent mechanism controls SETD3 protein levels during the cell cycle and attenuates its oncogenic role in liver tumorigenesis.
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Affiliation(s)
- Xiaoqing Cheng
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072
| | - Yuan Hao
- the Department of General Surgery, Xinhua Hospital affiliated with Shanghai Jiaotong University School of Medicine, Shanghai 200092,
| | - Wenjie Shu
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072
| | - Mengjie Zhao
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072
| | - Chen Zhao
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072
| | - Yuan Wu
- the Department of Radiotherapy, Hubei Cancer Hospital, Wuhan 430079
| | - Xiaodan Peng
- the Department of Oncology, Shenzhen Hospital of Peking University, Shenzhen 518083
| | - Pinfang Yao
- the Department of Radiotherapy, Hubei Cancer Hospital, Wuhan 430079
| | - Daibiao Xiao
- the Medical Research Institute, Wuhan University, Wuhan 430071, and
| | - Guoliang Qing
- the Medical Research Institute, Wuhan University, Wuhan 430071, and
| | - Zhengying Pan
- the Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Lei Yin
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072
| | - Desheng Hu
- the Department of Radiotherapy, Hubei Cancer Hospital, Wuhan 430079,
| | - Hai-Ning Du
- From the Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072,
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Jiménez C, Jara-Acevedo M, Corchete LA, Castillo D, Ordóñez GR, Sarasquete ME, Puig N, Martínez-López J, Prieto-Conde MI, García-Álvarez M, Chillón MC, Balanzategui A, Alcoceba M, Oriol A, Rosiñol L, Palomera L, Teruel AI, Lahuerta JJ, Bladé J, Mateos MV, Orfão A, San Miguel JF, González M, Gutiérrez NC, García-Sanz R. A Next-Generation Sequencing Strategy for Evaluating the Most Common Genetic Abnormalities in Multiple Myeloma. J Mol Diagn 2016; 19:99-106. [PMID: 27863261 DOI: 10.1016/j.jmoldx.2016.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/04/2016] [Accepted: 08/12/2016] [Indexed: 12/16/2022] Open
Abstract
Identification and characterization of genetic alterations are essential for diagnosis of multiple myeloma and may guide therapeutic decisions. Currently, genomic analysis of myeloma to cover the diverse range of alterations with prognostic impact requires fluorescence in situ hybridization (FISH), single nucleotide polymorphism arrays, and sequencing techniques, which are costly and labor intensive and require large numbers of plasma cells. To overcome these limitations, we designed a targeted-capture next-generation sequencing approach for one-step identification of IGH translocations, V(D)J clonal rearrangements, the IgH isotype, and somatic mutations to rapidly identify risk groups and specific targetable molecular lesions. Forty-eight newly diagnosed myeloma patients were tested with the panel, which included IGH and six genes that are recurrently mutated in myeloma: NRAS, KRAS, HRAS, TP53, MYC, and BRAF. We identified 14 of 17 IGH translocations previously detected by FISH and three confirmed translocations not detected by FISH, with the additional advantage of breakpoint identification, which can be used as a target for evaluating minimal residual disease. IgH subclass and V(D)J rearrangements were identified in 77% and 65% of patients, respectively. Mutation analysis revealed the presence of missense protein-coding alterations in at least one of the evaluating genes in 16 of 48 patients (33%). This method may represent a time- and cost-effective diagnostic method for the molecular characterization of multiple myeloma.
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Affiliation(s)
- Cristina Jiménez
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - María Jara-Acevedo
- DNA Sequencing Service, University of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Luis A Corchete
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | | | | | - María E Sarasquete
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Noemí Puig
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Joaquín Martínez-López
- Hematology Department, 12 de Octubre Hospital, Unit of Cancer Research Innovation Spain (CRIS), Spanish National Cancer Research Center (CNIO), University of Madrid, Madrid, Spain
| | - María I Prieto-Conde
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - María García-Álvarez
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - María C Chillón
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Ana Balanzategui
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Miguel Alcoceba
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Albert Oriol
- Catalan Institute of Oncology, Josep Carreras Institute, Germans Trias i Pujol Hospital, Barcelona, Spain
| | - Laura Rosiñol
- Research Biomedical Institute August Pi i Sunyer, Clinical Hospital of Barcelona, Barcelona, Spain
| | | | | | - Juan J Lahuerta
- Hematology Department, 12 de Octubre Hospital, Unit of Cancer Research Innovation Spain (CRIS), Spanish National Cancer Research Center (CNIO), University of Madrid, Madrid, Spain
| | - Joan Bladé
- Research Biomedical Institute August Pi i Sunyer, Clinical Hospital of Barcelona, Barcelona, Spain
| | - María V Mateos
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Alberto Orfão
- DNA Sequencing Service, University of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Jesús F San Miguel
- Center for Applied Medical Research, University of Navarra Hospital, Institute of Health Research of Navarra (IDISNA), Pamplona, Spain
| | - Marcos González
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain.
| | - Norma C Gutiérrez
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), Salamanca, Spain
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Hyperhaploidy is a novel high-risk cytogenetic subgroup in multiple myeloma. Leukemia 2016; 31:637-644. [PMID: 27694925 DOI: 10.1038/leu.2016.253] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 07/20/2016] [Accepted: 08/19/2016] [Indexed: 12/13/2022]
Abstract
Hyperhaploid clones (24-34 chromosomes) were identified in 33 patients with multiple myeloma (MM), demonstrating a novel numerical cytogenetic subgroup. Strikingly, all hyperhaploid karyotypes were found to harbor monosomy 17p, the single most important risk stratification lesion in MM. A catastrophic loss of nearly a haploid set of chromosomes results in disomies of chromosomes 3, 5, 7, 9, 11, 15, 18, 19 and 21, the same basic set of odd-numbered chromosomes found in trisomy in hyperdiploid myeloma. All other autosomes are found in monosomy, resulting in additional clinically relevant monosomies of 1p, 6q, 13q and 16q. Hypotriploid subclones (58-68 chromosomes) were also identified in 11 of the 33 patients and represent a duplication of the hyperhaploid clone. Analysis of clones utilizing interphase fluorescence in situ hybridization (iFISH), metaphase FISH and spectral karyotyping identified either monosomy 17 or del17p in all patients. Amplification of 1q21 was identified in eight patients, demonstrating an additional high-risk marker. Importantly, our findings indicate that current iFISH strategies may be uninformative or ambiguous in the detection of these clones, suggesting this patient subgroup maybe underreported. Overall survival for patients with hyperhaploid clones was poor, with a 5-year survival rate of 23.1%. These findings identify a distinct numerical subgroup with cytogenetically defined high-risk disease.
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Coccaro N, Tota G, Anelli L, Zagaria A, Casieri P, Cellamare A, Minervini CF, Minervini A, Cumbo C, Impera L, Brunetti C, Orsini P, Parciante E, Mestice A, Specchia G, Albano F. MYEOV gene overexpression in primary plasma cell leukemia with t(11;14)(q13;q32). Oncol Lett 2016; 12:1460-1464. [PMID: 27446453 DOI: 10.3892/ol.2016.4759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/26/2016] [Indexed: 12/25/2022] Open
Abstract
Primary plasma cell leukemia (pPCL) is an uncommon form of plasma cell dyscrasia, and the most aggressive of the human monoclonal gammopathies. The t(11;14)(q13;q32) rearrangement is the most common alteration in pPCL, promoting cyclin D1 (CCND1) gene overexpression caused by its juxtaposition with the immunoglobulin heavy locus chromosome region. The myeloma overexpressed (MYEOV) gene maps very close to the CCND1 gene on chromosome 11, but its overexpression is rarely observed in multiple myeloma. The present study describes a case of pPCL with t(11;14) characterized by a breakpoint on der(11), unlike the one usually observed. Droplet digital polymerase chain reaction analysis revealed overexpression of CCND1 and MYEOV. To the best of our knowledge, MYEOV gene overexpression has never been previously described in pPCL.
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Affiliation(s)
- Nicoletta Coccaro
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Paola Casieri
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Angelo Cellamare
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | | | - Angela Minervini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Cosimo Cumbo
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Claudia Brunetti
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Paola Orsini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Anna Mestice
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, I-70124 Bari, Italy
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Xu H, Fei D, Zong S, Fan Z. MicroRNA-154 inhibits growth and invasion of breast cancer cells through targeting E2F5. Am J Transl Res 2016; 8:2620-2630. [PMID: 27398145 PMCID: PMC4931156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
Accumulating evidence suggested that microRNA-154 (miR-154) might play important roles in the development of various cancer types. However, the role of miR-154 in breast cancer progression remains largely unknown. Here, miR-154 expression level was measured via quantitative real-time RT-PCR (qRT-PCR) in 36 pairs of human breast cancer tissues and adjacent normal breast tissues and in a panel of human breast cancer cell lines. Cell proliferation, cycle, migration, and invasion were assessed by CCK8 assay, flow cytometer assay, wound healing assay and transwell invasion assay, respectively. Luciferase reporter assay and Western blot was used to verify E2F transcription factor 5 protein (E2F5) as a novel target gene of miR-154. Our results showed that miR-154 was frequently downregulated in breast cancer tissues and cell lines. Overexpression of miR-154 in MCF-7 cells significantly inhibited cell proliferation, migration, and invasion, and increased cell arrest at G0/G1 stage in vitro. E2F5 was identified as a target of miR-154, and its expression was inversely correlated with miR-154 expression in clinical breast cancer tissues. In addition, downregulation of E2F5 in MCF7 cells had similar effect on cell proliferation, cycle, migration and invasion by miR-154 induced. These findings indicate that miR-154 acts as a tumor suppressor by targeting E2F5, suggesting miR-154 as a potential therapeutic target for the treatment of breast cancer.
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Affiliation(s)
- Hui Xu
- Department of Breast Surgery, The First Hospital of Jilin UniversityChangchun 130021, China
| | - Dan Fei
- Department of Ultrasonographic, China-Japan Union Hospital of Jilin UniversityChangchun 130033, China
| | - Shan Zong
- Department of Breast Surgery, The First Hospital of Jilin UniversityChangchun 130021, China
| | - Zhimin Fan
- Department of Breast Surgery, The First Hospital of Jilin UniversityChangchun 130021, China
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Common genetic variants in 11q13.3 and 9q22.33 are associated with molecular subgroups of multiple myeloma. Leukemia 2015; 29:2418-21. [PMID: 26308770 DOI: 10.1038/leu.2015.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Tian E, Børset M, Sawyer JR, Brede G, Våtsveen TK, Hov H, Waage A, Barlogie B, Shaughnessy JD, Epstein J, Sundan A. Allelic mutations in noncoding genomic sequences construct novel transcription factor binding sites that promote gene overexpression. Genes Chromosomes Cancer 2015. [PMID: 26220195 DOI: 10.1002/gcc.22280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The growth and survival factor hepatocyte growth factor (HGF) is expressed at high levels in multiple myeloma (MM) cells. We report here that elevated HGF transcription in MM was traced to DNA mutations in the promoter alleles of HGF. Sequence analysis revealed a previously undiscovered single-nucleotide polymorphism (SNP) and crucial single-nucleotide variants (SNVs) in the promoters of myeloma cells that produce large amounts of HGF. The allele-specific mutations functionally reassembled wild-type sequences into the motifs that affiliate with endogenous transcription factors NFKB (nuclear factor kappa-B), MZF1 (myeloid zinc finger 1), and NRF-2 (nuclear factor erythroid 2-related factor 2). In vitro, a mutant allele that gained novel NFKB-binding sites directly responded to transcriptional signaling induced by tumor necrosis factor alpha (TNFα) to promote high levels of luciferase reporter. Given the recent discovery by genome-wide sequencing (GWS) of numerous non-coding mutations in myeloma genomes, our data provide evidence that heterogeneous SNVs in the gene regulatory regions may frequently transform wild-type alleles into novel transcription factor binding properties to aberrantly interact with dysregulated transcriptional signals in MM and other cancer cells.
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Affiliation(s)
- Erming Tian
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Magne Børset
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Immunology and Transfusion Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Jeffrey R Sawyer
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Gaute Brede
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thea K Våtsveen
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Håkon Hov
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bart Barlogie
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | | | - Joshua Epstein
- The Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Anders Sundan
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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