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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [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] [Received: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Sánchez-Marín D, Silva-Cázares MB, Porras-Reyes FI, García-Román R, Campos-Parra AD. Breaking paradigms: Long non-coding RNAs forming gene fusions with potential implications in cancer. Genes Dis 2024; 11:101136. [PMID: 38292185 PMCID: PMC10825296 DOI: 10.1016/j.gendis.2023.101136] [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] [Received: 03/28/2023] [Revised: 08/16/2023] [Accepted: 09/10/2023] [Indexed: 02/01/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides with dynamic regulatory functions. They interact with a wide range of molecules such as DNA, RNA, and proteins to modulate diverse cellular functions through several mechanisms and, if deregulated, they can lead to cancer development and progression. Recently, it has been described that lncRNAs are susceptible to form gene fusions with mRNAs or other lncRNAs, breaking the paradigm of gene fusions consisting mainly of protein-coding genes. However, their biological significance in the tumor phenotype is still uncertain. Therefore, their recent identification opens a new line of research to study their biological role in tumorigenesis, and their potential as biomarkers with clinical relevance or as therapeutic targets. The present study aimed to review the lncRNA fusions identified so far and to know which of them have been associated with a potential function. We address the current challenges to deepen their study as well as the reasons why they represent a future therapeutic window in cancer.
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Affiliation(s)
- David Sánchez-Marín
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04360, México
| | - Macrina Beatriz Silva-Cázares
- Unidad Académica Multidisciplinaria Región Altiplano, Universidad Autónoma de San Luis Potosí (UASLP), Carretera a Cedral Km 5+600, Ejido San José de la Trojes, Matehuala, San Luis Potosí, C.P. 78760, México
| | - Fany Iris Porras-Reyes
- Servicio de Anatomía Patológica, Instituto Nacional de Cancerología (INCan), Niño Jesús, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Rebeca García-Román
- Instituto de Salud Pública, Universidad Veracruzana (UV), Av. Dr Luis, Dr. Castelazo Ayala s/n, Col. Industrial Ánimas, Xalapa, Veracruz, C.P. 91190, México
| | - Alma D. Campos-Parra
- Instituto de Salud Pública, Universidad Veracruzana (UV), Av. Dr Luis, Dr. Castelazo Ayala s/n, Col. Industrial Ánimas, Xalapa, Veracruz, C.P. 91190, México
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Koduru P, Chen W, Fuda F, Kaur G, Awan F, John S, Garcia R, Gagan J. RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241230262. [PMID: 38371338 PMCID: PMC10874141 DOI: 10.1177/2632010x241230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
Background Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.
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Affiliation(s)
- Prasad Koduru
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weina Chen
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Franklin Fuda
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gurbakhash Kaur
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Farrukh Awan
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel John
- Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rolando Garcia
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey Gagan
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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Ismail NH, Mussa A, Al-Khreisat MJ, Mohamed Yusoff S, Husin A, Al-Jamal HAN, Johan MF, Islam MA. Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma. Noncoding RNA 2023; 9:68. [PMID: 37987364 PMCID: PMC10660696 DOI: 10.3390/ncrna9060068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
The dysregulation of non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), leads to the development and advancement of multiple myeloma (MM). miRNAs, in particular, are paramount in post-transcriptional gene regulation, promoting mRNA degradation and translational inhibition. As a result, miRNAs can serve as oncogenes or tumor suppressors depending on the target genes. In MM, miRNA disruption could result in abnormal gene expression responsible for cell growth, apoptosis, and other biological processes pertinent to cancer development. The dysregulated miRNAs inhibit the activity of tumor suppressor genes, contributing to disease progression. Nonetheless, several miRNAs are downregulated in MM and have been identified as gene regulators implicated in extracellular matrix remodeling and cell adhesion. miRNA depletion potentially facilitates the tumor advancement and resistance of therapeutic drugs. Additionally, lncRNAs are key regulators of numerous cellular processes, such as gene expression, chromatin remodeling, protein trafficking, and recently linked MM development. The lncRNAs are uniquely expressed and influence gene expression that supports MM growth, in addition to facilitating cellular proliferation and viability via multiple molecular pathways. miRNA and lncRNA alterations potentially result in anomalous gene expression and interfere with the regular functioning of MM. Thus, this review aims to highlight the dysregulation of these ncRNAs, which engender novel therapeutic modalities for the treatment of MM.
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Affiliation(s)
- Nor Hayati Ismail
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ali Mussa
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, Omdurman 11111, Sudan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Shafini Mohamed Yusoff
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Azlan Husin
- Department of Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Hamid Ali Nagi Al-Jamal
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin (UniSZA), Kuala Nerus 21300, Terengganu, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Md Asiful Islam
- WHO Collaborating Centre for Global Women’s Health, Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Liu W, Zuo B, Liu W, Huo Y, Zhang N, Yang M. Long non-coding RNAs in non-small cell lung cancer: implications for preventing therapeutic resistance. Biochim Biophys Acta Rev Cancer 2023; 1878:188982. [PMID: 37734560 DOI: 10.1016/j.bbcan.2023.188982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
Lung cancer has the highest mortality and morbidity rates among all cancers worldwide. Despite many complex treatment options, including radiotherapy, chemotherapy, targeted drugs, immunotherapy, and combinations of these treatments, efficacy is low in cases of resistance to therapy, metastasis, and advanced disease, contributing to low overall survival. There is a pressing need for the discovery of novel biomarkers and therapeutic targets for the early diagnosis of lung cancer and to determine the efficacy and outcomes of drug treatments. There is now substantial evidence for the diagnostic and prognostic value of long noncoding RNAs (lncRNAs). This review briefly discusses recent findings on the roles and mechanisms of action of lncRNAs in the responses to therapy in non-small cell lung cancer.
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Affiliation(s)
- Wenjuan Liu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China
| | - Bingli Zuo
- Human Resources Department, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China
| | - Wenting Liu
- Department of Neurology, Weifang People's Hospital, Weifang, Shandong Province 261041, China
| | - Yanfei Huo
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province 211166, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province 211166, China.
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Severgnini M, D’Angiò M, Bungaro S, Cazzaniga G, Cifola I, Fazio G. Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia. Cancers (Basel) 2022; 14:cancers14143523. [PMID: 35884588 PMCID: PMC9315513 DOI: 10.3390/cancers14143523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Acute lymphoblastic leukemia (ALL) is the most frequent childhood cancer. In recent years, broad application of NGS technologies enabled the discovery of novel genomically defined ALL. In this study, as a proof-of-principle, we applied RNA-seq technology to comprehensively profile the transcriptional landscape of a collection of 10 childhood BCP-ALL cases, and performed a deep bioinformatics analysis including several publicly available datasets, in order to characterize their full spectrum of transcriptional events. The paired-end RNA sequencing of our BCP-ALL pediatric cohort revealed a total of 9001 raw fusion events, which, after filtering, resulted in 245 candidate fusions. Overall, 235 out of 245 events were intra-chromosomal fusions, among which 229 involved two contiguous or overlapping genes, also known as conjoined genes (CGs). Among them, we identified a subset of 14 CGs (6.1%) exclusively expressed in leukemic cases but neither in solid cancers nor in normal samples. These events could be suggestive of a novel mechanism of transcriptional regulation in childhood leukemia and may represent novel potential leukemia-specific biomarkers. Abstract Acute lymphoblastic leukemia (ALL) is the most frequent childhood cancer. For the last three decades, conventional cytogenetic and molecular approaches allowed the identification of genetic abnormalities having prognostic and therapeutic relevance. Although the current cure rate in pediatric B cell acute leukemia is approximately 90%, it remains one of the leading causes of mortality in childhood. Furthermore, in the contemporary protocols, chemotherapy intensity was raised to the maximal levels of tolerability, and further improvements in the outcome will depend on the characterization and reclassification of the disease, as well as on the development of new targeted drugs. The recent technological advances in genome-wide profiling techniques have allowed the exploration of the molecular heterogeneity of this disease, even though some potentially interesting biomarkers such as conjoined genes have not been deeply investigated yet. In the present study, we performed the transcriptome sequencing (RNA-seq) of 10 pediatric B cell precursor (BCP)-ALL cases with different risk (four standard- and six high-risk patients) enrolled in the Italian AIEOP-BFM ALL2000 protocol, in order to characterize the full spectrum of transcriptional events and to identify novel potential genetic mechanisms sustaining their different early response to therapy. Total RNA was extracted from primary leukemic blasts and RNA-seq was performed by Illumina technology. Bioinformatics analysis focused on fusion transcripts, originated from either inter- or intra-chromosomal structural rearrangements. Starting from a raw list of 9001 candidate events, by employing a custom-made bioinformatics pipeline, we obtained a short list of 245 candidate fusions. Among them, 10 events were compatible with chromosomal translocations. Strikingly, 235/245 events were intra-chromosomal fusions, 229 of which involved two contiguous or overlapping genes, resulting in the so-called conjoined genes (CGs). To explore the specificity of these events in leukemia, we performed an extensive bioinformatics meta-analysis and evaluated the presence of the fusions identified in our 10 BCP-ALL cohort in several other publicly available RNA-seq datasets, including leukemic, solid tumor and normal sample collections. Overall, 14/229 (6.1%) CGs were found to be exclusively expressed in leukemic cases, suggesting an association between CGs and leukemia. Moreover, CGs were found to be common events both in standard- and high-risk BCP-ALL patients and it might be suggestive of a novel potential transcriptional regulation mechanism active in leukemic cells.
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Affiliation(s)
- Marco Severgnini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 20054 Milano, Italy; (M.S.); (I.C.)
| | - Mariella D’Angiò
- School of Medicine and Surgery, Università degli Studi di Milano Bicocca, 20126 Milano, Italy;
- Tettamanti Research Center, University of Milan Bicocca, 20900 Monza, Italy;
| | - Silvia Bungaro
- Ospedale San Gerardo, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), 20900 Monza, Italy;
| | - Giovanni Cazzaniga
- School of Medicine and Surgery, Università degli Studi di Milano Bicocca, 20126 Milano, Italy;
- Tettamanti Research Center, University of Milan Bicocca, 20900 Monza, Italy;
- Correspondence: ; Tel.: +39-039-233-3661
| | - Ingrid Cifola
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 20054 Milano, Italy; (M.S.); (I.C.)
| | - Grazia Fazio
- Tettamanti Research Center, University of Milan Bicocca, 20900 Monza, Italy;
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Wu F, Zhu Y, Zhou C, Gui W, Li H, Lin X. Regulation mechanism and pathogenic role of lncRNA plasmacytoma variant translocation 1 (PVT1) in human diseases. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Karami Fath M, Karimfar N, Fazlollahpour Naghibi A, Shafa S, Ghasemi Shiran M, Ataei M, Dehghanzadeh H, Nabi Afjadi M, Ghadiri T, Payandeh Z, Tarhriz V. Revisiting characteristics of oncogenic extrachromosomal DNA as mobile enhancers on neuroblastoma and glioma cancers. Cancer Cell Int 2022; 22:200. [PMID: 35614494 PMCID: PMC9131661 DOI: 10.1186/s12935-022-02617-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/18/2022] [Indexed: 12/21/2022] Open
Abstract
Cancer can be induced by a variety of possible causes, including tumor suppressor gene failure and proto-oncogene hyperactivation. Tumor-associated extrachromosomal circular DNA has been proposed to endanger human health and speed up the progression of cancer. The amplification of ecDNA has raised the oncogene copy number in numerous malignancies according to whole-genome sequencing on distinct cancer types. The unusual structure and function of ecDNA, and its potential role in understanding current cancer genome maps, make it a hotspot to study tumor pathogenesis and evolution. The discovery of the basic mechanisms of ecDNA in the emergence and growth of malignancies could lead researchers to develop new cancer therapies. Despite recent progress, different aspects of ecDNA require more investigation. We focused on the features, and analyzed the bio-genesis, and origin of ecDNA in this review, as well as its functions in neuroblastoma and glioma cancers.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Nastaran Karimfar
- Faculty of Veterinary Medicine, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | | | - Shahriyar Shafa
- School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Melika Ghasemi Shiran
- Department of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mehran Ataei
- Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran
| | | | - Mohsen Nabi Afjadi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
| | - Tahereh Ghadiri
- Department of Neuroscience and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran. .,Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran. .,Neurosiences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Zahra Payandeh
- Department Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, Stockholm, Sweden.
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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Isa R, Horinaka M, Tsukamoto T, Mizuhara K, Fujibayashi Y, Taminishi-Katsuragawa Y, Okamoto H, Yasuda S, Kawaji-Kanayama Y, Matsumura-Kimoto Y, Mizutani S, Shimura Y, Taniwaki M, Sakai T, Kuroda J. The Rationale for the Dual-Targeting Therapy for RSK2 and AKT in Multiple Myeloma. Int J Mol Sci 2022; 23:ijms23062919. [PMID: 35328342 PMCID: PMC8949999 DOI: 10.3390/ijms23062919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Multiple myeloma (MM) is characterized by remarkable cytogenetic/molecular heterogeneity among patients and intraclonal diversity even in a single patient. We previously demonstrated that PDPK1, the master kinase of series of AGC kinases, is universally active in MM, and plays pivotal roles in cell proliferation and cell survival of myeloma cells regardless of the profiles of cytogenetic and genetic abnormalities. This study investigated the therapeutic efficacy and mechanism of action of dual blockade of two major PDPK1 substrates, RSK2 and AKT, in MM. The combinatory treatment of BI-D1870, an inhibitor for N-terminal kinase domain (NTKD) of RSK2, and ipatasertib, an inhibitor for AKT, showed the additive to synergistic anti-tumor effect on human MM-derived cell lines (HMCLs) with active RSK2-NTKD and AKT, by enhancing apoptotic induction with BIM and BID activation. Moreover, the dual blockade of RSK2 and AKT exerted robust molecular effects on critical gene sets associated with myeloma pathophysiologies, such as those with MYC, mTOR, STK33, ribosomal biogenesis, or cell-extrinsic stimuli of soluble factors, in HMCLs. These results provide the biological and molecular rationales for the dual-targeting strategy for RSK2 and AKT, which may overcome the therapeutic difficulty due to cytogenetic/molecular heterogeneity in MM.
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Affiliation(s)
- Reiko Isa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Mano Horinaka
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (M.H.); (S.Y.); (T.S.)
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Kentaro Mizuhara
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yoko Taminishi-Katsuragawa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Haruya Okamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Shusuke Yasuda
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (M.H.); (S.Y.); (T.S.)
| | - Yuka Kawaji-Kanayama
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Shinsuke Mizutani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Toshiyuki Sakai
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (M.H.); (S.Y.); (T.S.)
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (R.I.); (T.T.); (K.M.); (Y.F.); (Y.T.-K.); (H.O.); (Y.K.-K.); (Y.M.-K.); (S.M.); (Y.S.); (M.T.)
- Correspondence:
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10
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Karami Fath M, Akbari Oryani M, Ramezani A, Barjoie Mojarad F, Khalesi B, Delazar S, Anjomrooz M, Taghizadeh A, Taghizadeh S, Payandeh Z, Pourzardosht N. Extra chromosomal DNA in different cancers: Individual genome with important biological functions. Crit Rev Oncol Hematol 2021; 166:103477. [PMID: 34534658 DOI: 10.1016/j.critrevonc.2021.103477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 12/21/2022] Open
Abstract
Cancer can be caused by various factors, including the malfunction of tumor suppressor genes and the hyper-activation of proto-oncogenes. Tumor-associated extrachromosomal circular DNA (eccDNA) has been shown to adversely affect human health and accelerate malignant actions. Whole-genome sequencing (WGS) on different cancer types suggested that the amplification of ecDNA has increased the oncogene copy number in various cancers. The unique structure and function of ecDNA, its profound significance in cancer, and its help in the comprehension of current cancer genome maps, renders it as a hotspot to explore the tumor pathogenesis and evolution. Illumination of the basic mechanisms of ecDNA may provide more insights into cancer therapeutics. Despite the recent advances, different features of ecDNA require further elucidation. In the present review, we primarily discussed the characteristics, biogenesis, genesis, and origin of ecDNA and later highlighted its functions in both tumorigenesis and therapeutic resistance of different cancers.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mahsa Akbari Oryani
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arefeh Ramezani
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Barjoie Mojarad
- Department of Radiology, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Sina Delazar
- Department of Radiology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehran Anjomrooz
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Arvin Taghizadeh
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Taghizadeh
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran.
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11
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Ikeda S, Tagawa H. Impact of hypoxia on the pathogenesis and therapy resistance in multiple myeloma. Cancer Sci 2021; 112:3995-4004. [PMID: 34310776 PMCID: PMC8486179 DOI: 10.1111/cas.15087] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
Multiple myeloma (MM) is a refractory plasma cell tumor. In myeloma cells, the transcription factor IRF4, the master regulator of plasma cells, is aberrantly upregulated and plays an essential role in oncogenesis. IRF4 forms a positive feedback loop with MYC, leading to additional tumorigenic properties. In recent years, molecular targeted therapies have contributed to a significant improvement in the prognosis of MM. Nevertheless, almost all patients experience disease progression, which is thought to be a result of treatment resistance induced by various elements of the bone marrow microenvironment. Among these, the hypoxic response, one of the key processes for cellular homeostasis, induces hypoxia‐adapted traits such as undifferentiation, altered metabolism, and dissemination, leading to drug resistance. These inductions are caused by ectopic gene expression changes mediated by the activation of hypoxia‐inducible factors (HIFs). By contrast, the expression levels of IRF4 and MYC are markedly reduced by hypoxic stress. Notably, an anti‐apoptotic capability is usually acquired under both normoxic and hypoxic conditions, but the mechanism is distinct. This fact strongly suggests that myeloma cells may survive by switching their dependent regulatory factors from IRF4 and MYC (normoxic bone marrow region) to HIF (hypoxic bone marrow microenvironment). Therefore, to achieve deep remission, combination therapeutic agents, which are complementarily effective against both IRF4‐MYC‐dominant and HIF‐dominated fractions, may become an important therapeutic strategy for MM.
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Affiliation(s)
- Sho Ikeda
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroyuki Tagawa
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
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12
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Varier KM, Dhandapani H, Liu W, Song J, Wang C, Hu A, Ben-David Y, Shen X, Li Y, Gajendran B. An immunotherapeutic approach to decipher the role of long non-coding RNAs in cancer progression, resistance and epigenetic regulation of immune cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:242. [PMID: 34303380 PMCID: PMC8305593 DOI: 10.1186/s13046-021-01997-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Immunotherapeutic treatments are gaining attention due to their effective anti-tumor response. Particularly, the revolution of immune checkpoint inhibitors (ICIs) produces promising outcomes for various cancer types. However, the usage of immunotherapy is limited due to its low response rate, suggesting that tumor cells escape the immune surveillance. Rapid advances in transcriptomic profiling have led to recognize immune-related long non-coding RNAs (LncRNAs), as regulators of immune cell-specific gene expression that mediates immune stimulatory as well as suppression of immune response, indicating LncRNAs as targets to improve the efficacy of immunotherapy against tumours. Moreover, the immune-related LncRNAs acting as epigenetic modifiers are also under deep investigation. Thus, herein, is a summarised knowledge of LncRNAs and their regulation in the adaptive and innate immune system, considering their importance in autophagy and predicting putative immunotherapeutic responses.
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Affiliation(s)
- Krishnapriya M Varier
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hemavathi Dhandapani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India.,Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Jialei Song
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Xiangchun Shen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Yanmei Li
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
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13
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Wang Y, Huang R, Zheng G, Shen J. Small ring has big potential: insights into extrachromosomal DNA in cancer. Cancer Cell Int 2021; 21:236. [PMID: 33902601 PMCID: PMC8077740 DOI: 10.1186/s12935-021-01936-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/13/2021] [Indexed: 12/23/2022] Open
Abstract
Recent technical advances have led to the discovery of novel functions of extrachromosomal DNA (ecDNA) in multiple cancer types. Studies have revealed that cancer-associated ecDNA shows a unique circular shape and contains oncogenes that are more frequently amplified than that in linear chromatin DNA. Importantly, the ecDNA-mediated amplification of oncogenes was frequently found in most cancers but rare in normal tissues. Multiple reports have shown that ecDNA has a profound impact on oncogene activation, genomic instability, drug sensitivity, tumor heterogeneity and tumor immunology, therefore may offer the potential for cancer diagnosis and therapeutics. Nevertheless, the underlying mechanisms and future applications of ecDNA remain to be determined. In this review, we summarize the basic concepts, biological functions and molecular mechanisms of ecDNA. We also provide novel insights into the fundamental role of ecDNA in cancer.
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Affiliation(s)
- Yihao Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Guopei Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
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14
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Matsumoto Y, Tsukamoto T, Chinen Y, Shimura Y, Sasaki N, Nagoshi H, Sato R, Adachi H, Nakano M, Horiike S, Kuroda J, Taki T, Tashiro K, Taniwaki M. Detection of novel and recurrent conjoined genes in non-Hodgkin B-cell lymphoma. J Clin Exp Hematop 2021; 61:71-77. [PMID: 33883344 PMCID: PMC8265495 DOI: 10.3960/jslrt.20033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For this study, we investigated comprehensive expression of conjoined genes (CGs) in
non-Hodgkin B-cell lymphoma (B-NHL) cell line KPUM-UH1 by using paired-end RNA sequencing.
Furthermore, we analyzed the expression of these transcripts in an additional 21 cell lines, 37
primary samples of various malignancies and peripheral blood mononuclear cells of four normal
individuals. Seventeen CGs were detected in KPUM-UH1: CTBS-GNG5,
SRP9-EPHX1, RMND5A-ANAPC, OTX1-EHBP1,
ATF2-CHN1, PRKAA1-TTC33, LARP1-MRPL22,
LOC105379697-BAK1, TIAM2-SCAF8,
SPAG1-VPS13B, WBP1L-CNNM2, NARS2-GAB2,
CTSC-RAB38, VAMP1-CD27-AS1, LRRC37A2-NSF,
UBA2-WTIP and ZNF600-ZNF611. To our knowledge, 10 of these
genes have not been previously reported. The various characteristics of the CGs included in-
and out-of-frame fusions, chimeras involving non-coding RNA and transcript variants. A finding
of note was that LARP1-MRPL2 was characterized as in-frame fusion and was
recurrently expressed in B-NHL samples. In this study, variety of CGs was expressed both in
malignant and normal cells, some of which might be specific to lymphoma.
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Affiliation(s)
- Yosuke Matsumoto
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Hematology, Fukuchiyama City Hospital, Fukuchiyama, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nana Sasaki
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Sato
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroko Adachi
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohiko Taki
- Department of Medical Technology, Kyorin University Faculty of Health Science, Tokyo, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
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15
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Tolomeo D, Agostini A, Visci G, Traversa D, Storlazzi CT. PVT1: A long non-coding RNA recurrently involved in neoplasia-associated fusion transcripts. Gene 2021; 779:145497. [PMID: 33600954 DOI: 10.1016/j.gene.2021.145497] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022]
Abstract
NGS technologies and bioinformatics tools allow the rapid identification of chimeric transcripts in cancer. More than 40,000 fusions are so far reported in the literature; however, for most of them, the role in oncogenesis is still not fully understood. This is the case for fusions involving the long non-coding RNA (lncRNA) Plasmacytoma variant translocation 1 (PVT1) (8q24.21). This lncRNA displays oncogenic functions in several cancer types interacting with microRNAs and proteins, but the role of PVT1 fusion transcripts is more obscure. These chimeras have been identified in both hematological malignancies and solid tumors, mainly arising from rearrangements and/or amplification of the 8q24 chromosomal region. In this review, we detail the full spectrum of PVT1 fusions in cancer, summarizing current knowledge about their genesis, function, and role as biomarkers.
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Affiliation(s)
- Doron Tolomeo
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
| | - Antonio Agostini
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124 Bari, Italy.
| | - Grazia Visci
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
| | - Debora Traversa
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
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16
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Ding T, Deng R, Huang T. Long non-coding RNA T cell factor 7 is associated with increased disease risk and poor prognosis, and promotes cell proliferation, attenuates cell apoptosis and miR-200c expression in multiple myeloma. Oncol Lett 2021; 21:129. [PMID: 33552250 PMCID: PMC7798040 DOI: 10.3892/ol.2020.12390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
The aim of the present study was to investigate the association of long non-coding RNA T cell factor 7 (lncRNA TCF7) with disease risk, prognosis and its cellular function in multiple myeloma (MM). A total of 132 de novo symptomatic patients with MM and 50 controls were enrolled. Plasma cells from patients with MM and controls were separated from bone marrow samples to detect lncRNA TCF7 expression using reverse transcription-quantitative PCR. In addition, treatment responses, event-free survival (EFS) and overall survival (OS) were measured. The effects of lncRNA TCF7 on proliferation, apoptosis and microRNA-200c (miR-200c) expression were assessed by gain- and loss-of-function experiments in RPMI-8226 and U-266 cells. The results demonstrated that lncRNA TCF7 expression was upregulated in patients with MM compared with controls, and the receiver operating characteristic curve revealed that lncRNA TCF7 could distinguish patients with MM from controls with an area under the curve of 0.793 (95% CI, 0.725-0.861). In patients with MM, high lncRNA TCF7 expression was associated with higher β2-microglobulin, more advanced International Staging System stage and increased t (14; 16) mutations. Furthermore, it was demonstrated that lncRNA TCF7 was downregulated in patients with complete response (CR) compared with patients without CR. Furthermore, high lncRNA TCF7 expression predicted worse EFS and OS. lncRNA TCF7 also promoted cell proliferation, whereas it reduced cell apoptosis and miR-200c expression in RPMI-8226 and U-266 cells. In conclusion, the present results suggested that lncRNA TCF7 may be used as a potential biomarker and as a treatment target for MM.
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Affiliation(s)
- Tianling Ding
- Department of Hematology, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, P.R. China
| | - Ruoyu Deng
- Shanghai Qeejen Bio-tech Institution, Shanghai 200434, P.R. China
| | - Ting Huang
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
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17
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Wilson C, Kanhere A. 8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer. Int J Mol Sci 2021; 22:1094. [PMID: 33499210 PMCID: PMC7865353 DOI: 10.3390/ijms22031094] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 01/17/2023] Open
Abstract
The majority of the human genome is comprised of non-protein-coding genes, but the relevance of non-coding RNAs in complex diseases has yet to be fully elucidated. One class of non-coding RNAs is long non-coding RNAs or lncRNAs, many of which have been identified to play a range of roles in transcription and translation. While the clinical importance of the majority of lncRNAs have yet to be identified, it is puzzling that a large number of disease-associated genetic variations are seen in lncRNA genes. The 8q24.21 locus is rich in lncRNAs and very few protein-coding genes are located in this region. Interestingly, the 8q24.21 region is also a hot spot for genetic variants associated with an increased risk of cancer. Research focusing on the lncRNAs in this area of the genome has indicated clinical relevance of lncRNAs in different cancers. In this review, we summarise the lncRNAs in the 8q24.21 region with respect to their role in cancer and discuss the potential impact of cancer-associated genetic polymorphisms on the function of lncRNAs in initiation and progression of cancer.
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Affiliation(s)
| | - Aditi Kanhere
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK;
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18
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Taniue K, Akimitsu N. The Functions and Unique Features of LncRNAs in Cancer Development and Tumorigenesis. Int J Mol Sci 2021; 22:E632. [PMID: 33435206 PMCID: PMC7826647 DOI: 10.3390/ijms22020632] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Over the past decades, research on cancer biology has focused on the involvement of protein-coding genes in cancer development. Long noncoding RNAs (lncRNAs), which are transcripts longer than 200 nucleotides that lack protein-coding potential, are an important class of RNA molecules that are involved in a variety of biological functions. Although the functions of a majority of lncRNAs have yet to be clarified, some lncRNAs have been shown to be associated with human diseases such as cancer. LncRNAs have been shown to contribute to many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, protein and RNA. Here we describe the literature regarding the biogenesis and features of lncRNAs. We also present an overview of the current knowledge regarding the roles of lncRNAs in cancer from the view of various aspects of cellular homeostasis, including proliferation, survival, migration and genomic stability. Furthermore, we discuss the methodologies used to identify the function of lncRNAs in cancer development and tumorigenesis. Better understanding of the molecular mechanisms involving lncRNA functions in cancer is critical for the development of diagnostic and therapeutic strategies against tumorigenesis.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Cancer Genomics and Precision Medicine, Division of Gastroenterology and Hematology-Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa 078-8510, Hokkaido, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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19
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Aprile M, Katopodi V, Leucci E, Costa V. LncRNAs in Cancer: From garbage to Junk. Cancers (Basel) 2020; 12:cancers12113220. [PMID: 33142861 PMCID: PMC7692075 DOI: 10.3390/cancers12113220] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing-based transcriptomics has significantly redefined the concept of genome complexity, leading to the identification of thousands of lncRNA genes identification of thousands of lncRNA genes whose products possess transcriptional and/or post-transcriptional regulatory functions that help to shape cell functionality and fate. Indeed, it is well-established now that lncRNAs play a key role in the regulation of gene expression through epigenetic and posttranscriptional mechanims. The rapid increase of studies reporting lncRNAs alteration in cancers has also highlighted their relevance for tumorigenesis. Herein we describe the most prominent examples of well-established lncRNAs having oncogenic and/or tumor suppressive activity. We also discuss how technical advances have provided new therapeutic strategies based on their targeting, and also report the challenges towards their use in the clinical settings.
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Affiliation(s)
- Marianna Aprile
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Valerio Costa
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
- Correspondence:
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20
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Zhou X, Zhan L, Huang K, Wang X. The functions and clinical significance of circRNAs in hematological malignancies. J Hematol Oncol 2020; 13:138. [PMID: 33069241 PMCID: PMC7568356 DOI: 10.1186/s13045-020-00976-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023] Open
Abstract
With covalently closed circular structures, circular RNAs (circRNAs) were once misinterpreted as by-products of mRNA splicing. Being abundant, stable, highly conserved, and tissue-specific, circRNAs are recently identified as a type of regulatory RNAs. CircRNAs bind to certain miRNAs or proteins to participate in gene transcription and translation. Emerging evidence has indicated that the dysregulation of circRNAs is closely linked to the tumorigenesis and treatment response of hematological malignancies. CircRNAs play critical roles in various biological processes, including tumorigenesis, drug resistance, tumor metabolism, autophagy, pyroptosis, and ferroptosis. The N6-methyladenosine modification of circRNAs and discovery of fusion-circRNAs provide novel insights into the functions of circRNAs. Targeting circRNAs in hematological malignancies will be an attractive treatment strategy. In this review, we systematically summarize recent advances toward the novel functions and molecular mechanisms of circRNAs in hematological malignancies, and highlight the potential clinical applications of circRNAs as novel biomarkers and therapeutic targets for future exploration.
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Affiliation(s)
- Xiangxiang Zhou
- Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China. .,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China. .,School of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China. .,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, People's Republic of China. .,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, People's Republic of China. .,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, 251006, People's Republic of China.
| | - Linquan Zhan
- Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China
| | - Kai Huang
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China. .,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China. .,School of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China. .,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, People's Republic of China. .,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, People's Republic of China. .,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, 251006, People's Republic of China.
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21
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Handa H, Honma K, Oda T, Kobayashi N, Kuroda Y, Kimura-Masuda K, Watanabe S, Ishihara R, Murakami Y, Masuda Y, Tahara KI, Takei H, Kasamatsu T, Saitoh T, Murakami H. Long Noncoding RNA PVT1 Is Regulated by Bromodomain Protein BRD4 in Multiple Myeloma and Is Associated with Disease Progression. Int J Mol Sci 2020; 21:ijms21197121. [PMID: 32992461 PMCID: PMC7583953 DOI: 10.3390/ijms21197121] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are deregulated in human cancers and are associated with disease progression. Plasmacytoma Variant Translocation 1 (PVT1), a lncRNA, is located adjacent to the gene MYC, which has been linked to multiple myeloma (MM). PVT1 is expressed in MM and is associated with carcinogenesis. However, its role and regulation remain uncertain. We examined PVT1/MYC expression using real-time PCR in plasma cells purified from 59 monoclonal gammopathy of undetermined significance (MGUS) and 140 MM patients. The MM cell lines KMS11, KMS12PE, OPM2, and RPMI8226 were treated with JQ1, an MYC super-enhancer inhibitor, or MYC inhibitor 10058-F4. The expression levels of PVT1 and MYC were significantly higher in MM than in MGUS (p < 0.0001) and were positively correlated with disease progression (r = 0.394, p < 0.0001). JQ1 inhibited cell proliferation and decreased the expression levels of MYC and PVT1. However, 10054-F4 did not alter the expression level of PVT1. The positive correlation between MYC and PVT1 in patients, the synchronous downregulation of MYC and PVT1 by JQ1, and the lack of effect of the MYC inhibitor on PVT1 expression suggest that the expression of these two genes is co-regulated by a super-enhancer. Cooperative effects between these two genes may contribute to MM pathogenesis and progression.
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Affiliation(s)
- Hiroshi Handa
- Department of Hematology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (N.K.); (K.-i.T.); (H.T.)
- Correspondence: ; Tel.: +81-27-220-8166; Fax: +81-27-220-8173
| | - Kazuki Honma
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Tsukasa Oda
- Institute of Molecular and Cellular Regulation, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan;
| | - Nobuhiko Kobayashi
- Department of Hematology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (N.K.); (K.-i.T.); (H.T.)
| | - Yuko Kuroda
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Kei Kimura-Masuda
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Saki Watanabe
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Rei Ishihara
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Yuki Murakami
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Yuta Masuda
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Ken-ichi Tahara
- Department of Hematology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (N.K.); (K.-i.T.); (H.T.)
| | - Hisashi Takei
- Department of Hematology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (N.K.); (K.-i.T.); (H.T.)
| | - Tetsuhiro Kasamatsu
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Takayuki Saitoh
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
| | - Hirokazu Murakami
- Department of Laboratory Science, Gunma University Graduate School of Health Science, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan; (K.H.); (Y.K.); (K.K.-M.); (S.W.); (R.I.); (Y.M.); (Y.M.); (T.K.); (T.S.); (H.M.)
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22
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Li P, Han X, Xie Y, Liu Y. Long Noncoding RNA Plasmacytoma Variant Translocation 1 Is Increased in Multiple Myeloma and Correlates With Lower Induction Response. Technol Cancer Res Treat 2020. [PMCID: PMC7436793 DOI: 10.1177/1533033820935496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objective: This study aimed to investigate the correlation of long noncoding RNA plasmacytoma variant translocation 1 with clinical features and prognosis in patients with multiple myeloma. Methods: The bone marrow samples were collected from 128 patients with de novo symptomatic multiple myeloma (before initial treatment) and 30 healthy donors (on the enrollment). Long noncoding RNA plasmacytoma variant translocation 1 expression in bone marrow-derived plasma cells was detected by reverse transcription quantitative polymerase chain reaction. In patients with multiple myeloma, their demographics and clinical features before treatment were collected; induction treatment response (complete response and overall response rate) and survival profiles (progression-free survival and overall survival) were assessed. Results: Expression of long noncoding RNA plasmacytoma variant translocation 1 was increased in patients with multiple myeloma compared to healthy donors. Receiver-operating characteristic curve showed that long noncoding RNA plasmacytoma variant translocation 1 distinguished patients with multiple myeloma from healthy donors with an area under the curve of 0.884 (95% confidence interval: 0.829-0.940). In patients with multiple myeloma, high expression of long noncoding RNA plasmacytoma variant translocation 1 correlated with elevated β-2 microglobulin, increased International Staging System stage, and raised Del (17p), but it did not correlate with other biochemical indexes or chromosomal abnormalities. Furthermore, long noncoding RNA plasmacytoma variant translocation 1 high expression patients presented with decreased complete response and overall response rate compared to long noncoding RNA plasmacytoma variant translocation 1 low expression patients, and high expression of long noncoding RNA plasmacytoma variant translocation 1 predicted unfavorable progression-free survival as well overall survival in patients with multiple myeloma. Conclusion: Long noncoding RNA plasmacytoma variant translocation 1 might be a potential biomarker for the supervision of disease progression and prognosis in patients with multiple myeloma.
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Affiliation(s)
- Pei Li
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiyao Han
- Department of Hematology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yinghua Xie
- Department of Hematology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yihan Liu
- Department of Hematology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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23
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Ota A, Hanamura I, Karnan S, Inaguma S, Takei N, Lam VQ, Mizuno S, Kanasugi J, Wahiduzzaman M, Rahman ML, Hyodo T, Konishi H, Tsuzuki S, Ikeda H, Takami A, Hosokawa Y. Novel Interleukin-6 Inducible Gene PDZ-Binding Kinase Promotes Tumor Growth of Multiple Myeloma Cells. J Interferon Cytokine Res 2020; 40:389-405. [PMID: 32721246 PMCID: PMC7462034 DOI: 10.1089/jir.2020.0111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) remains an intractable hematological malignancy, despite recent advances in anti-MM drugs. Here, we show that role of PDZ binding kinase (PBK) in MM tumor growth. We identified that interleukin-6 (IL-6) readily increases PBK expression. Kaplan–Meier analysis showed that the MM patients with higher expression of PBK have a significant shorter survival time compared with those with moderate/lower expression of PBK. Knockout of PBK dramatically suppressed in vivo tumor growth in MM cells, while genome editing of PBK changing from asparagine to serine substitution (rs3779620) slightly suppresses the tumor formation. Mechanistically, loss of PBK increased the number of apoptotic cells with concomitant decrease in the phosphorylation level of Stat3 as well as caspase activities. A novel PBK inhibitor OTS514 significantly decreased KMS-11-derived tumor growth. These findings highlight the novel oncogenic role of PBK in tumor growth of myeloma, and it might be a novel therapeutic target for the treatment of patients with MM.
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Affiliation(s)
- Akinobu Ota
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Ichiro Hanamura
- Division of Hematology, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Sivasundaram Karnan
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Shingo Inaguma
- Department of Pathology, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Norio Takei
- Institute for Animal Experimentation, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Vu Quang Lam
- Division of Hematology, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Shohei Mizuno
- Division of Hematology, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Jo Kanasugi
- Division of Hematology, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Md Wahiduzzaman
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Md Lutfur Rahman
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Toshinori Hyodo
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Hiroyuki Konishi
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Shinobu Tsuzuki
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Hiroshi Ikeda
- Department of Pathology, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Akiyoshi Takami
- Division of Hematology, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Yoshitaka Hosokawa
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
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24
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Benetatos L, Benetatou A, Vartholomatos G. Long non-coding RNAs and MYC association in hematological malignancies. Ann Hematol 2020; 99:2231-2242. [PMID: 32621182 DOI: 10.1007/s00277-020-04166-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) have an established role in cell biology. Among their functions is the regulation of hematopoiesis. They characterize the different stages of hematopoiesis in a more lineage-restricted expression pattern than coding mRNAs. They affect hematopoietic stem cell renewal, proliferation, and differentiation of committed progenitors by interacting with master regulators transcription factors. Among these transcription factors, MYC has a prominent role. Similar to MYC's transcriptional activation/amplification of protein coding genes, MYC also regulates lncRNAs' expression profile, while it is also regulated by lncRNAs. Both myeloid and lymphoid malignancies are prone to the association of MYC with lncRNAs. Such interaction inhibits apoptosis, enhances cell proliferation, deregulates metabolism, and promotes genomic instability and resistance to treatment. In this review, we discuss the recent findings that encompass the crosstalk between lncRNAs and describe the pathways that very probably have a pathogenetic role in both acute and chronic hematologic malignancies.
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Affiliation(s)
| | - Agapi Benetatou
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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25
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Smith SC, Qdaisat TZS, Althof PA, Dave BJ, Sanmann JN. MECOM rearrangement involving the MYC locus: Two additional patients with the rare translocation, t(3;8)(q26.2;q24), and molecular review. Leuk Res 2020; 95:106387. [PMID: 32535247 DOI: 10.1016/j.leukres.2020.106387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/31/2022]
Abstract
A relatively small subset of myeloid neoplasms involve rearrangements of cytoband 3q26.2. Such rearrangements are often in response to therapy and carry a poor prognosis. The ectopic expression of MECOM is the result of such translocations. To date, thirty-three t(3;8)(q26.2;q24) cases have been reported; we contribute two patients with confirmed MECOM and MYC rearrangements. Both patients presented with pancytopenia and were diagnosed with myelodysplastic/myeloproliferative disorders. In addition to translocation t(3;8), Patient 1 possessed a derivative chromosome 5, while Patient 2 possessed monosomy 7; neither patient's clonal abnormalities resolved in follow-up studies. Of the previous 33 cases, one exhibited 5q loss, while monosomy 7 was found in fifteen. These findings contribute to the small number of reported cases with t(3;8) translocations. We also speculate about the molecular mechanisms associated with this translocation.
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Affiliation(s)
- Scott C Smith
- University of Nebraska Medical Center, United States; Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, Omaha, NE, United States
| | - Tareq Z S Qdaisat
- University of Nebraska Medical Center, United States; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Pamela A Althof
- University of Nebraska Medical Center, United States; Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, Omaha, NE, United States
| | - Bhavana J Dave
- University of Nebraska Medical Center, United States; Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, Omaha, NE, United States
| | - Jennifer N Sanmann
- University of Nebraska Medical Center, United States; Human Genetics Laboratory, Munroe-Meyer Institute for Genetics and Rehabilitation, Omaha, NE, United States.
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26
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Ghetti M, Vannini I, Storlazzi CT, Martinelli G, Simonetti G. Linear and circular PVT1 in hematological malignancies and immune response: two faces of the same coin. Mol Cancer 2020; 19:69. [PMID: 32228602 PMCID: PMC7104523 DOI: 10.1186/s12943-020-01187-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Non coding RNAs (ncRNAs) have emerged as regulators of human carcinogenesis by affecting the expression of key tumor suppressor genes and oncogenes. They are divided into short and long ncRNAs, according to their length. Circular RNAs (circRNAs) are included in the second group and were recently discovered as being originated by back-splicing, joining either single or multiple exons, or exons with retained introns. The human Plasmacytoma Variant Translocation 1 (PVT1) gene maps on the long arm of chromosome 8 (8q24) and encodes for 52 ncRNAs variants, including 26 linear and 26 circular isoforms, and 6 microRNAs. PVT1 genomic locus is 54 Kb downstream to MYC and several interactions have been described among these two genes, including a feedback regulatory mechanism. MYC-independent functions of PVT1/circPVT1 have been also reported, especially in the regulation of immune responses. We here review and discuss the role of both PVT1 and circPVT1 in the hematopoietic system. No information is currently available concerning their transforming ability in hematopoietic cells. However, present literature supports their cooperation with a more aggressive and/or undifferentiated cell phenotype, thus contributing to cancer progression. PVT1/circPVT1 upregulation through genomic amplification or rearrangements and/or increased transcription, provides a proliferative advantage to malignant cells in acute myeloid leukemia, acute promyelocytic leukemia, Burkitt lymphoma, multiple myeloma (linear PVT1) and acute lymphoblastic leukemia (circPVT1). In addition, PVT1 and circPVT1 regulate immune responses: the overexpression of the linear form in myeloid derived suppressor cells induced immune tolerance in preclinical tumor models and circPVT1 showed immunosuppressive properties in myeloid and lymphoid cell subsets. Overall, these recent data on PVT1 and circPVT1 functions in hematological malignancies and immune responses reflect two faces of the same coin: involvement in cancer progression by promoting a more aggressive phenotype of malignant cells and negative regulation of the immune system as a novel potential therapy-resistance mechanism.
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Affiliation(s)
- Martina Ghetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Ivan Vannini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
| | | | - Giovanni Martinelli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
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27
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Martínez-Barriocanal Á, Arango D, Dopeso H. PVT1 Long Non-coding RNA in Gastrointestinal Cancer. Front Oncol 2020; 10:38. [PMID: 32083000 PMCID: PMC7005105 DOI: 10.3389/fonc.2020.00038] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 01/09/2020] [Indexed: 12/24/2022] Open
Abstract
Whole genome and transcriptome sequencing technologies have led to the identification of many long non-coding RNAs (lncRNAs) and stimulated the research of their role in health and disease. LncRNAs participate in the regulation of critical signaling pathways including cell growth, motility, apoptosis, and differentiation; and their expression has been found dysregulated in human tumors. Thus, lncRNAs have emerged as new players in the initiation, maintenance and progression of tumorigenesis. PVT1 (plasmacytoma variant translocation 1) lncRNA is located on chromosomal 8q24.21, a large locus frequently amplified in human cancers and predictive of increased cancer risk in genome-wide association studies (GWAS). Combined, colorectal and gastric adenocarcinomas are the most frequent tumor malignancies and also the leading cause of cancer-related deaths worldwide. PVT1 expression is elevated in gastrointestinal tumors and correlates with poor patient prognosis. In this review, we discuss the mechanisms of action underlying PVT1 oncogenic role in colorectal and gastric cancer such as MYC upregulation, miRNA production, competitive endogenous RNA (ceRNA) function, protein stabilization, and epigenetic regulation. We also illustrate the potential role of PVT1 as prognostic biomarker and its relationship with resistance to current chemotherapeutic treatments.
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Affiliation(s)
- Águeda Martínez-Barriocanal
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Group of Molecular Oncology, IRB Lleida, Lleida, Spain
| | - Diego Arango
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Group of Molecular Oncology, IRB Lleida, Lleida, Spain
| | - Higinio Dopeso
- Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
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28
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p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis. Mol Cell 2020; 77:761-774.e8. [PMID: 31973890 DOI: 10.1016/j.molcel.2019.12.014] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/20/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
The tumor suppressor p53 transcriptionally activates target genes to suppress cellular proliferation during stress. p53 has also been implicated in the repression of the proto-oncogene Myc, but the mechanism has remained unclear. Here, we identify Pvt1b, a p53-dependent isoform of the long noncoding RNA (lncRNA) Pvt1, expressed 50 kb downstream of Myc, which becomes induced by DNA damage or oncogenic signaling and accumulates near its site of transcription. We show that production of the Pvt1b RNA is necessary and sufficient to suppress Myc transcription in cis without altering the chromatin organization of the locus. Inhibition of Pvt1b increases Myc levels and transcriptional activity and promotes cellular proliferation. Furthermore, Pvt1b loss accelerates tumor growth, but not tumor progression, in an autochthonous mouse model of lung cancer. These findings demonstrate that Pvt1b acts at the intersection of the p53 and Myc transcriptional networks to reinforce the anti-proliferative activities of p53.
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29
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Matsumoto Y, Chinen Y, Shimura Y, Nagoshi H, Sasaki N, Muramatsu A, Kuriyama K, Ohshiro M, Hirakawa Y, Iwai T, Uchiyama H, Taki T, Horiike S, Kuroda J, Taniwaki M. Recurrent intragenic exon rearrangements of SOBP and AUTS2 in non-Hodgkin B-cell lymphoma. Int J Hematol 2019; 111:75-83. [PMID: 31686349 DOI: 10.1007/s12185-019-02766-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 11/28/2022]
Abstract
Expression of intragenic exon rearrangements (IERs) has reportedly been detected in both normal and cancer cells. However, there have been few reports of occurrence of these rearrangements specific to neoplasms including malignant lymphoma. In this study, we detected IERs of ten genes (NBPF8, SOBP, AUTS2, RAB21, SPATA13, ABCC4, WDR7, PHLPP1, NFATC1 and MAGED1) in non-Hodgkin B cell lymphoma (B-NHL) cell line KPUM-UH1 using a high-resolution single nucleotide polymorphism array and reverse transcription polymerase chain reaction using reversely directed divergent primers within exons involved in genomic intragenic gains followed by sequencing analysis. Among them, the IERs involved in SOBP (6q21) exon 2 and 3 and AUTS2 (7q11.22) exon 2-4 were the molecular lesions specific to tumors and were frequently detected in B-NHL samples. These IERs constitute novel genetic alterations of B-NHL, which might be associated with tumorigenesis and be useful as genetic biological markers.
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Affiliation(s)
- Yosuke Matsumoto
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan.
| | - Yoshiaki Chinen
- Department of Hematology, Fukuchiyama City Hospital, Fukuchiyama, Japan.,Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Hiroshima University, Hiroshima, Japan
| | - Nana Sasaki
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Ayako Muramatsu
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Kodai Kuriyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Muneo Ohshiro
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Yoshiko Hirakawa
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Toshiki Iwai
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Hitoji Uchiyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Tomohiko Taki
- Department of Medical Technology, Kyorin University, Faculty of Health Science, Tokyo, Japan.,Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Xiong X, Yuan J, Zhang N, Zheng Y, Liu J, Yang M. Silencing of lncRNA PVT1 by miR-214 inhibits the oncogenic GDF15 signaling and suppresses hepatocarcinogenesis. Biochem Biophys Res Commun 2019; 521:478-484. [PMID: 31677796 DOI: 10.1016/j.bbrc.2019.10.137] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
Abstract
The prognosis for hepatocellular carcinoma (HCC) is dismal. Long noncoding RNA PVT1 has been linked to malignancies and might be a deleterious therapy target. However, the key events controlling its expression in HCC remain undetermined. Here, we address how PVT1 is fine-regulated and its downstream signaling in hepatoma cells. Interestingly, we found that c-Myc and P53 could divergently regulate PVT1 transcription. Oncoprotein c-Myc enhances PVT1 expression, whereas P53 suppresses its expression. We also identified miR-214 as a crucial, negative regulator of PVT1. Consistently, high miR-214 levels were significantly correlated with diminished PVT1 expression in HCC specimens. Silencing of PVT1 by ectopic miR-214 or siRNAs markedly inhibited viability and invasion of HCC cells. In opposition, inhibition of endogenous miR-214 promoted PVT1 expression and enhanced cell proliferation. Notably, oncogenic GDF15 is a potential downstream target of the miR-214-PVT1 signaling. Collectively, our results show that the c-Myc/P53/miR-214-PVT1-GDF15 axis is implicated in HCC development, shedding light on the mechanistic actions of PVT1 and representing potential targets for HCC clinical intervention.
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Affiliation(s)
- Xiangyu Xiong
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Jupeng Yuan
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Nasha Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Yan Zheng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Jibing Liu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
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31
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Chi Y, Wang D, Wang J, Yu W, Yang J. Long Non-Coding RNA in the Pathogenesis of Cancers. Cells 2019; 8:cells8091015. [PMID: 31480503 PMCID: PMC6770362 DOI: 10.3390/cells8091015] [Citation(s) in RCA: 509] [Impact Index Per Article: 101.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 12/24/2022] Open
Abstract
The incidence and mortality rate of cancer has been quickly increasing in the past decades. At present, cancer has become the leading cause of death worldwide. Most of the cancers cannot be effectively diagnosed at the early stage. Although there are multiple therapeutic treatments, including surgery, radiotherapy, chemotherapy, and targeted drugs, their effectiveness is still limited. The overall survival rate of malignant cancers is still low. It is necessary to further study the mechanisms for malignant cancers, and explore new biomarkers and targets that are more sensitive and effective for early diagnosis, treatment, and prognosis of cancers than traditional biomarkers and methods. Long non-coding RNAs (lncRNAs) are a class of RNA transcripts with a length greater than 200 nucleotides. Generally, lncRNAs are not capable of encoding proteins or peptides. LncRNAs exert diverse biological functions by regulating gene expressions and functions at transcriptional, translational, and post-translational levels. In the past decade, it has been demonstrated that the dysregulated lncRNA profile is widely involved in the pathogenesis of many diseases, including cancer, metabolic disorders, and cardiovascular diseases. In particular, lncRNAs have been revealed to play an important role in tumor growth and metastasis. Many lncRNAs have been shown to be potential biomarkers and targets for the diagnosis and treatment of cancers. This review aims to briefly discuss the latest findings regarding the roles and mechanisms of some important lncRNAs in the pathogenesis of certain malignant cancers, including lung, breast, liver, and colorectal cancers, as well as hematological malignancies and neuroblastoma.
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Affiliation(s)
- Yujing Chi
- Department of Central Laboratory & Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China
| | - Di Wang
- Department of Central Laboratory & Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China
| | - Junpei Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-coding RNA Medicine, Beijing 100191, China
| | - Weidong Yu
- Department of Central Laboratory & Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-coding RNA Medicine, Beijing 100191, China.
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Ghafouri-Fard S, Omrani MD, Taheri M. Long noncoding RNA PVT1: A highly dysregulated gene in malignancy. J Cell Physiol 2019; 235:818-835. [PMID: 31297833 DOI: 10.1002/jcp.29060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022]
Abstract
Recent studies have verified the contribution of several long noncoding RNAs (lncRNAs) in the carcinogenesis. Among the highly acknowledged lncRNAs is the human homolog of the plasmacytoma variant translocation gene, which is called PVT1. PVT1 resides near Myc oncogene and regulates the oncogenic process through modulation of several signaling pathways, such as TGF-β, Wnt/ β-catenin, PI3K/AKT, and mTOR pathways. This lncRNA has a circular form as well. Expression analyses and functional studies have appraised the oncogenic roles of PVT1 and circPVT1. Experiments in several cancer cell lines have shown that PVT1 silencing suppresses cancer cell proliferation, whereas its overexpression has the opposite effect. Its silencing has led to the accumulation of cells in the G0/G1 phase and diminished the number of cells in the S phase. Moreover, genome-wide association studies have signified the role of single nucleotide polymorphisms of this lncRNA in conferring risk of lymphoma in different populations. In the current study, we have summarized recent data about the role of PVT1 and circPVT1 in the carcinogenesis process.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Cui YS, Song YP, Fang BJ. The role of long non-coding RNAs in multiple myeloma. Eur J Haematol 2019; 103:3-9. [PMID: 30985973 DOI: 10.1111/ejh.13237] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 12/12/2022]
Abstract
Multiple myeloma (MM) is still an incurable disease, and its pathogenesis involves cytogenetics and epigenetics. In recent years, the roles of long non-coding RNAs (lncRNAs) in MM have been deeply studied by scholars. LncRNAs are defined as a class of non-protein-coding transcripts greater than 200 nucleotides in length, which are involved in a large spectrum of biological processes, including proliferation, differentiation, apoptosis, invasion, and chromatin remodeling. However, little is known about the specific mechanisms of these lncRNAs. They can act as oncogenic and/or tumor-suppressive factors in the development and progression of MM. But that how do they work remains unclear. In this review, the recent progress in the study of functional lncRNAs associated with MM was summarized and the present knowledge about their expression and roles was discussed, to provide guidance for the in-depth functional study of lncRNAs.
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Affiliation(s)
- Yu-Shan Cui
- Department of Hematology, Henan Institute of Haematology, Henan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong-Ping Song
- Department of Hematology, Henan Institute of Haematology, Henan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Bai-Jun Fang
- Department of Hematology, Henan Institute of Haematology, Henan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
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Mizuno Y, Chinen Y, Tsukamoto T, Takimoto-Shimomura T, Matsumura-Kimoto Y, Fujibayashi Y, Kuwahara-Ota S, Fujino T, Nishiyama D, Shimura Y, Kobayashi T, Horiike S, Taniwaki M, Kuroda J. A novel method of amplified fluorescent in situ hybridization for detection of chromosomal microdeletions in B cell lymphoma. Int J Hematol 2019; 109:593-602. [PMID: 30830578 DOI: 10.1007/s12185-019-02617-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/09/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022]
Abstract
Chromosomal microdeletions frequently cause loss of prognostically relevant tumor suppressor genes in hematologic malignancies; however, detection of minute deletions by conventional methods for chromosomal analysis, such as G-banding and fluorescence in situ hybridization (FISH), is difficult due to their low resolution. Here, we describe a new diagnostic modality that enables detection of chromosomal microdeletions, using CDKN2A gene deletion in B cell lymphomas (BCLs) as an example. In this method, which we refer to as amplified-FISH (AM-FISH), a 31-kb fluorescein isothiocyanate (FITC)-conjugated DNA probe encoding only CDKN2A was first hybridized with the chromosome, and then labeled with Alexa Fluor 488-conjugated anti-FITC secondary antibody to increase sensitivity. CDKN2A signals were equally identifiable by AM-FISH and conventional FISH in normal mononuclear blood cells. In contrast, when two BCL cell lines lacking CDKN2A were analyzed, CDKN2A signals were not detected by AM-FISH, whereas conventional FISH yielded false signals. Furthermore, AM-FISH detected CDKN2A deletions in two BCL patients with 9p21 microdeletions, which were not detected by conventional FISH. These results suggest that AM-FISH is a highly sensitive, specific, and simple method for diagnosis of chromosomal microdeletions.
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Affiliation(s)
- Yoshimi Mizuno
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan.
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tomoko Takimoto-Shimomura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Saeko Kuwahara-Ota
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Takahiro Fujino
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Daichi Nishiyama
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
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35
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Butova R, Vychytilova-Faltejskova P, Souckova A, Sevcikova S, Hajek R. Long Non-Coding RNAs in Multiple Myeloma. Noncoding RNA 2019; 5:ncrna5010013. [PMID: 30682861 PMCID: PMC6468639 DOI: 10.3390/ncrna5010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Multiple myeloma (MM) is the second most common hematooncological disease of malignant plasma cells in the bone marrow. While new treatment brought unprecedented increase of survival of patients, MM pathogenesis is yet to be clarified. Increasing evidence of expression of long non-coding RNA molecules (lncRNA) linked to development and progression of many tumors suggested their important role in tumorigenesis. To date, over 15,000 lncRNA molecules characterized by diversity of function and specificity of cell distribution were identified in the human genome. Due to their involvement in proliferation, apoptosis, metabolism, and differentiation, they have a key role in the biological processes and pathogenesis of many diseases, including MM. This review summarizes current knowledge of non-coding RNAs (ncRNA), especially lncRNAs, and their role in MM pathogenesis. Undeniable involvement of lncRNAs in MM development suggests their potential as biomarkers.
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Affiliation(s)
- Romana Butova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | | | - Adela Souckova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Sabina Sevcikova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Roman Hajek
- Department of Hematooncology, University Hospital Ostrava and Faculty of Medicine, University Ostrava, 70852 Ostrava, Czech Republic.
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Hussain T, Liu B, Shrock MS, Williams T, Aldaz CM. WWOX, the FRA16D gene: A target of and a contributor to genomic instability. Genes Chromosomes Cancer 2018; 58:324-338. [PMID: 30350478 DOI: 10.1002/gcc.22693] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/10/2018] [Indexed: 12/20/2022] Open
Abstract
WWOX is one of the largest human genes spanning over 1.11 Mbp in length at chr16q23.1-q23.2 and containing FRA16D, the second most common chromosomal fragile site. FRA16D is a hot spot of genomic instability, prone to breakage and for causing germline and somatic copy number variations (CNVs). Consequentially WWOX is frequent target for deletions in cancer. Esophageal, stomach, colon, bladder, ovarian, and uterine cancers are those most commonly affected by WWOX deep focal deletions. WWOX deletions significantly correlate with various clinicopathological features in esophageal carcinoma. WWOX is also a common target for translocations in multiple myeloma. By mapping R-loop (RNA:DNA hybrid) forming sequences (RFLS) we observe this to be a consistent feature aligning with germline and somatic CNV break points at the edges and core of FRA16D spanning from introns 5 to 8 of WWOX. Germline CNV polymorphisms affecting WWOX are extremely common in humans across different ethnic groups. Importantly, structural variants datasets allowed us to identify a specific hot spot for germline duplications and deletions within intron 5 of WWOX coinciding with the 5' edge of the FRA16D core and various RFLS. Recently, multiple pathogenic CNVs spanning WWOX have been identified associated with neurological conditions such as autism spectrum disorder, infantile epileptic encephalopathies, and other developmental anomalies. Loss of WWOX function has recently been associated with DNA damage repair abnormalities, increased genomic instability, and resistance to chemoradiotherapy. The described observations place WWOX both as a target of and a contributor to genomic instability. Both of these aspects will be discussed in this review.
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Affiliation(s)
- Tabish Hussain
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Morgan S Shrock
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Terence Williams
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - C Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
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Zhang Y, Yang G, Luo Y. Long non-coding RNA PVT1 promotes glioma cell proliferation and invasion by targeting miR-200a. Exp Ther Med 2018; 17:1337-1345. [PMID: 30680011 DOI: 10.3892/etm.2018.7083] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 12/14/2022] Open
Abstract
Glioma is a type of malignant tumor accounting for 80% of all brain cancer morbidity. The long non-coding RNA (lncRNA) PVT1 has been demonstrated to be an oncogenic lncRNA in other types of cancer. However, the role of PVT1 in glioma is still unknown. The aim of the present study was to investigate the role of PVT1 in glioma, and its potential association with microRNA (miR)-200a. miR-200a mimics and small interfering (si)RNA transfection were utilized to construct miR-200a overexpression and knockdown models to investigate the effect of miR-200a on glioma cells. Slow-virus infection was used to transfect cells. Western blotting and reverse transcription-quantitative polymerase chain reaction were applied for the quantitative analysis of mRNA and protein expression. Apoptosis of podocytes was detected by terminal deoxynucleotidyl-transferase-mediated dUTP nick end labelling staining. PVT1 expression in glioma was upregulated. In vitro, PVT1 silencing via transfection with si-PVT1 suppressed proliferation and invasion and induced G0/G1 phase arrest. Luciferase reporter assay revealed the association between miR-200a and the PVT1 3'-untranslated region. Furthermore, experiments examining both miR-200a and PVT1 indicated that miR-200a could reverse the effects of PVT1 on glioma cell phenotypes. The present study reveals the overexpression of PVT1 in glioma tissue and cells and the oncogenic role of PVT1 in gliomagenesis via sponging miR-200a, thus providing a potential biomarker for the early detection of glioma and prognosis prediction.
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Affiliation(s)
- Yonghong Zhang
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Gang Yang
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yicheng Luo
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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38
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Mizuno S, Hanamura I, Ota A, Karnan S, Kanasugi J, Nakamura A, Takasugi S, Uchino K, Horio T, Goto M, Murakami S, Gotou M, Yamamoto H, Watarai M, Shikami M, Hosokawa Y, Miwa H, Taniwaki M, Ueda R, Nitta M, Takami A. Establishment and characterization of a novel vincristine-resistant diffuse large B-cell lymphoma cell line containing the 8q24 homogeneously staining region. FEBS Open Bio 2018; 8:1977-1991. [PMID: 30524948 PMCID: PMC6275272 DOI: 10.1002/2211-5463.12538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/27/2022] Open
Abstract
Chromosome band 8q24 is the most frequently amplified locus in various types of cancers. MYC has been identified as the primary oncogene at the 8q24 locus, whereas a long noncoding gene, PVT1, which lies adjacent to MYC, has recently emerged as another potential oncogenic regulator at this position. In this study, we established and characterized a novel cell line, AMU‐ML2, from a patient with diffuse large B‐cell lymphoma (DLBCL), displaying homogeneously staining regions at the 8q24 locus. Fluorescence in situ hybridization clearly detected an elevation in MYC copy numbers corresponding to the homogenously staining region. In addition, a comparative genomic hybridization analysis using high‐resolution arrays revealed that the 8q24 amplicon size was 1.4 Mb, containing the entire MYC and PVT1 regions. We also demonstrated a loss of heterozygosity for TP53 at 17p13 in conjunction with a TP53 frameshift mutation. Notably, AMU‐ML2 cells exhibited resistance to vincristine, and cell proliferation was markedly inhibited by MYC‐shRNA‐mediated knockdown. Furthermore, genes involved in cyclin D, mTOR, and Ras signaling were downregulated following MYC knockdown, suggesting that MYC expression was closely associated with tumor cell growth. In conclusion, AMU‐ML2 cells are uniquely characterized by homogenously staining regions at the 8q24 locus, thus providing useful insights into the pathogenesis of DLBCL with 8q24 abnormalities.
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Affiliation(s)
- Shohei Mizuno
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Ichiro Hanamura
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Akinobu Ota
- Department of Biochemistry Aichi Medical University Japan
| | | | - Jo Kanasugi
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Ayano Nakamura
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Souichi Takasugi
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Kaori Uchino
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Tomohiro Horio
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Mineaki Goto
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Satsuki Murakami
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Mayuko Gotou
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Hidesuke Yamamoto
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Masaya Watarai
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Masato Shikami
- Department of Hematology Daiyukai General Hospital Aichi Japan
| | | | | | - Masafumi Taniwaki
- Department of Hematology and Oncology Graduate School of Medical Science Kyoto Prefectural University of Medicine Japan
| | - Ryuzo Ueda
- Department of Tumor Immunology Aichi Medical University School of Medicine Japan
| | - Masakazu Nitta
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Akiyoshi Takami
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
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39
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Yang Q, Shen X, Su Z, Ju S. Emerging roles of noncoding RNAs in multiple myeloma: A review. J Cell Physiol 2018; 234:7957-7969. [PMID: 30370557 DOI: 10.1002/jcp.27547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/13/2018] [Indexed: 01/06/2023]
Abstract
Multiple myeloma (MM) is a hematologic malignancy characterized by unrestricted secretion of monoclonal immunoglobulin and uncontrolled plasma cell proliferation. Extra-medullary infiltration and drug resistance are two major obstacles in the treatment of MM. To solve these problems, it is necessary to elucidate the underlying pathological mechanisms and find new therapeutic targets. Noncoding RNAs (ncRNAs), which were once considered "transcriptional noise," have been recognized as crucial regulators in the process of tumorigenesis including MM. Increasing evidence has shown that ncRNAs participate in MM pathogenesis via a series of complex cellular or extracellular processes. This review article summarizes examples of ncRNAs involved in myelosis and discusses their potential as biomarkers and therapeutic targets in the diagnosis and treatment of myelosis.
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Affiliation(s)
- Qian Yang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China.,Medical School of Nantong University, Nantong, China
| | - Xianjuan Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhangyao Su
- Medical School of Nantong University, Nantong, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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40
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Takimoto-Shimomura T, Nagoshi H, Maegawa S, Fujibayashi Y, Tsukamoto T, Matsumura-Kimoto Y, Mizuno Y, Chinen Y, Mizutani S, Shimura Y, Horiike S, Taniwaki M, Kobayashi T, Kuroda J. Establishment and Characteristics of a Novel Mantle Cell Lymphoma-derived Cell Line and a Bendamustine-resistant Subline. Cancer Genomics Proteomics 2018; 15:213-223. [PMID: 29695404 DOI: 10.21873/cgp.20080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/AIM Bendamustine hydrochloride (BH) is a key therapeutic agent for mantle cell lymphoma (MCL), while the mechanism underlying BH-resistance has not been verified. MATERIALS AND METHODS We compared molecular/biological characteristics of a newly-generated MCL-derived cell line KPUM-YY1 and its BH-resistant subline KPUM-YY1R. RESULTS The growth-inhibitory IC50 for BH was 20 μM in KPUM-YY1 cells, while cell proliferation was not inhibited by up to 60 μM BH in KPUM-YY1R cells. Compared to KPUM-YY1 cells, gene expression profiling in KPUM-YY1R cells revealed up-regulation of 312 genes, including ABCB1 encoding P-glycoprotein (P-gp), and microsomal glutathione S-transferase 1 (MGST1). Addition of either a P-gp inhibitor or a GST inhibitor, at least partly, restored sensitivity to BH in KPUM-YY1R cells. In addition, KPUM-YY1R cells showed cross-resistance against various anti-MCL chemotherapeutics. CONCLUSION BH resistance is mediated by overlapping mechanisms with overexpression of ABCB1 and MGST1, and is potentially accompanied by multidrug resistance in MCL.
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Affiliation(s)
- Tomoko Takimoto-Shimomura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hisao Nagoshi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Saori Maegawa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshimi Mizuno
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shinsuke Mizutani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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41
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Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell 2018; 173:1398-1412.e22. [PMID: 29731168 PMCID: PMC5984165 DOI: 10.1016/j.cell.2018.03.068] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/08/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Abstract
Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers suggest alternative mechanisms. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.
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MESH Headings
- Animals
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- CRISPR-Cas Systems
- Carcinogenesis/genetics
- Cell Line, Tumor
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromatin
- DNA, Neoplasm/genetics
- Enhancer Elements, Genetic
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, myc
- Humans
- Mice
- Mice, Inbred NOD
- Mutation
- Neoplasm Transplantation
- Promoter Regions, Genetic
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Transcription, Genetic
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Affiliation(s)
- Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Y Grace Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jeewon Kim
- Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Jing He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Stephanie A Nevins
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Breast Cancer Program, CRUK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 2QQ, UK
| | - S John Liu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA 94121, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
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42
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miR-1204 targets VDR to promotes epithelial-mesenchymal transition and metastasis in breast cancer. Oncogene 2018; 37:3426-3439. [DOI: 10.1038/s41388-018-0215-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 11/09/2017] [Accepted: 02/09/2018] [Indexed: 11/08/2022]
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43
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Arun G, Diermeier SD, Spector DL. Therapeutic Targeting of Long Non-Coding RNAs in Cancer. Trends Mol Med 2018; 24:257-277. [PMID: 29449148 PMCID: PMC5840027 DOI: 10.1016/j.molmed.2018.01.001] [Citation(s) in RCA: 424] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/09/2018] [Accepted: 01/14/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a significant population of the human transcriptome. Many lncRNAs exhibit cell- and/or tissue/tumor-specific expression, making them excellent candidates for therapeutic applications. In this review we discuss examples of lncRNAs that demonstrate the diversity of their function in various cancer types. We also discuss recent advances in nucleic acid drug development with a focus on oligonucleotide-based therapies as a novel approach to inhibit tumor progression. The increased success rates of nucleic acid therapeutics provide an outstanding opportunity to explore lncRNAs as viable therapeutic targets to combat various aspects of cancer progression.
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Affiliation(s)
- Gayatri Arun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; These authors contributed equally
| | - Sarah D Diermeier
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; These authors contributed equally
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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44
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MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences. Leukemia 2018; 32:2152-2166. [PMID: 29467491 PMCID: PMC6170393 DOI: 10.1038/s41375-018-0033-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/27/2017] [Accepted: 11/13/2017] [Indexed: 01/05/2023]
Abstract
Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene amplification in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of high-resolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp). This revealed that different MYC-dmin architectures can coexist within the same leukemic cell population, indicating a step-wise evolution rather than a single event origin, such as through chromothripsis. This was supported also by the analysis of the chromothripsis criteria, that poorly matched the model in our samples. Furthermore, we found that dmin could evolve toward ring chromosomes stabilized by neocentromeres. Surprisingly, amplified genes (mainly PVT1) frequently participated in fusion transcripts lacking a corresponding DNA template. We also detected a significant overexpression of the circular RNA of PVT1 (circPVT1) in AML-amp cases versus AML with a normal karyotype. Our results show that 8q24 amplicons in AML are surprisingly plastic DNA structures with an unexpected association to novel fusion transcripts and circular RNAs.
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45
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Lin M, Lee PL, Chiu L, Chua C, Ban KHK, Lin AHF, Chan ZL, Chung TH, Yan B, Chng WJ. Identification of novel fusion transcripts in multiple myeloma. J Clin Pathol 2018; 71:708-712. [PMID: 29453220 DOI: 10.1136/jclinpath-2017-204961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/06/2018] [Indexed: 01/21/2023]
Abstract
AIMS Multiple myeloma (MM) is a heterogeneous disease characterised by genetically complex abnormalities. The classical mutational spectrum includes recurrent chromosomal aberrations and gene-level mutations. Recurrent translocations involving the IGH gene such as t(11;14), t(4;14) and t(14;16) are well known. However, the presence of complex genetic abnormalities raises the possibility that fusions other than the recurrent IGH translocations exist. We therefore employed a targeted RNA-sequencing panel to identify novel putative fusions in a local cohort of MM. METHODS Targeted RNA-sequencing was performed on 21 patient samples using the Illumina TruSight RNA Pan-Cancer Panel (comprising 1385 genes). Fusion calls were generated from the Illumina RNA-Sequencing Alignment software (V.1.0.0). These samples had conventional cytogenetic and fluorescence in situ hybridisation data for the common recurrent chromosomal abnormalities (t(11;14), t(4;14), t(14;16) and 17p13 deletion). The MMRF CoMMpass dataset was analysed using the TopHat-fusion pipeline. RESULTS A total of 10 novel fusions were identified by the TruSight RNA Pan-Cancer Panel. Two of these fusions, HGF/CACNA2D1 and SMC3/MXI1, were validated by reverse transcription PCR and Sanger sequencing as they involve genes that may have biological relevance in MM genesis. Four of these (MAP2K4/MAP2K4P1) are likely to be spurious secondary to misalignment of reads to a pseudogene. One record of the HGF/CACNA2D1 fusion was identified from the MMRF CoMMpass dataset. CONCLUSIONS The identification of novel fusions offers insights into the biology of MM and might have clinical relevance. Further functional studies are required to determine the biological and clinical relevance of these novel fusions.
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Affiliation(s)
- Mingxuan Lin
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Peak Ling Lee
- Department of Laboratory Medicine, Cytogenetics Laboratory, National University Health System, Singapore, Singapore
| | - Lily Chiu
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Constance Chua
- Department of Laboratory Medicine, Cytogenetics Laboratory, National University Health System, Singapore, Singapore
| | - Kenneth H K Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Adeline H F Lin
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Zit Liang Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore.,Translational Centre for Development and Research, National University Health System, Singapore, Singapore
| | - Wee-Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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46
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Elotuzumab for the Treatment of Relapsed or Refractory Multiple Myeloma, with Special Reference to its Modes of Action and SLAMF7 Signaling. Mediterr J Hematol Infect Dis 2018. [PMID: 29531651 PMCID: PMC5841936 DOI: 10.4084/mjhid.2018.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Elotuzumab, targeting signaling lymphocytic activation molecule family 7 (SLAMF7), has been approved in combination with lenalidomide and dexamethasone (ELd) for relapsed/refractory multiple myeloma (MM) based on the findings of the phase III randomized trial ELOQUENT-2 (NCT01239797). Four-year follow-up analyses of ELOQUENT-2 have demonstrated that progression-free survival was 21% in ELd versus 14% in Ld. Elotuzumab binds a unique epitope on the membrane IgC2 domain of SLAMF7, exhibiting a dual mechanism of action: natural killer (NK) cell-mediated antibody-dependent cellular cytotoxicity (ADCC) and enhancement of NK cell activity. The ADCC is mediated through engagement between Fc portion of elotuzumab and FcgRIIIa/CD16 on NK cells. Enhanced NK cell cytotoxicity results from phosphorylation of the immunoreceptor tyrosine-based switch motif (ITSM) that is induced via elotuzumab binding and recruits the SLAM-associated adaptor protein EAT-2. The coupling of EAT-2 to the phospholipase Cg enzymes SH2 domain leads to enhanced Ca2+ influx and MAPK/Erk pathway activation, resulting in granule polarization and enhanced exocytosis in NK cells. Elotuzumab does not stimulate the proliferation of MM cells due to a lack of EAT-2. The inhibitory effects of elotuzumab on MM cell growth are not induced by the lack of CD45, even though SHP-2, SHP-1, SHIP-1, and Csk may be recruited to phosphorylated ITSM of SLAMF7. ELd improves PFS in patients with high-risk cytogenetics, i.e. t(4;14), del(17p), and 1q21 gain/amplification. Since the immune state is paralytic in advanced MM, the efficacy of ELd with minimal toxicity may bring forward for consideration of its use in the early stages of the disease.
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47
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Huang SS, Chang NS. Phosphorylation/de-phosphorylation in specific sites of tumor suppressor WWOX and control of distinct biological events. Exp Biol Med (Maywood) 2018; 243:137-147. [PMID: 29310447 DOI: 10.1177/1535370217752350] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Abnormal differentiation and growth of hematopoietic stem cells cause the development of hematopoietic diseases and hematopoietic malignancies. However, the molecular events underlying leukemia development are not well understood. In our recent study, we have demonstrated that calcium ionophore and phorbol ester force the differentiation of T lymphoblastic leukemia. The event involves a newly identified IκBα/WWOX/ERK signaling, in which WWOX is Ser14 phosphorylated. Additional evidence also reveals that pS14-WWOX is involved in enhancing cancer progression and metastasis and facilitating neurodegeneration. In this mini-review, we update the current knowledge for the functional roles of WWOX under physiological and pathological settings, and provide new insights regarding pS14-WWOX in T leukemia cell maturation, and switching the anticancer pY33-WWOX to pS14-WWOX for cancer promotion and disease progression. Impact statement WWOX was originally designated as a tumor suppressor. However, human newborns deficient in WWOX do not spontaneously develop tumors. Activated WWOX with Tyr33 phosphorylation is present in normal tissues and organs. However, when pY33-WWOX is overly induced under stress conditions, it becomes apoptotic to eliminate damaged cells. Notably, WWOX with Ser14 phosphorylation is upregulated in the lesions of cancer, as well as in the brain hippocampus and cortex with Alzheimer's disease. Suppression of pS14-WWOX by Zfra reduces cancer growth and mitigates Alzheimer's disease progression, suggesting that pS14-WWOX facilitates disease progression. pS14-WWOX can be regarded as a marker of disease progression.
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Affiliation(s)
- Shenq-Shyang Huang
- 1 Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC.,2 Graduate Program of Biotechnology in Medicine, Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Nan-Shan Chang
- 1 Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, ROC.,3 Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA.,4 Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan, ROC
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48
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Xu H, Gong J, Liu H. High expression of lncRNA PVT1 independently predicts poor overall survival in patients with primary uveal melanoma. PLoS One 2017; 12:e0189675. [PMID: 29244840 PMCID: PMC5731763 DOI: 10.1371/journal.pone.0189675] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/30/2017] [Indexed: 02/07/2023] Open
Abstract
The plasmacytoma variant translocation 1 gene (PVT1) plays an oncogenic role in the initiation and progression of multiple cancers. In this study, by using deep-sequencing data and follow-up data in the Cancer Genome Atlas-Uveal melanomas (TCGA-UVM), we assessed the association between the expression of PVT1 and clinicopathological characteristics of patients with uveal melanoma, the mechanism of its dysregulation and its prognostic value. Results showed that high PVT1 expression group had a higher proportion of epithelioid cell dominant disease (a more malignant histological subtype than spindle cell dominant disease) and more cases of extrascleral extension (a risk factor for metastasis) compared with the low PVT1 expression group. 61 out of 80 cases (76.3%) of primary uveal melanoma had PVT1 amplification in TCGA-UVM. In addition, PVT1 expression was strongly and negatively correlated with its methylation status (Pearson's r = -0.712, Spearman's r = -0.806). By performing univariate and multivariate analysis, we found that high PVT1 expression was an independent predictor of poor OS in patients with uveal melanoma (HR: 12.015, 95%CI: 1.854-77.876, p = 0.009). Based on these findings, we infer that PVT1 expression is modulated by both DNA amplification and methylation and its expression might serve as a valuable and specific prognostic biomarker in terms of OS in uveal melanoma.
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Affiliation(s)
- Haiming Xu
- Department of Ophthalmology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jingwen Gong
- Department of Ophthalmology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Hui Liu
- Department of Ophthalmology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
- * E-mail:
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49
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Wu P, Li T, Li R, Jia L, Zhu P, Liu Y, Chen Q, Tang D, Yu Y, Li C. 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations. Nat Commun 2017; 8:1937. [PMID: 29203764 PMCID: PMC5715138 DOI: 10.1038/s41467-017-01793-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 10/17/2017] [Indexed: 01/06/2023] Open
Abstract
The Hi-C method is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. Here, we integrate Hi-C, whole-genome sequencing (WGS) and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations. We find that CNV breakpoints significantly overlap with topologically associating domain (TAD) boundaries. Compared to normal B cells, the numbers of TADs increases by 25% in MM, the average size of TADs is smaller, and about 20% of genomic regions switch their chromatin A/B compartment types. In summary, we report a 3D genome interaction map of aneuploid MM cells and reveal the relationship among CNVs, translocations, 3D genome reorganization, and gene expression regulation. Chromosome conformation capture techniques enable the study of genome organization in cancer cells. Here, the authors use Hi-C, WGS, and RNA-seq to study the 3D genome of multiple myeloma and find that genome disorganization is associated with copy number variations and changes in gene expression.
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Affiliation(s)
- Pengze Wu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Tingting Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ruifeng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Lumeng Jia
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ping Zhu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yifang Liu
- PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qing Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Daiwei Tang
- PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuezhou Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China. .,Center for Statistical Science, Peking University, Beijing, 100871, China.
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50
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Qiu M, Feng D, Zhang H, Xia W, Xu Y, Wang J, Dong G, Zhang Y, Yin R, Xu L. Comprehensive analysis of lncRNA expression profiles and identification of functional lncRNAs in lung adenocarcinoma. Oncotarget 2017; 7:16012-22. [PMID: 26918601 PMCID: PMC4941294 DOI: 10.18632/oncotarget.7559] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 02/07/2016] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence has highlighted the critical roles of long non-coding RNAs (lncRNAs) as biomarkers and therapeutic targets for cancer. Here, we characterized lncRNA expression profile in lung adenocarcinoma (LUAD). A training-validation method was applied to identify differentially expressed lncRNAs between LUAD samples and normal samples. 856 differentially expressed lncRNAs were identified. Bioinformatics analyses showed that these lncRNAs were located nearby transcription start sites and key regulators of cancer and these lncRNAs were involved in many critical biological processes. We found the lung cancer associated lncRNA 6 (LCAL6) was significantly unregulated and predicted survival in LUAD. Silence of LCAL6 inhibited LUAD tumor cell growth both in vitro and in vivo. To summary, we comprehensively analyze lncRNA expression profile in LUAD and provide resources for further search for clinical biomarkers and therapeutic targets of LUAD.
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Affiliation(s)
- Mantang Qiu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Dongjie Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Haitian Zhang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Wenjia Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Youtao Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Jie Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,Department of Scientific Research, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,Department of Scientific Research, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Yewei Zhang
- Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Rong Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Lin Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
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