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Ali A, Mahla SB, Reza V, Hossein A, Bahareh K, Mohammad H, Fatemeh S, Mostafa AB, Leili R. MicroRNAs: Potential prognostic and theranostic biomarkers in chronic lymphocytic leukemia. EJHAEM 2024; 5:191-205. [PMID: 38406506 PMCID: PMC10887358 DOI: 10.1002/jha2.849] [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: 06/26/2023] [Revised: 12/13/2023] [Accepted: 12/29/2023] [Indexed: 02/27/2024]
Abstract
Small noncoding ribonucleic acids called microRNAs coordinate numerous critical physiological and biological processes such as cell division, proliferation, and death. These regulatory molecules interfere with the function of many genes by binding the 3'-UTR region of target mRNAs to inhibit their translation or even degrade them. Given that a large proportion of miRNAs behave as either tumor suppressors or oncogenes, any genetic or epigenetic aberration changeing their structure and/or function could initiate tumor formation and development. An example of such cancers is chronic lymphocytic leukemia (CLL), the most prevalent adult leukemia in Western nations, which is caused by unregulated growth and buildup of defective cells in the peripheral blood and lymphoid organs. Genetic alterations at cellular and molecular levels play an important role in the occurrence and development of CLL. In this vein, it was noted that the development of this disease is noticeably affected by changes in the expression and function of miRNAs. Many studies on miRNAs have shown that these molecules are pivotal in the prognosis of different cancers, including CLL, and their epigenetic alterations (e.g., methylation) can predict disease progression and response to treatment. Furthermore, miRNAs are involved in the development of drug resistance in CLL, and targeting these molecules can be considered a new therapeutic approach for the treatment of this disease. MiRNA screening can offer important information on the etiology and development of CLL. Considering the importance of miRNAs in gene expression regulation, their application in the diagnosis, prognosis, and treatment of CLL is reviewed in this paper.
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Affiliation(s)
- Afgar Ali
- Research Center for Hydatid Disease in IranKerman University of Medical SciencesKermanIran
| | - Sattarzadeh Bardsiri Mahla
- Stem Cells and Regenerative Medicine Innovation CenterKerman University of Medical SciencesKermanIran
- Department of Hematology and Laboratory Sciences, Faculty of Allied Medical SciencesKerman University of Medical SciencesKermanIran
| | - Vahidi Reza
- Research Center for Hydatid Disease in IranKerman University of Medical SciencesKermanIran
| | - Arezoomand Hossein
- Department of Hematology and Laboratory Sciences, Faculty of Allied Medical SciencesKerman University of Medical SciencesKermanIran
| | - Kashani Bahareh
- Department of Medical Genetics, School of MedicineTehran University of Medical SciencesTehranIran
| | - Hosseininaveh Mohammad
- Research Center for Hydatid Disease in IranKerman University of Medical SciencesKermanIran
| | - Sharifi Fatemeh
- Research Center of Tropical and Infectious DiseasesKerman University of Medical SciencesKermanIran
| | - Amopour Bahnamiry Mostafa
- Department of Research and Development, Production and Research ComplexPasteur Institute of IranTehranIran
| | - Rouhi Leili
- Student Research CommitteeKerman University of Medical SciencesKermanIran
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Fishov H, Muchtar E, Salmon‐Divon M, Dispenzieri A, Zvida T, Schneider C, Bender B, Duek A, Leiba M, Shpilberg O, Hershkovitz‐Rokah O. AL amyloidosis clonal plasma cells are regulated by microRNAs and dependent on anti-apoptotic BCL2 family members. Cancer Med 2023; 12:8199-8210. [PMID: 36694297 PMCID: PMC10134277 DOI: 10.1002/cam4.5621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Noncoding RNAs such as microRNAs (miRNAs) have attracted attention as biological pathway regulators, which differ from chromosomal translocations and gene point mutations. Their involvement in the molecular mechanisms underlying light chain (AL) amyloidosis pathogenesis is yet to be elucidated. AIMS To decipher specific miRNA expression profile in AL-amyloidosis and to examine how miRNAs are involved in AL pathogenesis. METHODS The expression profile of miRNAs and mRNA from bone marrow (BM)-derived CD138+ cells were determined using the NanoString nCounter assay and RNA-Seq, respectively. The effect of aberrantly expressed miRNAs on potential molecular targets was analyzed by qRT-PCR, Western blot, Mito-potential assay, and Annexin-PI staining. RESULTS Genes which were significantly differentially expressed between AL-amyloidosis and MM, were found to be involved in cell growth and apoptotic mechanisms. Specifically, BCL2L1, MCL1, and BCL2 were upregulated in AL-amyloidosis compared with MM and controls. The levels of miR-181a-5p and miR-9-5p, which regulate the above-mentioned genes, were lower in BM samples from AL-amyloidosis compared with controls, providing a mechanism for BCL2 family gene upregulation. When miR-9-5p and miR-181a-5p were overexpressed in ALMC1 cells, BCL2L1, MCL1, and BCL2 were downregulated and induced apoptosis. Treatment of ALMC-1 cells with venetoclax, (BCL-2 inhibitor), resulted in the upregulation of those miRNAs, the downregulation of BCL2, MCL1, and BCL2L1 mRNA and protein levels, and subsequent apoptosis. CONCLUSION Our findings suggest that miR-9-5p and miR-181a-5p act as tumor-suppressors whose downregulation induces anti-apoptotic mechanisms underlying the pathogenesis of AL-amyloidosis. The study highlights the post-transcriptional regulation in AL-amyloidosis and provides pathogenetic evidence for the potential use of BCL-2 inhibitors in this disease.
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Affiliation(s)
- Hila Fishov
- Department of Molecular Biology, Faculty of Natural SciencesAriel UniversityArielIsrael
- Translational Research Lab, Assuta Medical CentersTel‐AvivIsrael
| | - Eli Muchtar
- Division of HematologyDepartment of Internal Medicine, Mayo ClinicRochesterMinnesotaUSA
| | - Mali Salmon‐Divon
- Department of Molecular Biology, Faculty of Natural SciencesAriel UniversityArielIsrael
- Adelson School of MedicineAriel UniversityArielIsrael
| | - Angela Dispenzieri
- Division of HematologyDepartment of Internal Medicine, Mayo ClinicRochesterMinnesotaUSA
| | - Tal Zvida
- Department of Molecular Biology, Faculty of Natural SciencesAriel UniversityArielIsrael
- Translational Research Lab, Assuta Medical CentersTel‐AvivIsrael
| | | | | | - Adrian Duek
- Institute of HematologyAssuta Ashdod University Hospital, Faculty of Health Science Ben‐Gurion University of the NegevBeer ShevaIsrael
| | - Merav Leiba
- Institute of HematologyAssuta Ashdod University Hospital, Faculty of Health Science Ben‐Gurion University of the NegevBeer ShevaIsrael
| | - Ofer Shpilberg
- Translational Research Lab, Assuta Medical CentersTel‐AvivIsrael
- Adelson School of MedicineAriel UniversityArielIsrael
- Institute of Hematology, Assuta Medical CentersTel‐AvivIsrael
| | - Oshrat Hershkovitz‐Rokah
- Department of Molecular Biology, Faculty of Natural SciencesAriel UniversityArielIsrael
- Translational Research Lab, Assuta Medical CentersTel‐AvivIsrael
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Behera JK, Bhattacharya M, Mishra P, Mishra A, Dash AA, Kar NB, Behera B, Patra BC. Regulatory role of miRNAs in Wnt signaling pathway linked with cardiovascular diseases. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100133. [PMID: 36568258 PMCID: PMC9780067 DOI: 10.1016/j.crphar.2022.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/15/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are discovered in science about 23 years ago. These are short, a series of non-coding, single-stranded and evolutionary conserved RNA molecules found in eukaryotic cells. It involved post-transcriptional fine-tune protein expression and repressing the target of mRNA in different biological processes. These miRNAs binds with the 3'-UTR region of specific mRNAs to phosphorylate the mRNA degradation and inhibit the translation process in various tissues. Therefore, aberrant expression in miRNAs induces numerous cardiovascular diseases and developmental defects. Subsequently, the miRNAs and Wnt singling pathway are regulating a cellular process in cardiac development and regeneration, maintain the homeostasis and associated heart diseases. In Wnt signaling pathway majority of the signaling components are expressed and regulated by miRNAs, whereas the inhibition or dysfunction of the Wnt signaling pathway induces cardiovascular diseases. Moreover, inadequate studies about the important role of miRNAs in heart development and diseases through Wnt signaling pathway has been exist still now. For this reason in present review we summarize and update the involvement of miRNAs and the role of Wnt signaling in cardiovascular diseases. We have discussed the mechanism of miRNA functions which regulates the Wnt components in cellular signaling pathway. The fundamental understanding of Wnt signaling regulation and mechanisms of miRNAs is quite essential for study of heart development and related diseases. This approach definitely enlighten the future research to provide a new strategy for formulation of novel therapeutic approaches against cardiovascular diseases.
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Affiliation(s)
- Jiban Kumar Behera
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756089, Odisha, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756089, Odisha, India
| | - Pabitra Mishra
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756089, Odisha, India
| | - Akansha Mishra
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756089, Odisha, India
| | - Adya Anindita Dash
- Department of Biosciences and Biotechnology, Fakir Mohan University, Vyasa Vihar, Balasore, 756089, Odisha, India
| | - Niladri Bhusan Kar
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756089, Odisha, India
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Vyasa Vihar, Balasore, 756089, Odisha, India
| | - Bidhan Chandra Patra
- Department of Zoology, Vidyasagar University, Midnapore, 721102, West Bengal, India
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Sbirkov Y, Vergov B, Mehterov N, Sarafian V. miRNAs in Lymphocytic Leukaemias-The miRror of Drug Resistance. Int J Mol Sci 2022; 23:ijms23094657. [PMID: 35563051 PMCID: PMC9103677 DOI: 10.3390/ijms23094657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
Refractory disease and relapse remain the main causes of cancer therapy failure. Refined risk stratification, treatment regimens and improved early diagnosis and detection of minimal residual disease have increased cure rates in malignancies like childhood acute lymphoblastic leukaemia (ALL) to 90%. Nevertheless, overall survival in the context of drug resistance remains poor. The regulatory role of micro RNAs (miRNAs) in cell differentiation, homeostasis and tumorigenesis has been under extensive investigation in different cancers. There is accumulating data demonstrating the significance of miRNAs for therapy outcomes in lymphoid malignancies and some direct demonstrations of the interplay between these small molecules and drug response. Here, we summarise miRNAs' impact on chemotherapy resistance in adult and paediatric ALL and chronic lymphocytic leukaemia (CLL). The main focus of this review is on the modulation of particular signaling pathways like PI3K-AKT, transcription factors such as NF-κB, and apoptotic mediators, all of which are bona fide and pivotal elements orchestrating the survival of malignant lymphocytic cells. Finally, we discuss the attractive strategy of using mimics, antimiRs and other molecular approaches pointing at miRNAs as promising therapeutic targets. Such novel strategies to circumvent ALL and CLL resistance networks may potentially improve patients' responses and survival rates.
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Affiliation(s)
- Yordan Sbirkov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: (Y.S.); (V.S.)
| | - Bozhidar Vergov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: (Y.S.); (V.S.)
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Das D, Karthik N, Taneja R. Crosstalk Between Inflammatory Signaling and Methylation in Cancer. Front Cell Dev Biol 2021; 9:756458. [PMID: 34901003 PMCID: PMC8652226 DOI: 10.3389/fcell.2021.756458] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023] Open
Abstract
Inflammation is an intricate immune response against infection and tissue damage. While the initial immune response is important for preventing tumorigenesis, chronic inflammation is implicated in cancer pathogenesis. It has been linked to various stages of tumor development including transformation, proliferation, angiogenesis, and metastasis. Immune cells, through the production of inflammatory mediators such as cytokines, chemokines, transforming growth factors, and adhesion molecules contribute to the survival, growth, and progression of the tumor in its microenvironment. The aberrant expression and secretion of pro-inflammatory and growth factors by the tumor cells result in the recruitment of immune cells, thus creating a mutual crosstalk. The reciprocal signaling between the tumor cells and the immune cells creates and maintains a successful tumor niche. Many inflammatory factors are regulated by epigenetic mechanisms including DNA methylation and histone modifications. In particular, DNA and histone methylation are crucial forms of transcriptional regulation and aberrant methylation has been associated with deregulated gene expression in oncogenesis. Such deregulations have been reported in both solid tumors and hematological malignancies. With technological advancements to study genome-wide epigenetic landscapes, it is now possible to identify molecular mechanisms underlying altered inflammatory profiles in cancer. In this review, we discuss the role of DNA and histone methylation in regulation of inflammatory pathways in human cancers and review the merits and challenges of targeting inflammatory mediators as well as epigenetic regulators in cancer.
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Affiliation(s)
- Dipanwita Das
- Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nandini Karthik
- Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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de Assis CS, Silva AS, Dos Santos Nunes MK, Filho JM, do Nascimento RAF, Gomes CNAP, de Queiroga Evangelista IW, de Oliveira NFP, Persuhn DC. Methylation Profile of miR-9-1 and miR-9-1/-9-3 as Potential Biomarkers of Diabetic Retinopathy. Curr Diabetes Rev 2021; 17:e123120189795. [PMID: 33388023 DOI: 10.2174/1573399817666210101104326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/17/2020] [Accepted: 10/23/2020] [Indexed: 11/22/2022]
Abstract
AIMS Analysis of the relationship between the methylation profile of miR-9-1 or miRs -9-1 / -9-3 and diabetic retinopathy. BACKGROUND Diabetic Retinopathy (DR) is a frequent complication of Diabetes mellitus and it has a decisive impact on the quality of life, as it is one of the biggest causes of blindness in the adult population. Levels of microRNA-9 have been shown to be related to diabetes but little is known about its involvement with DR in humans. OBJECTIVE To analyze the relationship between the methylation profile of miR-9-1 or miRs -9-1/-9-3 and DR. METHODS 103 patients diagnosed with diabetes for 5 to 10 years were analyzed. The data were categorized according to clinical, biochemical, lifestyle and anthropometric parameters. DNA extracted from leukocyte samples was used to determine the methylation profile of miRs-9-1 and -9-3 using a specific methylation PCR assay. RESULTS miR-9-1 methylation was related to diabetic retinopathy, indicating that methylation of this miR increases the chances of presenting retinopathy up to 5 times. In our analyses, diabetics with lower levels of creatinine and CRP showed significant reductions (99% and 97%) in presenting DR. Methylation of both miRs-9-1 and 9-3 methylated increases the chances of presenting DR by 8 times; in addition, a sedentary lifestyle can increase the risk for the same complication by up to 6 times. CONCLUSION Our results suggest that both methylation of miR-9-1 and e miRs-9-1 / 9-3 favors DR in patients with diabetes in a period of 5 to 10 years of diagnosis.
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Affiliation(s)
| | | | - Mayara Karla Dos Santos Nunes
- Post-Graduation Program in Development and Technological Innovation of Medicines (DITM), Federal University of Paraiba, Joao Pessoa, Brazil
| | - João Modesto Filho
- Department of Internal Medicine, Federal University of Paraiba, Joao Pessoa, Brazil
| | | | | | | | | | - Darlene Camati Persuhn
- Department of Molecular Biology and Post-Graduation Program in Nutrition Science, Federal University of Paraiba, Joao Pessoa, Brazil
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Chebly A, Chouery E, Ropio J, Kourie HR, Beylot-Barry M, Merlio JP, Tomb R, Chevret E. Diagnosis and treatment of lymphomas in the era of epigenetics. Blood Rev 2020; 48:100782. [PMID: 33229141 DOI: 10.1016/j.blre.2020.100782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/05/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Lymphomas represent a heterogeneous group of cancers characterized by clonal lymphoproliferation. Over the past decades, frequent epigenetic dysregulations have been identified in hematologic malignancies including lymphomas. Many of these impairments occur in genes with established roles and well-known functions in the regulation and maintenance of the epigenome. In hematopoietic cells, these dysfunctions can result in abnormal DNA methylation, erroneous chromatin state and/or altered miRNA expression, affecting many different cellular functions. Nowadays, it is evident that epigenetic dysregulations in lymphoid neoplasms are mainly caused by genetic alterations in genes encoding for enzymes responsible for histone or chromatin modifications. We summarize herein the recent epigenetic modifiers findings in lymphomas. We focus also on the most commonly mutated epigenetic regulators and emphasize on actual epigenetic therapies.
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Affiliation(s)
- Alain Chebly
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Eliane Chouery
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon
| | - Joana Ropio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Porto University, Institute of Biomedical Sciences of Abel Salazar, 4050-313 Porto, Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Institute of Molecular Pathology and Immunology (Ipatimup), Cancer Biology group, 4200-465 Porto, Portugal
| | - Hampig Raphael Kourie
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Hematology-Oncology Department, Beirut, Lebanon
| | - Marie Beylot-Barry
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Dermatology Department, 33000 Bordeaux, France
| | - Jean-Philippe Merlio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France; Bordeaux University Hospital Center, Tumor Bank and Tumor Biology Laboratory, 33600 Pessac, France
| | - Roland Tomb
- Saint Joseph University, Faculty of Medicine, Medical Genetics Unit (UGM), Beirut, Lebanon; Saint Joseph University, Faculty of Medicine, Dermatology Department, Beirut, Lebanon
| | - Edith Chevret
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, F-33000 Bordeaux, France.
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Zhang MY, Calin GA, Yuen KS, Jin DY, Chim CS. Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy. Clin Epigenetics 2020; 12:150. [PMID: 33076962 PMCID: PMC7574348 DOI: 10.1186/s13148-020-00926-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/25/2020] [Indexed: 12/24/2022] Open
Abstract
Background miR-342-3p, localized to 14q32, is a tumor suppressor miRNA implicated in carcinogenesis. Given the presence of a promotor-associated CpG island for its host gene, EVL, we hypothesized that intronic miR-342-3p is a tumor suppressor co-regulated with host gene by promoter DNA methylation in B cell lymphoma. Results By bisulfite pyrosequencing-verified methylation-specific PCR (MSP), EVL/MIR342 methylation was detected in five (50%) lymphoma cell lines but not normal peripheral blood and tonsils. EVL/MIR342 methylation correlated with repression of both miR-342-3p and EVL in cell lines. In completely methylated SU-DHL-16 cells, 5-AzadC treatment resulted in promoter demethylation and re-expression of miR-342-3p and EVL. In 132 primary lymphoma samples, EVL/MIR342 was preferentially methylated in B cell lymphomas (N = 68; 68.7%) than T cell lymphoma (N = 8; 24.2%) by MSP (P < 0.0001). Moreover, EVL/MIR342 methylation was associated with lower miR-342-3p expression in 79 primary NHL (P = 0.0443). In SU-DHL-16 cells, the tumor suppressor function of miR-342-3p was demonstrated by the inhibition of cellular proliferation and increase of cell death upon over-expression of miR-342-3p. Mechanistically, overexpression of miR-342-3p resulted in a decrease of LC3-II, a biomarker of autophagy, which was pro-survival for SU-DHL-16. Pre-treatment with 3-methyladenine, an autophagy inhibitor, abrogated tumor suppression associated with miR-342-3p overexpression. By luciferase assay, MAP1LC3B, a precursor of LC3-II, was confirmed as a direct target of miR-342-3p. Finally, in SU-DHL-16 cells, overexpression of miR-342-3p downregulated the known target DNMT1, with promoter demethylation and re-expression of tumor suppressor E-cadherin. Conclusions Intronic miR-342-3p is co-regulated with its host gene EVL by tumor-specific promoter DNA methylation in B cell lymphoma. The tumor suppressor function of miR-342-3p was mediated via inhibition of pro-survival autophagy by targeting MAP1LC3B and downregulation of DNMT1 with demethylation and re-expression of tumor suppressor genes.
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Affiliation(s)
- Min Yue Zhang
- Division of Hematology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kit San Yuen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
| | - Dong Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
| | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong.
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Tomesz A, Szabo L, Molnar R, Deutsch A, Darago R, Mathe D, Budan F, Ghodratollah N, Varjas T, Nemeth B, Kiss I. Effect of 7,12-Dimethylbenz(α)anthracene on the Expression of miR-330, miR-29a, miR-9-1, miR-9-3 and the mTORC1 Gene in CBA/Ca Mice. In Vivo 2020; 34:2337-2343. [PMID: 32871758 DOI: 10.21873/invivo.12046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND/AIM Development of malignant tumors is preceded by molecular biological events. Our aim was to establish an assay panel by using miRNAs and other genes for the rapid screening of potential carcinogens or chemopreventive agents. MATERIALS AND METHODS Six male and 6 female CBA/Ca mice received 20 mg/bwkg 7,12-dimethylbenz(α)anthracene (DMBA) intraperitoneally, and 24 h later RNA was isolated from parenchymal organs. Expression of miR-330, miR-29a, miR-9-1, miR-9-3 and mTORC1 was analysed by real time polymerase chain reaction and compared to non-treated controls. RESULTS DMBA caused significant alterations in the expression of the studied genes. The most profound changes were the strongly elevated miR-9-3 and mTORC1 expressions in female mice in all organs studied. CONCLUSION miR-9-3 and mTORC1 expression in female mice were found to be the most suitable biomarkers for rapid identification of possible carcinogenic effects.
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Affiliation(s)
- Andras Tomesz
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary .,Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Laszlo Szabo
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary.,Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Richard Molnar
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary.,Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Arpad Deutsch
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Richard Darago
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Domokos Mathe
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ferenc Budan
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary.,Institute of Environmental Engineering, University of Pannonia, Veszprém, Hungary
| | | | - Timea Varjas
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Balazs Nemeth
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Istvan Kiss
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
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Li Z, Kumar S, Jin DY, Calin GA, Chng WJ, Siu KL, Poon MW, Chim CS. Epigenetic silencing of long non-coding RNA BM742401 in multiple myeloma: impact on prognosis and myeloma dissemination. Cancer Cell Int 2020; 20:403. [PMID: 32855620 PMCID: PMC7446116 DOI: 10.1186/s12935-020-01504-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/18/2020] [Indexed: 12/31/2022] Open
Abstract
Background Long non-coding RNA (lncRNA) BM742401 is a tumor suppressor in gastric cancer and chronic lymphocytic leukemia. As the promoter and coding region of BM742401 are fully embedded in a CpG island, we hypothesized that BM742401 is a tumor suppressor lncRNA epigenetically silenced by promoter DNA methylation in multiple myeloma. Methods Methylation-specific PCR and quantitative bisulfite pyrosequencing were performed to detect the methylation of BM742401 in normal plasma cells, myeloma cell lines and primary myeloma samples. The expression of BM742401 was measured by qRT-PCR. The function of BM742401 in multiple myeloma cells was analyzed by lentivirus transduction followed by migration assay. Results BM742401 methylation was detected in 10 (66.7%) myeloma cell lines but not normal plasma cells, and inversely correlated with expression of BM742401. In primary samples, BM742401 methylation was detected in 3 (12.5%) monoclonal gammopathy of undetermined significance, 9 (15.8%) myeloma at diagnosis and 8 (17.0%) myeloma at relapse/progression. Moreover, BM742401 methylation at diagnosis was associated with inferior overall survival (median OS: 25 vs. 39 months; P = 0.0496). In myeloma cell line JJN-3, stable overexpression of BM742401 by lentivirus transduction resulted in reduced cell migration (P = 0.0001) but not impacting cell death or proliferation. Conclusions This is the first report of tumor-specific methylation-mediated silencing of BM742401 in myeloma, which is likely an early event in myelomagenesis with adverse impact on overall survival. Moreover, BM742401 is a tumor suppressor lncRNA by inhibiting myeloma cell migration, hence implicated in myeloma plasma cell homing, metastasis and disease progression.
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Affiliation(s)
- Zhenhai Li
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China.,Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, China
| | - Shaji Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN USA
| | - Dong-Yan Jin
- School of Biomedical Sciences, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Wee-Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
| | - Kam-Leung Siu
- School of Biomedical Sciences, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Ming-Wai Poon
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, China
| | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, China
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11
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Chakraborty C, Sharma AR, Sharma G, Lee SS. The Interplay among miRNAs, Major Cytokines, and Cancer-Related Inflammation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:606-620. [PMID: 32348938 PMCID: PMC7191126 DOI: 10.1016/j.omtn.2020.04.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022]
Abstract
Inflammation is closely related with the progression of cancer and is an indispensable component that orchestrates the tumor microenvironment. Studies suggest that different mediator and cellular effectors, including cytokines (interleukins, tumor necrosis factor-α [TNF-α], transforming growth factor-β [TGF-β], and granulocyte macrophage colony-stimulating factor [GM-CSF]), chemokines, as well as some transcription factors (nuclear factor κB [NF-κB], signal transducer and activator of transcription 3 [STAT3], hypoxia-inducible factor-1α [HIF1α]), play a crucial role during cancer-related inflammation (CRI). MicroRNAs (miRNAs) are the key components of cellular physiology. They play notable roles during posttranscriptional gene regulation and, thus, might have a potential role in controlling the inflammatory cascade during cancer progression. Taking into consideration the role identified for miRNAs in relation to inflammatory cytokines, we have tried to review their participation in neoplastic progression. Additionally, the involvement of miRNAs with some important transcription factors (NF-κB, STAT3, HIF1α) and proteins (cyclooxygenase-2 [COX-2], inducible nitric oxide synthase [iNOS]) closely associated with inflammation during cancer has also been discussed. A clear insight into the responsibility of miRNAs in cytokine signaling and inflammation related to CRI could project them as new therapeutic molecules, which could lead to improved treatment of CRI in the near future.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126, India; Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
| | - Garima Sharma
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
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12
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Wu X, Zou S, Wu F, He Z, Kong W. Role of microRNA in inner ear stem cells and related research progress. AMERICAN JOURNAL OF STEM CELLS 2020; 9:16-24. [PMID: 32419976 PMCID: PMC7218733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Deafness is one of the major global health problems that seriously affects the quality of human life. At present, there are no successful treatments for deafness caused by cochlear hair cell (HC) damage. The irreversibility of mammalian hearing impairment is that the inner ear's sensory epithelium cannot repair lost hair cells and neurons through spontaneous regeneration. The goal of stem cell therapy for sensorineural hearing loss is to reconstruct the damaged inner ear structure and achieve functional repair. microRNA (miRNA), as a class of highly conserved endogenous non-coding small RNAs, plays an important role in the development of cochlea and HCs. miRNA also participates in the regulation of stem cell proliferation and differentiation, and plays an important role in the process of regeneration of inner ear HCs, miRNA has a broad application prospect of clinical treatment of hearing loss, which is conducive to solving the medical problem of inner ear HC regeneration.
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Affiliation(s)
- Xia Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, P. R. China
| | - Shengyu Zou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, P. R. China
| | - Fan Wu
- Otorhinolaryngology Department, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University107 West Yan Jiang Road, Guangzhou 510120, P. R. China
| | - Zuhong He
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, P. R. China
| | - Weijia Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, P. R. China
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13
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Luo J, Xie Y, Zheng Y, Wang C, Qi F, Hu J, Xu Y. Comprehensive insights on pivotal prognostic signature involved in clear cell renal cell carcinoma microenvironment using the ESTIMATE algorithm. Cancer Med 2020; 9:4310-4323. [PMID: 32311223 PMCID: PMC7300420 DOI: 10.1002/cam4.2983] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 01/30/2020] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence has highlighted that the immune and stromal cells formed the majority of tumor microenvironment (TME) which are served as important roles in tumor progression. In our study, we aimed to screen vital prognostic signature associated with TME in clear cell renal cell carcinoma (ccRCC). We obtained total 611 samples from TCGA database consisting of transcriptome profiles and clinical data. ESTIMATE algorithm was applied to estimate the infiltrating fractions of immune/stromal cells. We found that the immune scores revealed more prognostic significance in overall survival and positive associations with risk clinical factors than stromal scores. We carried out differential expression analysis between Immunescore and stromalscore groups to obtain the 72 intersect genes. Protein to protein interaction (PPI) network and functional analysis was performed to indicate potential altered pathways. Additionally, we further conducted multivariate Cox analysis to identify 12 hub genes associated highly with TME of ccRCC using a stepwise regression procedure. Accordingly, risk score was constructed from the multivariate Cox results and Receiver Operating Characteristic (ROC) curve was used to assess the predictive value (AUC = 0.781). The ccRCC patients with high risk scores suffered poor survival outcomes than that with low risk scores. In the validation cohort from GSE53757, TNFSF13B, CASP5, and GJB6 correlated positively with tumor stages, while FREM1 negatively correlated with tumor stages. Importantly, we further observed that TNFSF13B, CASP5 and XCR1 showed the remarkable correlations with tumor‐infiltrating immune cells. Taken together, our research identified specific signatures that related to the infiltration of stromal and immune cells in TME of ccRCC using the transciptome profiles, which reached a comprehensive understanding of tumor microenvironment in ccRCC.
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Affiliation(s)
- Jun Luo
- Department of Urology, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Yi Xie
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yuxiao Zheng
- Department of Urology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University, Nanjing, China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Feng Qi
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiateng Hu
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yaoting Xu
- Department of Urology, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, China
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14
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Wierzbinska JA, Toth R, Ishaque N, Rippe K, Mallm JP, Klett LC, Mertens D, Zenz T, Hielscher T, Seifert M, Küppers R, Assenov Y, Lutsik P, Stilgenbauer S, Roessner PM, Seiffert M, Byrd J, Oakes CC, Plass C, Lipka DB. Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL. Genome Med 2020; 12:29. [PMID: 32188505 PMCID: PMC7081711 DOI: 10.1186/s13073-020-00724-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
Background In cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset, and progression. The cancer epigenome is composed of the epigenetic patterns present in the tumor-initiating cell at the time of transformation, and the tumor-specific epigenetic alterations that are acquired during tumor initiation and progression. The precise dissection of these two components of the tumor epigenome will facilitate a better understanding of the biological mechanisms underlying malignant transformation. Chronic lymphocytic leukemia (CLL) originates from differentiating B cells, which undergo extensive epigenetic programming. This poses the challenge to precisely determine the epigenomic ground state of the cell-of-origin in order to identify CLL-specific epigenetic aberrations. Methods We developed a linear regression model, methylome-based cell-of-origin modeling (Methyl-COOM), to map the cell-of-origin for individual CLL patients based on the continuum of epigenomic changes during normal B cell differentiation. Results Methyl-COOM accurately maps the cell-of-origin of CLL and identifies CLL-specific aberrant DNA methylation events that are not confounded by physiologic epigenetic B cell programming. Furthermore, Methyl-COOM unmasks abnormal action of transcription factors, altered super-enhancer activities, and aberrant transcript expression in CLL. Among the aberrantly regulated transcripts were many genes that have previously been implicated in T cell biology. Flow cytometry analysis of these markers confirmed their aberrant expression on malignant B cells at the protein level. Conclusions Methyl-COOM analysis of CLL identified disease-specific aberrant gene regulation. The aberrantly expressed genes identified in this study might play a role in immune-evasion in CLL and might serve as novel targets for immunotherapy approaches. In summary, we propose a novel framework for in silico modeling of reference DNA methylomes and for the identification of cancer-specific epigenetic changes, a concept that can be broadly applied to other human malignancies. Electronic supplementary material Supplementary information accompanies this paper at 10.1186/s13073-020-00724-7.
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Affiliation(s)
- Justyna A Wierzbinska
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,The German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Naveed Ishaque
- The German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Karsten Rippe
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Jan-Philipp Mallm
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Lara C Klett
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Daniel Mertens
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Mechanisms of Leukemogenesis, DKFZ, Heidelberg, Germany
| | - Thorsten Zenz
- Experimental Hematology Lab, University Hospital Zurich, Zurich, Switzerland
| | | | - Marc Seifert
- Group Molecular Genetics, Essen University Hospital, Essen, Germany
| | - Ralf Küppers
- Group Molecular Genetics, Essen University Hospital, Essen, Germany
| | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | | | | | | | - John Byrd
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, USA
| | - Christopher C Oakes
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, USA
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,The German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Daniel B Lipka
- The German Cancer Consortium (DKTK), Heidelberg, Germany. .,Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Faculty of Medicine, Medical Center, Otto-von-Guericke-University, 39120, Magdeburg, Germany.
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15
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Javandoost E, Firoozi-Majd E, Rostamian H, Khakpoor-Koosheh M, Mirzaei HR. Role of microRNAs in Chronic Lymphocytic Leukemia Pathogenesis. Curr Med Chem 2020; 27:282-297. [PMID: 31544709 DOI: 10.2174/0929867326666190911114842] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/20/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are a group of small endogenous non-coding RNAs involved in many cancers and various cellular processes such as cellular growth, DNA methylation, apoptosis, and differentiation. 13q14.3 chromosomal region contains miR-15 and miR-16 and deletion of this region is a commonly reported aberration in Chronic Lymphoblastic Leukemia (CLL), suggesting miRNAs involvement in CLL pathogenesis. MicroRNAs are known as oncogenes and tumor suppressors in CLL which may also serve as markers of onset and progression of the disease. The most prevalent form of leukemia diagnosed in adults in the western world, chronic lymphocytic leukemia, accounts for one-third of all leukemias. CLL is characterized by the presence of B Cell Malignant Clones in secondary lymphoid tissues, peripheral blood and bone marrow. The precise etiology of CLL is remained to be known, however, a number of Chromosomal Abnormalities such as deletions of 13q14.3, 11q and 17p and trisomy 12 have been detected. In this review, we offer our prospect on how miRNAs are involved in the CLL pathogenesis and disease progression. Further understanding of the underlying mechanisms and regulation of CLL pathogenesis has underscored the need for further research regarding their role in this disease.
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Affiliation(s)
- Ehsan Javandoost
- Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Firoozi-Majd
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hosein Rostamian
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Khakpoor-Koosheh
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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16
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Wang LQ, Kumar S, Calin GA, Li Z, Chim CS. Frequent methylation of the tumour suppressor miR-1258 targeting PDL1: implication in multiple myeloma-specific cytotoxicity and prognostification. Br J Haematol 2020; 190:249-261. [PMID: 32079038 DOI: 10.1111/bjh.16517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/10/2020] [Indexed: 12/17/2022]
Abstract
miR-1258 is localised to the first intron of ZNF385B at chromosome 2q31.3. miR-1258 promoter methylation was studied in 147 samples including 10 normal buffy coat, eight normal bone marrow plasma cells, 16 human myeloma cell lines (HMCLs), 20 MGUS, 63 diagnostic myeloma, and 30 relapsed myeloma samples by methylation-specific PCR. In myeloma lines, miR-1258 methylation, verified by pyrosequencing, was detected in 62·5% HMCLs but not normal controls, and expression of miR-1258 correlated with that of ZNF385B. 5-Aza-2'-deoxycytidine resulted in promoter demethylation and ZNF385B/miR-1258 re-expression. Luciferase assay confirmed programmed cell death ligand-1 (PDL1) as a direct target of miR-1258. Over-expression of miR-1258 in completely methylated myeloma cells led to reduced cellular proliferation and enhanced apoptosis, hence a tumour suppressor role, in addition to repression of PDL1. In primary samples, miR-1258 methylation, with lower expression of miR-1258, was detected in 49·2% diagnostic myeloma, imparting an inferior PFS (P = 0·034) in addition to 50·0% relapsed myeloma but not MGUS. Therefore, miR-1258 is a tumour suppressor miRNA co-regulated with its host gene, and frequently hypermethylated in active myeloma instead of MGUS, hence acquired during myeloma progression. Methylation-mediated miR-1258 silencing led to overexpression of PDL1 and inferior PFS, implicating miR-1258 in the modulation of myeloma-specific cytotoxicity.
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Affiliation(s)
- Lu Q Wang
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Shaji Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenhai Li
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Chor S Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
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17
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Huang G, Liu X, Zhao X, Zhao J, Hao J, Ren J, Chen Y. MiR-9 promotes multiple myeloma progression by regulating TRIM56/NF-κB pathway. Cell Biol Int 2019; 43:1223-1233. [PMID: 30637864 DOI: 10.1002/cbin.11104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 01/11/2019] [Indexed: 12/14/2022]
Abstract
miR-9 has been reported to play a pivotal role in multiple human cancers by acting as an oncogene or tumor suppressor. In this study, we explored the possible role and molecular mechanism of miR-9 in multiple myeloma (MM). The miR-9 expression was examined by quantitative real-time polymerase chain reaction assay. Transfection with miR-9-mimics, miR-9-inhibitor, pcDNA-TRIM56, or si-TRIM56 into cells was used to change the expression levels of miR-9 and TRIM56. Western blot analysis was used to detect the expression of TRIM56, p65, p-p65, IκBα, and p-IκBα. The potential target of miR-9 was confirmed by luciferase reporter assay. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay, colony formation assay, and flow cytometry were used to assess the abilities of cell proliferation and apoptosis. miR-9 was upregulated in MM patients and cell lines, and miR-9 overexpression promoted proliferation and repressed apoptosis in MM cell lines. TRIM56 was confirmed as a target of miR-9. Moreover, TRIM56 reversed miR-9-mediated pro-proliferation and anti-apoptosis effect on MM cell lines. Furthermore, nuclear factor-κB (NF-κB) pathway was involved in miR-9/TRIM56-mediated regulation on MM cell lines. miR-9 promoted the development and progression of MM by regulating TRIM56/NF-κB pathway, thereby providing a potential microRNA-based target for MM therapy.
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Affiliation(s)
- Guoqiang Huang
- Department of Hematology, Hanzhong Central Hospital, Hanzhong, 723000, China
| | - Xiaopeng Liu
- Department of Hematology, Hanzhong Central Hospital, Hanzhong, 723000, China
| | - Xiaoying Zhao
- Department of Hematology, Hanzhong Central Hospital, Hanzhong, 723000, China
| | - Jing Zhao
- Department of Hematology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China
| | - Jinxia Hao
- Department of Hematology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China
| | - Juan Ren
- Department of Hematology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China
| | - Ying Chen
- Department of Hematology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China
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18
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Li Z, Wong KY, Calin GA, Chng WJ, Chan GCF, Chim CS. Epigenetic silencing of miR-340-5p in multiple myeloma: mechanisms and prognostic impact. Clin Epigenetics 2019; 11:71. [PMID: 31064412 PMCID: PMC6505104 DOI: 10.1186/s13148-019-0669-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/25/2019] [Indexed: 12/31/2022] Open
Abstract
Background miR-340-5p, localized to 5q35, is a tumor suppressor miRNA implicated in multiple cancers. As a CpG island is present at the putative promoter region of its host gene, RNF130, we hypothesized that the intronic miR-340-5p is a tumor suppressor miRNA epigenetically silenced by promoter DNA methylation of its host gene in multiple myeloma. Results By pyrosequencing-confirmed methylation-specific PCR, RNF130/miR-340 was methylated in 8/15 (53.3%) myeloma cell lines but not normal plasma cells. Methylation correlated inversely with the expression of both miR-340-5p and RNF130. In completely methylated WL-2 and RPMI-8226R cells, 5-AzadC treatment led to demethylation and re-expression of miR-340-5p. In primary samples, RNF130/miR-340 methylation was detected in 4 (22.2%) monoclonal gammopathy of undetermined significance, 15 (23.8%) diagnostic myeloma, and 7 (23.3%) relapsed myeloma. RNF130/miR-340 methylation at diagnosis was associated with inferior overall survival (median 27 vs. 68 months; P = 3.944E−5). In WL-2 cells, overexpression of miR-340-5p resulted in reduced cellular proliferation [MTS, P = 0.002; verified in KMS-12-PE (P = 0.002) and RPMI-8226R (P = 2.623E−05) cells], increased cell death (trypan blue, P = 0.005), and enhanced apoptosis by annexin V-PI staining. Moreover, by qRT-PCR, overexpression of miR-340-5p led to repression of both known targets (CCND1 and NRAS) and bioinformatically predicted targets in MAPK signaling (MEKK1, MEKK2, and MEKKK3) and apoptosis (MDM4 and XIAP), hence downregulation of phospho-ERK1/2 and XIAP by Western blot. Furthermore, by qRT-PCR, in CD138-sorted primary samples (n = 37), miR-340-5p and XIAP were inversely correlated (P = 0.002). By luciferase assay, XIAP was confirmed as a direct target of miR-340-5p via targeting of the distal but not proximal seed region binding site. Conclusions Collectively, tumor-specific methylation-mediated silencing of miR-340-5p is likely an early event in myelomagenesis with adverse survival impact, via targeting multiple oncogenes in MAPK signaling and apoptosis, thereby a tumor suppressive miRNA in myeloma. Electronic supplementary material The online version of this article (10.1186/s13148-019-0669-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenhai Li
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
| | - Kwan Yeung Wong
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Godfrey Chi-Fung Chan
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong.
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19
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Liu WL. MicroRNA-9 inhibits retinal neovascularization in rats with diabetic retinopathy by targeting vascular endothelial growth factor A. J Cell Biochem 2019; 120:8032-8043. [PMID: 30485520 DOI: 10.1002/jcb.28081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
Diabetic retinopathy (DR) is a leading cause of adult visual impairment and loss. This study aims to explore the effects of microRNA-9 (miR-9) on retinal neovascularization during DR by targeting the vascular endothelial growth factor A (VEGFA). DR rat models were successfully established. Retinal microvascular endothelial cells (RMECs) of DR rats were isolated and treated with miR-9 mimic, miR-9 inhibitor or small interfering RNA (siRNA)-VEGFA. The expressions of miR-9, VEGFA, and cluster of differentiation 31 (CD31) of the rats' tissues and cells were examined. The targeting relationship between miR-9 and VEGFA was testified. The tubule formation, the cell proliferation and the periodic distribution and apoptosis were evaluated after transfection. In the retinal tissues of DR rats, miR-9 expression decreased while the expression of VEGFA and CD31 increased. Notably, miR-9 targeted and inhibited VEGFA expression. In response to the treatment of miR-9 mimic and siRNA-VEGFA, a reduction was identified in CD31 expression, tubule formation, and proliferation of RMECs and cell ratio in the S phase, but an increase was observed in apoptosis rate of RMECs. The treatment of miR-9 inhibitor reversed the manifestations. Our study demonstrated that miR-9 could inhibit retinal neovascularization of DR and tubule formation, and promote apoptosis in RMECs by targeting VEGFA.
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Affiliation(s)
- Wen-Lan Liu
- Optometry Education & Research Office, College of Medical Technology, Xi'an Medical University, Xi'an, China
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20
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Roy R, Chatterjee A, Das D, Ray A, Singh R, Chattopadhyay E, Sarkar ND, Eccles M, Pal M, Maitra A, Roy B. Genome-wide miRNA methylome analysis in oral cancer: possible biomarkers associated with patient survival. Epigenomics 2019; 11:473-487. [PMID: 30875235 DOI: 10.2217/epi-2018-0078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM The methylome associated with miRNA loci was investigated in oral cancer to explore tobacco specific methylation and potential biomarkers for patient survival. METHODS Methylome data was generated from 16 pairs of cancer-normal tissues by reduced representation bisulfite sequencing method. Differentially methylated regions were identified using the DMAP pipeline. In silico validation and Kaplan-Meier survival analyses were performed on The Cancer Genome Atlas data based on our miRNA methylome data. RESULTS A total of 4310 unique differentially methylated regions, mapping to 144 miRNA loci, were identified. Three distinct groups of miRNAs were differentially methylated in cancer tissues from smokers, chewers and mixed habitués. Hypermethylation of miR-503, miR-200a/b, miR-320b and miR-489 was associated with worse 5-year survival. CONCLUSION Differential methylation patterns in miRNA loci are associated with poor survival underscoring their potential as predictive and prognostic biomarkers in oral cancer.
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Affiliation(s)
- Roshni Roy
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Aniruddha Chatterjee
- HB Division, Fred Hutchinson Cancer Research Centre, Seattle, WA 98109-1024, USA
| | - Debasis Das
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Anindita Ray
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Richa Singh
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Esita Chattopadhyay
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Navonil De Sarkar
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand.,Department of Oral & Maxillofacial Pathology, Guru Nanak Institute of Dental Science & Research, Kolkata, India
| | - Michael Eccles
- HB Division, Fred Hutchinson Cancer Research Centre, Seattle, WA 98109-1024, USA
| | - Mousumi Pal
- National Institute of Biomedical Genomics, Kalyani, 741251, India
| | - Arindam Maitra
- Human Genetics Unit, Indian Statistical Institute, 205 B.T. Road, Kolkata 700108, India
| | - Bidyut Roy
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
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21
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Hardeland R. Aging, Melatonin, and the Pro- and Anti-Inflammatory Networks. Int J Mol Sci 2019; 20:ijms20051223. [PMID: 30862067 PMCID: PMC6429360 DOI: 10.3390/ijms20051223] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/17/2022] Open
Abstract
Aging and various age-related diseases are associated with reductions in melatonin secretion, proinflammatory changes in the immune system, a deteriorating circadian system, and reductions in sirtuin-1 (SIRT1) activity. In non-tumor cells, several effects of melatonin are abolished by inhibiting SIRT1, indicating mediation by SIRT1. Melatonin is, in addition to its circadian and antioxidant roles, an immune stimulatory agent. However, it can act as either a pro- or anti-inflammatory regulator in a context-dependent way. Melatonin can stimulate the release of proinflammatory cytokines and other mediators, but also, under different conditions, it can suppress inflammation-promoting processes such as NO release, activation of cyclooxygenase-2, inflammasome NLRP3, gasdermin D, toll-like receptor-4 and mTOR signaling, and cytokine release by SASP (senescence-associated secretory phenotype), and amyloid-β toxicity. It also activates processes in an anti-inflammatory network, in which SIRT1 activation, upregulation of Nrf2 and downregulation of NF-κB, and release of the anti-inflammatory cytokines IL-4 and IL-10 are involved. A perhaps crucial action may be the promotion of macrophage or microglia polarization in favor of the anti-inflammatory phenotype M2. In addition, many factors of the pro- and anti-inflammatory networks are subject to regulation by microRNAs that either target mRNAs of the respective factors or upregulate them by targeting mRNAs of their inhibitor proteins.
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Affiliation(s)
- Rüdiger Hardeland
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, 37073 Göttingen, Germany.
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22
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Kiani S, Akhavan-Niaki H, Fattahi S, Kavoosian S, Babaian Jelodar N, Bagheri N, Najafi Zarrini H. Purified sulforaphane from broccoli (Brassica oleracea var. italica) leads to alterations of CDX1 and CDX2 expression and changes in miR-9 and miR-326 levels in human gastric cancer cells. Gene 2018; 678:115-123. [DOI: 10.1016/j.gene.2018.08.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/06/2018] [Indexed: 02/08/2023]
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23
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Xue Y, Li M, Liu D, Zhu Q, Chen H. Expression of miR-9 in the serum of patients with acute ischemic stroke and its effect on neuronal damage. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:5885-5892. [PMID: 31949675 PMCID: PMC6963079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/09/2018] [Indexed: 06/10/2023]
Abstract
BACKGROUND This research was aimed to measure the expression of miR-9 in serum of acute ischemic stroke (AIS) patients and explore the role of miR-9 on OGD-induced neuronal damage. METHODS In the present study, we measured the expression of miR-9 in serum of 65 AIS patients by real-time quantitative PCR (RT-qPCR) and the effect of miR-9 on oxygen-glucose deprivation (OGD)-induced neuronal injury was detected by CCK-8 in vitro. Western blot was used to measure the expression of protein. RESULTS We found that the serum level of miR-9 in 65 AIS patients was significantly higher than that in control group (no-AIS), and was positively correlated with NIHSS score (r=0.627, P<0.001), infarct volume ((r=0.576, P<0.001), serum IL-8 (r=0.376, P=0.002), TNF-α (r=0.418, P<0.001), IL-6 (r=0.545, P<0.001), and IL-1β (r=0.592, P<0.001). miR-9 expression levels were upregulated in cultured neurons with OGD treatment. The downregulation of miR-9 significantly alleviated OGD-induced neuronal injury. Dual-luciferase reporter assay demonstrated that SIRT1 was a target gene of miR-9, and miR-9 negatively regulated SIRT 1 expression and positively regulated p65 expression. CONCLUSIONS All in all, our data showed that downregulation of miR-9 protected neurons against OGD/R-induced injury by the SIRT1-mediated NF-kB pathway.
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Affiliation(s)
- Yufeng Xue
- Department of Neurology, Tai Zhou First People’s HospitalChina
| | - Min Li
- Department of Neurology, Tai Zhou First People’s HospitalChina
| | - Donghong Liu
- Department of Laboratory, Tai Zhou First People’s HospitalChina
| | - Qibing Zhu
- Department of Pharmacy, Tai Zhou First People’s HospitalChina
| | - Huijun Chen
- Department of Pharmacy, Tai Zhou First People’s HospitalChina
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24
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Bardin P, Marchal-Duval E, Sonneville F, Blouquit-Laye S, Rousselet N, Le Rouzic P, Corvol H, Tabary O. Small RNA and transcriptome sequencing reveal the role of miR-199a-3p in inflammatory processes in cystic fibrosis airways. J Pathol 2018; 245:410-420. [DOI: 10.1002/path.5095] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/11/2018] [Accepted: 04/26/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Pauline Bardin
- Sorbonne Université, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint Antoine (CRSA); Paris France
| | - Emmeline Marchal-Duval
- Sorbonne Université, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint Antoine (CRSA); Paris France
| | - Florence Sonneville
- Sorbonne Université, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint Antoine (CRSA); Paris France
| | - Sabine Blouquit-Laye
- Université de Versailles Saint Quentin en Yvelines; UFR des Sciences de la Santé, UMR 1173; Montigny-Le-Bretonneux France
| | - Nathalie Rousselet
- Sorbonne Université, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint Antoine (CRSA); Paris France
| | - Philippe Le Rouzic
- Sorbonne Université, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint Antoine (CRSA); Paris France
| | - Harriet Corvol
- Sorbonne Université, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint Antoine (CRSA); Paris France
- Hôpital Trousseau; Paediatric Respiratory Department, AP-HP; Paris France
| | - Olivier Tabary
- Sorbonne Université, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint Antoine (CRSA); Paris France
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25
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Liu K, Beck D, Thoms JAI, Liu L, Zhao W, Pimanda JE, Zhou X. Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. Bioinformatics 2018; 33:2622-2630. [PMID: 28472271 DOI: 10.1093/bioinformatics/btx280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/22/2017] [Indexed: 02/01/2023] Open
Abstract
Motivation Long non-coding RNAs (lncRNAs) have been implicated in the regulation of diverse biological functions. The number of newly identified lncRNAs has increased dramatically in recent years but their expression and function have not yet been described from most diseases. To elucidate lncRNA function in human disease, we have developed a novel network based method (NLCFA) integrating correlations between lncRNA, protein coding genes and noncoding miRNAs. We have also integrated target gene associations and protein-protein interactions and designed our model to provide information on the combined influence of mRNAs, lncRNAs and miRNAs on cellular signal transduction networks. Results We have generated lncRNA expression profiles from the CD34+ haematopoietic stem and progenitor cells (HSPCs) from patients with Myelodysplastic syndromes (MDS) and healthy donors. We report, for the first time, aberrantly expressed lncRNAs in MDS and further prioritize biologically relevant lncRNAs using the NLCFA. Taken together, our data suggests that aberrant levels of specific lncRNAs are intimately involved in network modules that control multiple cancer-associated signalling pathways and cellular processes. Importantly, our method can be applied to prioritize aberrantly expressed lncRNAs for functional validation in other diseases and biological contexts. Availability and implementation The method is implemented in R language and Matlab. Contact xizhou@wakehealth.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Keqin Liu
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Dominik Beck
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia.,Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Julie A I Thoms
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia
| | - Liang Liu
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Weiling Zhao
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - John E Pimanda
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia.,Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, 2007, Australia.,Department of Haematology, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Xiaobo Zhou
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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26
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Dos Santos Nunes MK, Silva AS, Wanderley de Queiroga Evangelista I, Modesto Filho J, Alves Pegado Gomes CN, Ferreira do Nascimento RA, Pordeus Luna RC, de Carvalho Costa MJ, Paulo de Oliveira NF, Camati Persuhn D. Analysis of the DNA methylation profiles of miR-9-3, miR-34a, and miR-137 promoters in patients with diabetic retinopathy and nephropathy. J Diabetes Complications 2018; 32:593-601. [PMID: 29674133 DOI: 10.1016/j.jdiacomp.2018.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/28/2018] [Accepted: 03/25/2018] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - João Modesto Filho
- Department of Internal Medicine, Federal University of Paraiba, Joao Pessoa, Brazil
| | | | | | | | - Maria José de Carvalho Costa
- Nutrition Science Department and Post-graduate Program in Nutrition Science, Federal University of Paraiba, Joao Pessoa, Brazil
| | | | - Darlene Camati Persuhn
- Department of Molecular Biology and Post-Graduation Program in Nutrition Science, Federal University of Paraiba, Joao Pessoa, Brazil.
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27
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Zang Y, Yu R, Bai Y, Chen X. MicroRNA-9 suppresses cancer proliferation and cell cycle progression in acute lymphoblastic leukemia with inverse association of neuropilin-1. J Cell Biochem 2018; 119:6604-6613. [PMID: 29693748 DOI: 10.1002/jcb.26799] [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: 12/17/2017] [Accepted: 02/21/2018] [Indexed: 12/26/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is one of the most common and most malign childhood cancers. In this work, we investigated the expression and function of human mature microRNA-9 (miR-9) in ALL. In ALL in vitro cell lines and in situ clinical specimens, gene expression of miR-9 was tested by qRT-PCR. MiR-9 was overexpressed in CEM/C1 and Molt-3 cells to investigate its possible anti-cancer effects on ALL in vitro proliferation, cell-cycle progression, and in vivo explant growth. The possible downstream target of miR-9, neuropilin-1 (NRP1), was examined by dual-luciferase activity assay, qRT-PCR, and Western blot. NRP1was upregulated in miR-9-overexpressed CEM/C1 and Molt-3 cells to investigate the functional involvement of NRP1 in miR-9-mediated regulation on ALL in vitro proliferation and cell-cycle progression. MiR-9 was downregulated in ALL cell lines and leukemic T-cells of ALL patients. Lentivirus-mediated miR-9 overexpression inhibited ALL in vitro proliferation, cell-cycle progression, and in vivo explant growth. NRP1 was confirmed be the downstream target of miR-9, and inversely modulated by miR-9 in ALL. NRP1 upregulation reversed the anti-cancer regulations of miR-9 on ALL in vitro proliferation and cell-cycle progression. MiR-9 is downregulated in ALL. Overexpressing miR-9 may inhibit ALL development, possible through its downstream target of NRP1.
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Affiliation(s)
- Yuzhu Zang
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Runhong Yu
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Yanliang Bai
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xiangli Chen
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, Henan, China
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28
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Silva MBD, Melo ARDS, Costa LDA, Barroso H, Oliveira NFPD. Global and gene-specific DNA methylation and hydroxymethylation in human skin exposed and not exposed to sun radiation. An Bras Dermatol 2018; 92:793-800. [PMID: 29364434 PMCID: PMC5786392 DOI: 10.1590/abd1806-4841.20175875] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/07/2016] [Indexed: 12/19/2022] Open
Abstract
Background epigenomes can be influenced by environmental factors leading to the
development of diseases. Objective To investigate the influence of sun exposure on global DNA methylation and
hydroxymethylation status and at specific sites of the miR-9-1, miR-9-3 and
MTHFR genes in skin samples of subjects with no history of skin
diseases. Methods Skin samples were obtained by punch on sun-exposed and sun-protected arm
areas from 24 corpses of 16-89 years of age. Genomic DNA was extracted from
skin samples that were ranked according to Fitzpatrick's criteria as light,
moderate, and dark brown. Global DNA methylation and hydroxymethylation and
DNA methylation analyses at specific sites were performed using ELISA and
MSP, respectively. Results No significant differences in global DNA methylation and hydroxymethylation
levels were found among the skin areas, skin types, or age. However,
gender-related differences were detected, where women showed higher
methylation levels. Global DNA methylation levels were higher than
hydroxymethylation levels, and the levels of these DNA modifications
correlated in skin tissue. For specific sites, no differences among the
areas were detected. Additional analyses showed no differences in the
methylation status when age, gender, and skin type were considered; however,
the methylation status of the miR-9-1 gene seems to be gender related. Study limitations there was no separation of dermis and epidermis and low sample size. Conclusion sun exposure does not induce changes in the DNA methylation and
hydroxymethylation status or in miR-9-1, miR-9-3 and MTHFR genes for the
studied skin types.
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Affiliation(s)
- Mikaelly Batista da Silva
- Center for Exact Sciences and Nature, Post-graduate Program in Cellular and Molecular Biology, Universidade Federal da Paraíba (UFPB) -Paraíba, (PB), Brazil
| | - Alanne Rayssa da Silva Melo
- Center for Exact Sciences and Nature, Post-graduate Program in Cellular and Molecular Biology, Universidade Federal da Paraíba (UFPB) -Paraíba, (PB), Brazil
| | - Ludimila de Araújo Costa
- Center for Exact Sciences and Nature, Post-graduate Program in Cellular and Molecular Biology, Universidade Federal da Paraíba (UFPB) -Paraíba, (PB), Brazil
| | - Haline Barroso
- Center for Exact Sciences and Nature, Post-graduate Program in Cellular and Molecular Biology, Universidade Federal da Paraíba (UFPB) -Paraíba, (PB), Brazil
| | - Naila Francis Paulo de Oliveira
- Center for Exact Sciences and Nature, Post-graduate Program in Cellular and Molecular Biology, Universidade Federal da Paraíba (UFPB) -Paraíba, (PB), Brazil
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29
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Nowek K, Wiemer EA, Jongen-Lavrencic M. The versatile nature of miR-9/9 * in human cancer. Oncotarget 2018; 9:20838-20854. [PMID: 29755694 PMCID: PMC5945517 DOI: 10.18632/oncotarget.24889] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/26/2018] [Indexed: 12/22/2022] Open
Abstract
miR-9 and miR-9* (miR-9/9*) were first shown to be expressed in the nervous system and to function as versatile regulators of neurogenesis. The variable expression levels of miR-9/9* in human cancer prompted researchers to investigate whether these small RNAs may also have an important role in the deregulation of physiological and biochemical networks in human disease. In this review, we present a comprehensive overview of the involvement of miR-9/9* in various human malignancies focusing on their opposing roles in supporting or suppressing tumor development and metastasis. Importantly, it is shown that the capacity of miR-9/9* to impact tumor formation is independent from their influence on the metastatic potential of tumor cells. Moreover, data suggest that miR-9/9* may increase malignancy of one cancer cell population at the expense of another. The functional versatility of miR-9/9* emphasizes the complexity of studying miRNA function and the importance to perform functional studies of both miRNA strands in a relevant cellular context. The possible application of miR-9/9* as targets for miRNA-based therapies is discussed, emphasizing the need to obtain a better understanding of the functional properties of these miRNAs and to develop safe delivery methods to target specific cell populations.
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Affiliation(s)
- Katarzyna Nowek
- Department of Hematology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erik A.C. Wiemer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mojca Jongen-Lavrencic
- Department of Hematology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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30
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Malpeli G, Barbi S, Greco C, Zupo S, Bertolaso A, Scupoli MT, Krampera M, Kamga PT, Croce CM, Scarpa A, Zamò A. MicroRNA signatures and Foxp3 + cell count correlate with relapse occurrence in follicular lymphoma. Oncotarget 2018; 9:19961-19979. [PMID: 29731996 PMCID: PMC5929439 DOI: 10.18632/oncotarget.24987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/30/2018] [Indexed: 12/29/2022] Open
Abstract
First line drug treatment of follicular lymphoma (FL) patients is followed by a highly variable disease-free time before relapse in about one third of patients. No molecular marker is able to predict efficiently the risk of relapse. We investigated the expression profile of microRNAs (miRNAs) by microarrays and of the tumor microenvironment by immunohistochemistry in 26 FLs and 12 reactive lymph nodes (rLN) as reference. Twenty-nine miRNAs were differentially expressed in FLs compared to rLNs and some of them discriminated grade 1 from 3a FLs. Both FLs and rLNs displayed molecular heterogeneity. FLs grouped into two clusters mostly driven by the tumor T-cell content. Among 21 drug-treated FL patients with an average follow-up of 13.5 years, eight cases relapsed. Twenty-six miRNAs discriminated between relapsed and non-relapsed FLs. Ten miRNAs also correlated with Foxp3+ cells number. Notably, Foxp3+ cells were significantly less in relapsed patients and lower Foxp3+ cell number associated with shorter time-to-relapse. Foxp3+ cells did not co-expressed follicular helper T-cell markers and were therefore classified as regulatory T cells rather than follicular regulatory T-cells. These findings introduce new knowledge about the relationship between miRNA alterations and infiltrating immune cells and show that Foxp3+ cells might be predictive of disease relapse.
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Affiliation(s)
- Giorgio Malpeli
- 1 Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Section of Surgery, University of Verona, Verona, Italy
- 2 Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Stefano Barbi
- 2 Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Corinna Greco
- 3 Department of Medicine, Section of Hematology, Stem Cell Research Laboratory, University of Verona, Italy
| | - Simonetta Zupo
- 4 Laboratory of Molecular Diagnostics, IRCCS-AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Anna Bertolaso
- 2 Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria Teresa Scupoli
- 5 Department of Medicine, Section of Hematology, University of Verona, Verona, Italy
| | - Mauro Krampera
- 3 Department of Medicine, Section of Hematology, Stem Cell Research Laboratory, University of Verona, Italy
| | - Paul Takam Kamga
- 3 Department of Medicine, Section of Hematology, Stem Cell Research Laboratory, University of Verona, Italy
| | - Carlo Maria Croce
- 6 Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Aldo Scarpa
- 2 Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- 7 Applied Research on Cancer-Network, ARC-NET, University of Verona, Verona, Italy
| | - Alberto Zamò
- 2 Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- 8 Department of Oncology, University of Torino, Torino, Italy
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31
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Epigenetic silencing of tumor suppressor long non-coding RNA BM742401 in chronic lymphocytic leukemia. Oncotarget 2018; 7:82400-82410. [PMID: 27689399 PMCID: PMC5347700 DOI: 10.18632/oncotarget.12252] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 09/20/2016] [Indexed: 11/25/2022] Open
Abstract
BM742401 is a tumor suppressor lncRNA downregulated in gastric cancer. As the promoter region and the entire transcript are embedded in a CpG island, we postulated that BM742401 is a tumor suppressor lncRNA inactivated by DNA methylation in chronic lymphocytic leukemia (CLL). The promoter of BM742401 was unmethylated in normal controls including three each of normal bone marrow, peripheral blood buffy coats, and CD19-sorted peripheral B-cells, but methylated in four (57.1%) CLL cell lines. Methylation of BM742401 correlated inversely with expression. In the completely methylated WAC3CD5+ CLL cells, 5-Aza-2′-deoxycytidine treatment led to promoter demethylation and re-expression of BM742401 transcript. Functionally, stable overexpression of BM742401 resulted in inhibition of cellular proliferation and enhanced apoptosis through caspase-9-dependent intrinsic but not caspase-8-dependent extrinsic apoptosis pathway, suggesting a tumor suppressor role of BM742401 in CLL. In primary CLL samples, methylation of BM742401 was detected in 43/98 (43.9%) of patients. Moreover, among CLL patients with standard-risk cytogenetic aberrations, methylation of BM742401 correlated with advanced Rai stage (≥ stage 2)(P = 0.002). Furthermore, BM742401 methylation was associated with miR-129-2 methylation (P = 0.05). BM742401 is a tumor suppressor lncRNA frequently methylated in CLL. The mechanism of BM742401 as a tumor suppressor warrants further studies.
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32
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Gao L, Cheng D, Yang J, Wu R, Li W, Kong AN. Sulforaphane epigenetically demethylates the CpG sites of the miR-9-3 promoter and reactivates miR-9-3 expression in human lung cancer A549 cells. J Nutr Biochem 2018. [PMID: 29525530 DOI: 10.1016/j.jnutbio.2018.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Increasing evidence suggests that epigenetic aberrations contribute to the development and progression of cancers such as lung cancer. The promoter region of miR-9-3 was recently found to be hypermethylated in lung cancer, resulting in down-regulation of miR-9-3 and poor patient prognosis. Sulforaphane (SFN), a natural compound that is obtained from cruciferous vegetables, has potent anticancer activities. In this study, we aimed to investigate the effect of SFN on restoring the miR-9-3 level in lung cancer A549 cells through epigenetic regulation. DNA methylation of the miR-9-3 promoter was examined using bisulfite genomic sequencing and methylated DNA immunoprecipitation analysis. The expression levels of miR-9-3 and several epigenetic modifying enzymes were measured using quantitative real-time polymerase chain reaction and Western blotting, respectively. The transcriptional activity of the miR-9-3 promoter was evaluated by patch methylation, and histone modifications were analyzed using chromatin immunoprecipitation (ChIP) assays. We found that CpG methylation was reduced in the miR-9-3 promoter and that miR-9-3 expression was increased after 5 days of treatment with SFN. In vitro methylation analysis showed that the methylated recombinant construct exhibited lower luciferase reporter activity than the unmethylated counterpart. ChIP assays revealed that SFN treatment increased H3K4me1 enrichment at the miR-9-3 promoter. Furthermore, SFN treatment attenuated enzymatic DNMT activity and DNMT3a, HDAC1, HDAC3, HDAC6 and CDH1 protein expression. Taken together, these findings indicate that SFN may exert its chemopreventive effects partly through epigenetic demethylation and restoration of miR-9-3.
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Affiliation(s)
- Linbo Gao
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David Cheng
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jie Yang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wenji Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Mansouri L, Wierzbinska JA, Plass C, Rosenquist R. Epigenetic deregulation in chronic lymphocytic leukemia: Clinical and biological impact. Semin Cancer Biol 2018; 51:1-11. [PMID: 29427646 DOI: 10.1016/j.semcancer.2018.02.001] [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: 06/08/2017] [Revised: 12/12/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023]
Abstract
Deregulated transcriptional control caused by aberrant DNA methylation and/or histone modifications is a hallmark of cancer cells. In chronic lymphocytic leukemia (CLL), the most common adult leukemia, the epigenetic 'landscape' has added a new layer of complexity to our understanding of this clinically and biologically heterogeneous disease. Early studies identified aberrant DNA methylation, often based on single gene promoter analysis with both biological and clinical impact. Subsequent genome-wide profiling studies revealed differential DNA methylation between CLLs and controls and in prognostics subgroups of the disease. From these studies, it became apparent that DNA methylation in regions outside of promoters, such as enhancers, is important for the regulation of coding genes as well as for the regulation of non-coding RNAs. Although DNA methylation profiles are reportedly stable over time and in relation to therapy, a higher epigenetic heterogeneity or 'burden' is seen in more aggressive CLL subgroups, albeit as non-recurrent 'passenger' events. More recently, DNA methylation profiles in CLL analyzed in relation to differentiating normal B-cell populations revealed that the majority of the CLL epigenome reflects the epigenomes present in the cell of origin and that only a small fraction of the epigenetic alterations represents truly CLL-specific changes. Furthermore, CLL patients can be grouped into at least three clinically relevant epigenetic subgroups, potentially originating from different cells at various stages of differentiation and associated with distinct outcomes. In this review, we summarize the current understanding of the DNA methylome in CLL, the role of histone modifying enzymes, highlight insights derived from animal models and attempts made to target epigenetic regulators in CLL along with the future directions of this rapidly advancing field.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden
| | - Justyna Anna Wierzbinska
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden.
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Li Z, Wong KY, Chan GCF, Chng WJ, Chim CS. Epigenetic silencing of EVL/miR-342 in multiple myeloma. Transl Res 2018; 192:46-53. [PMID: 29242101 DOI: 10.1016/j.trsl.2017.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/28/2022]
Abstract
miR-342-3p, localized to 14q32, is a tumor suppressor miRNA implicated in multiple cancers. As the promoter region of its host gene, EVL, is embedded in a CpG island, we postulated that miR-342-3p is an intronic miRNA co-regulated with its host gene by promoter DNA methylation in multiple myeloma (MM). By methylation-specific polymerase chain reaction, verified by quantitative bisulfite pyrosequencing, methylation of EVL/miR-342 was absent in all healthy controls (n = 10) and 12 of 15 (80%) human myeloma cell lines (HMCLs), but partially methylated in 3 of 15 (20%) HMCLs, including KMS-12-PE, OCI-MY5, and RPMI-8226R. In HMCLs, by real-time quantitative reverse transcription-polymerase chain reaction, methylation of EVL/miR-342 correlated with lower expression of both EVL (P = 0.013) and miR-342-3p (P = 0.023). Moreover, in KMS-12-PE and RPMI-8226R cells, both partially methylated for EVL/miR-342, 5-AzadC treatment led to demethylation of EVL/miR-342 and re-expression of miR-342-3p. Upon removal of 5-AzadC, continuous culture resulted in restoration of EVL/miR-342 methylation and downregulation of miR-342-3p. In primary samples, methylation of EVL/miR-342 was detected in 1 of 18 (5.6%) monoclonal gammopathy of undetermined significance (MGUS), 8 of 63 (12.7%) diagnostic MM, and 5 of 30 (16.7%) relapsed MM. EVL/miR-342 methylation was preferentially detected in IgD MM but not found to impact survival. Collectively, in MM, miR-342-3p is an intronic miRNA regulated by promoter DNA methylation of its host gene, EVL, in a tumor-specific manner. Methylation of EVL/miR-342 was present in consecutive stages of myelomagenesis including MGUS, diagnostic MM, and relapsed MM.
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Affiliation(s)
- Zhenhai Li
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Kwan Yeung Wong
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Godfrey Chi-Fung Chan
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong.
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Khosravi A, Alizadeh S, Jalili A, Shirzad R, Saki N. The impact of Mir-9 regulation in normal and malignant hematopoiesis. Oncol Rev 2018; 12:348. [PMID: 29774136 PMCID: PMC5939831 DOI: 10.4081/oncol.2018.348] [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: 12/25/2017] [Accepted: 03/01/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-9 (MiR-9) dysregulation has been observed in various cancers. Recently, MiR-9 is considered to have a part in hematopoiesis and hematologic malignancies. However, its importance in blood neoplasms is not yet well defined. Thus, this study was conducted in order to assess the significance of MiR-9 role in the development of hematologic neoplasia, prognosis, and treatment approaches. We have shown that a large number of MiR-9 targets (such as FOXOs, SIRT1, CCND1, ID2, CCNG1, Ets, and NFkB) play essential roles in leukemogenesis and that it is overexpressed in different leukemias. Our findings indicated MiR-9 downregulation in a majority of leukemias. However, its overexpression was reported in patients with dysregulated MiR-9 controlling factors (such as MLLr). Additionally, prognostic value of MiR-9 has been reported in some types of leukemia. This study generally emphasizes on the critical role of MiR-9 in hematologic malignancies as a prognostic factor and a therapeutic target.
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Affiliation(s)
- Abbas Khosravi
- Transfusion Research Center, High Institute for Research and Education in Transfusion Medi-cine, Tehran
| | - Shaban Alizadeh
- Hematology Department, Allied Medical School, Tehran University of Medical Sciences, Tehran
| | - Arsalan Jalili
- Department of Stem Cells and Developmental Biology at Cell Science Re-search Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran
| | - Reza Shirzad
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran
| | - Najmaldin Saki
- Thalassemia & Hemoglobinopathy Research Center, Research Institute of Health, Ahvaz Jun-dishapur University of Medical Sciences, Ahvaz, Iran
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Li Z, Wong KY, Chan GCF, Chim CS. Epigenetic silencing of LPP/miR-28 in multiple myeloma. J Clin Pathol 2017; 71:253-258. [PMID: 28775176 PMCID: PMC5868533 DOI: 10.1136/jclinpath-2017-204501] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 12/15/2022]
Abstract
Aims miR-28-5- is a tumour suppressor microRNA implicated in cancers. As a CpG island is absent in miR-28-5- but present in its host gene, LPP (LIM domain containing preferred translocation partner in lipoma), we hypothesized that miR-28-5p is epigenetically silenced by promoter DNA methylation of its host gene in multiple myeloma. Methods Methylation-specific PCR, verified by quantitative bisulfite pyrosequencing, was employed to study methylation of LPP/miR-28 in healthy controls (n=10), human myeloma cell lines (HMCLs) (n=15), and primary myeloma marrow samples at diagnosis (n=49) and at relapse (n=18). Quantitative reverse transcription PCR was used to investigate expression of miR-28-5p, LPP and CCND1. Results LPP/miR-28 was completely unmethylated in all healthy controls and 12 (80%) HMCLs, but partially methylated in three (20%) HMCLs. Methylation of LPP/miR-28 correlated with low expression of miR-285p (p=0.012) and LPP (p=0.037) in HMCLs. In RPMI-8226R cells, in which LPP/miR-28 was partially methylated, 5-AzadC treatment led to demethylation of LPP/miR-28 and re-expression of both miR-28-5p (p=0.0007) and LPP (p=0.0007), whereas continuous culture without 5-AzadC restored LPP/miR-28 methylation and reduced expression of both miR-28-5p (p=0.0013) and LPP (p=0.0025). Moreover, a known miR-28-5p target, CCND1, was expressed at higher levels in HMCLs with LPP/miR-28 methylation than those without, consistent with a tumour suppressor role of miR-28-5p in myeloma. However, in primary samples, LPP/miR-28 was methylated in two (4.1%) at diagnosis, whereas none at relapse. Conclusions This is the first report of epigenetic regulation of the intronic miR-28-5p expression by promoter DNA methylation of its host gene, hence warrants further study in different cancers.
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Affiliation(s)
- Zhenhai Li
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Kwan Yeung Wong
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Godfrey Chi-Fung Chan
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
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Mirzaei H, Fathullahzadeh S, Khanmohammadi R, Darijani M, Momeni F, Masoudifar A, Goodarzi M, Mardanshah O, Stenvang J, Jaafari MR, Mirzaei HR. State of the art in microRNA as diagnostic and therapeutic biomarkers in chronic lymphocytic leukemia. J Cell Physiol 2017; 233:888-900. [PMID: 28084621 DOI: 10.1002/jcp.25799] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/12/2017] [Indexed: 12/11/2022]
Abstract
Early diagnostic is one of the most important steps in cancer therapy which helps to design and choose a better therapeutic approach. The finding of biomarkers in various levels including genomics, transcriptomics, and proteomics levels could provide better treatment for various cancers such as chronic lymphocytic leukemia (CLL). The CLL is the one of main lymphoid malignancies which is specified by aggregation of mature B lymphocytes. Among different biomarkers (e.g., CD38, chromosomes abnormalities, ZAP-70, TP53, and microRNA [miRNA]), miRNAs have appeared as new diagnostic and therapeutic biomarkers in patients with the CLL disease. Multiple lines of evidence indicated that deregulation of miRNAs could be associated with pathological events which are present in the CLL. These molecules have an effect on a variety of targets such as Bcl2, c-fos, c-Myc, TP53, TCL1, and STAT3 which play critical roles in the CLL pathogenesis. It has been shown that expression of miRNAs could lead to the activation of B cells and B cell antigen receptor (BCR). Moreover, exosomes containing miRNAs are one of the other molecules which could contribute to BCR stimulation and progression of CLL cells. Hence, miRNAs and exosomes released from CLL cells could be used as potential diagnostic and therapeutic biomarkers for CLL. This critical review focuses on a very important aspect of CLL based on biomarker discovery covers the pros and cons of using miRNAs as important diagnostics and therapeutics biomarkers for this deadly disease.
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Affiliation(s)
- Hamed Mirzaei
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sima Fathullahzadeh
- Medical Biotechnology Research Center, Ashkezar Branch, Islamic Azad University, Ashkezar, Yazd, Iran
| | - Razieh Khanmohammadi
- Department of pediatric dentistry, School of dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Mansoreh Darijani
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Momeni
- Applied Physiology Research Center, Isfahan Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Aria Masoudifar
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Goodarzi
- Faculty of Bioscience Engineering, Department of Biosystems, Katholieke Universiteit Leuven - KULeuven, Heverlee, Belgium
| | - Omid Mardanshah
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jan Stenvang
- Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Reza Mirzaei
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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NF-κB in Hematological Malignancies. Biomedicines 2017; 5:biomedicines5020027. [PMID: 28561798 PMCID: PMC5489813 DOI: 10.3390/biomedicines5020027] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 12/30/2022] Open
Abstract
NF-κB (Nuclear Factor Κ-light-chain-enhancer of activated B cells) transcription factors are critical regulators of immunity, stress response, apoptosis, and differentiation. Molecular defects promoting the constitutive activation of canonical and non-canonical NF-κB signaling pathways contribute to many diseases, including cancer, diabetes, chronic inflammation, and autoimmunity. In the present review, we focus our attention on the mechanisms of NF-κB deregulation in hematological malignancies. Key positive regulators of NF-κB signaling can act as oncogenes that are often prone to chromosomal translocation, amplifications, or activating mutations. Negative regulators of NF-κB have tumor suppressor functions, and are frequently inactivated either by genomic deletions or point mutations. NF-κB activation in tumoral cells is also driven by the microenvironment or chronic signaling that does not rely on genetic alterations.
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Li Y, Zhao L, Li N, Miao Y, Zhou H, Jia L. miR-9 regulates the multidrug resistance of chronic myelogenous leukemia by targeting ABCB1. Oncol Rep 2017; 37:2193-2200. [DOI: 10.3892/or.2017.5464] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/08/2017] [Indexed: 11/06/2022] Open
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MicroRNA expression patterns and target prediction in multiple myeloma development and malignancy. Genes Genomics 2017; 39:533-540. [PMID: 28458781 PMCID: PMC5387019 DOI: 10.1007/s13258-017-0518-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/24/2017] [Indexed: 12/27/2022]
Abstract
Epigenetic changes have emerged as key causes in the development and progression of multiple myeloma (MM). In this study, global microRNA (miRNA) expression profiling were performed for 27 MM (19 specimens and 8 cell lines) and 3 normal controls by microarray. miRNA-targets were identified by integrating the miRNA expression profiles with mRNA expression profiles of the matched samples (unpublished data). Two miRNAs were selected for verification by RT-qPCR (miR-150-5p and miR-4430). A total of 1791 and 8 miRNAs were over-expressed and under-expressed, respectively in MM compared to the controls (fold change ≥2.0; p < 0.05). The miRNA-mRNA integrative analysis revealed inverse correlation between 5 putative target genes (RAD54L, CCNA2, CYSLTR2, RASGRF2 and HKDC1) and 15 miRNAs (p < 0.05). Most of the differentially expressed miRNAs are involved in survival, proliferation, migration, invasion and drug resistance in MM. Some have never been described in association with MM (miR-33a, miR-9 and miR-211). Interestingly, our results revealed 2 miRNAs, which are closely related to B cell differentiation (miR-150 and miR-125b). For the first time, we suggest that miR-150 might be potential negative regulator for two critical cell cycle control genes, RAD54L and CCNA2, whereas miR-125b potentially target RAS and CysLT signaling proteins, namely RASGRF2 and CYSLTR2, respectively. This study has enhanced our understanding on the pathobiology of MM and opens up new avenues for future research in myelomagenesis.
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Gao HY, Huo FC, Wang HY, Pei DS. MicroRNA-9 inhibits the gastric cancer cell proliferation by targeting TNFAIP8. Cell Prolif 2017; 50. [PMID: 28127811 DOI: 10.1111/cpr.12331] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AND OBJECTIVES MicroRNA-9 is frequently dysregulated in many human carcinoma types, including gastric cancer (GC). Previous studies demonstrated that the expression of TNFAIP8 in GC is correlated with tumour occurrence, development, invasion, metastasis and prognosis. However, till now, the relationship between MicroRNA-9 and TNFAIP8 in GC has not been reported. MATERIALS AND METHODS Levels of miR-9 and TNFAIP8 expression in GC tissues and in human GC cell lines were studied using qualitative real-time PCR (qRT-PCR) and Western blotting. Cell viability was detected using the CCK-8 and clone formation assays. A dual-luciferase reporter system was used to confirm the target gene of miR-9. RESULTS We found that the expression level of MicroRNA-9 in GC tissues and cell lines was significantly lower than that in adjacent non-cancerous tissues and human immortalized gastric epithelial cell (GES) line, respectively. In addition, overexpression of MicroRNA-9 markedly inhibited GC cell proliferation in vitro and tumour growth in vivo. Further experiments revealed that TNFAIP8 was a direct and functional target of MicroRNA-9 in GC and overexpression of MicroRNA-9 obviously down-regulated the expression of TNFAIP8, which was involved in the gastric carcinogenesis and cancer progression. CONCLUSION Our results suggested that MicroRNA-9-TNFAIP8 might represent a promising diagnostic biomarker for GC patients and could be a potential therapeutic target in the prevention and treatment of GC.
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Affiliation(s)
- Hong-Yu Gao
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical University, Xuzhou, China
| | - Fu-Chun Huo
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical University, Xuzhou, China
| | - Hai-Yan Wang
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical University, Xuzhou, China.,Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical University, Xuzhou, China.,Department of Pathology, Xuzhou Medical University, Xuzhou, China
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Epigenetic basis of cancer health disparities: Looking beyond genetic differences. Biochim Biophys Acta Rev Cancer 2017; 1868:16-28. [PMID: 28108348 DOI: 10.1016/j.bbcan.2017.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/07/2017] [Accepted: 01/16/2017] [Indexed: 12/18/2022]
Abstract
Despite efforts at various levels, racial health disparities still exist in cancer patients. These inequalities in incidence and/or clinical outcome can only be explained by a multitude of factors, with genetic basis being one of them. Several investigations have provided convincing evidence to support epigenetic regulation of cancer-associated genes, which results in the differential transcriptome and proteome, and may be linked to a pre-disposition of individuals of certain race/ethnicity to early or more aggressive cancers. Recent technological advancements and the ability to quickly analyze whole genome have aided in these efforts, and owing to their relatively easy detection, methylation events are much well-characterized, than the acetylation events, across human populations. The early trend of investigating a pre-determined set of genes for differential epigenetic regulation is paving way for more unbiased screening. This review summarizes our current understanding of the epigenetic events that have been tied to the racial differences in cancer incidence and mortality. A better understanding of the epigenetics of racial diversity holds promise for the design and execution of novel strategies targeting the human epigenome for reducing the disparity gaps.
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression mainly at the posttranscriptional level. Similar to protein-coding genes, their expression is also controlled by genetic and epigenetic mechanisms. Disruption of these control processes leads to abnormal expression of miRNAs in cancer. In this chapter, we discuss the supportive links between miRNAs and epigenetics in the context of carcinogenesis. miRNAs can be epigenetically regulated by DNA methylation and/or specific histone modifications. However, they can themselves (epi-miRNAs) repress key enzymes that drive epigenetic remodeling and also bind to complementary sequences in gene promoters, recruiting specific protein complexes that modulate chromatin structure and gene expression. All these issues affect the transcriptional landscape of cells. Most important, in the cancer clinical scenario, knowledge about miRNAs epigenetic dysregulation can not only be beneficial as a prognostic biomarker, but can also help in the design of new therapeutic approaches.
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Affiliation(s)
- Catia Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain.
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Costa LDA, da Silva ICB, Mariz BALA, da Silva MB, Freitas-Ribeiro GM, de Oliveira NFP. Influence of smoking on methylation and hydroxymethylation levels in global DNA and specific sites of KRT14 , KRT19 , MIR-9-3 and MIR-137 genes of oral mucosa. Arch Oral Biol 2016; 72:56-65. [DOI: 10.1016/j.archoralbio.2016.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 06/08/2016] [Accepted: 08/10/2016] [Indexed: 12/14/2022]
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45
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Fu L, Shi J, Liu A, Zhou L, Jiang M, Fu H, Xu K, Li D, Deng A, Zhang Q, Pang Y, Guo Y, Hu K, Zhou J, Wang Y, Huang W, Jing Y, Dou L, Wang L, Xu K, Ke X, Nervi C, Li Y, Yu L. A minicircuitry of microRNA-9-1 and RUNX1-RUNX1T1 contributes to leukemogenesis in t(8;21) acute myeloid leukemia. Int J Cancer 2016; 140:653-661. [PMID: 27770540 DOI: 10.1002/ijc.30481] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 09/13/2016] [Accepted: 10/11/2016] [Indexed: 01/28/2023]
Abstract
MicroRNA-9-1(miR-9-1) plays an important role in the mechanism that regulates the lineage fate of differentiating hematopoietic cells. Recent studies have shown that miR-9-1 is downregulated in t (8; 21) AML. However, the pathogenic mechanisms underlying miR-9-1 downregulation and the RUNX1-RUNX1T1 fusion protein, generated from the translocation of t (8; 21) in AML, remain unclear. RUNX1-RUNX1T1 can induce leukemogenesis through resides in and functions as a stable RUNX1-RUNX1T1-containing transcription factor complex. In this study, we demonstrate that miR-9-1 expression increases significantly after the treatment of RUNX1-RUNX1T1 (+) AML cell lines with decitabine (a DNMT inhibitor) and trichostatin A (an HDAC inhibitor). In addition, we show that RUNX1-RUNX1T1 triggers the heterochromatic silencing of miR-9-1 by binding to RUNX1-binding sites in the promoter region of miR-9-1 and recruiting chromatin-remodeling enzymes, DNMTs, and HDACs, contributing to hypermethylation of miR-9-1 in t (8; 21) AML. Furthermore, because RUNX1, RUNX1T1, and RUNX1-RUNX1T1 are all regulated by miR-9-1, the silencing of miR-9-1 enhances the oncogenic activity of these genes. Besides, overexpression of miR-9-1 induces differentiation and inhibits proliferation in t (8; 21) AML cell lines. In conclusion, our results indicate a feedback circuitry involving miR-9-1 and RUNX1-RUNX1T1, contributing to leukemogenesis in RUNX1-RUNX1T1 (+) AML cell lines.
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Affiliation(s)
- Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, 100191, China.,Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China.,Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Jinlong Shi
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, 100853, China
| | - Anqi Liu
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lei Zhou
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Mengmeng Jiang
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Huaping Fu
- Department of nuclear medicine, Chinese PLA General Hospital, Beijing, 100853, China
| | - Keman Xu
- College of medical laboratory science and technology, Harbin Medical University, Daqing, 163319, China
| | - Dandan Li
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Ailing Deng
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qingyi Zhang
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yifan Pang
- Department of Medicine, William Beaumont Hospital, Royal Oak, MI, 48073
| | - Yujie Guo
- College of Science, North China University of Technology, Beijing, 100144, China
| | - Kai Hu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, 100191, China
| | - Jiansuo Zhou
- Department of clinical laboratory, Peking University, Third Hospital, Beijing, 100191, China
| | - Yapeng Wang
- Department of reproduction center, Peking University, Third Hospital, Beijing, 100191, China
| | - Wenrong Huang
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yu Jing
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Liping Dou
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lili Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, 100191, China
| | - Clara Nervi
- Department of Medico-Surgical Sciences and Biotechnologies, University of Rome "La Sapienza" Polo Pontino, Latina, 04100, Italy
| | - Yonghui Li
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
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Epigenetic silencing of tumor suppressor miR-3151 contributes to Chinese chronic lymphocytic leukemia by constitutive activation of MADD/ERK and PIK3R2/AKT signaling pathways. Oncotarget 2016; 6:44422-36. [PMID: 26517243 PMCID: PMC4792566 DOI: 10.18632/oncotarget.6251] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 10/14/2015] [Indexed: 01/24/2023] Open
Abstract
We hypothesize that miR-3151, localized to a GWAS-identified chronic lymphocytic leukemia (CLL) risk locus (8q22.3), is a tumor suppressor miRNA silenced by promoter DNA methylation in CLL. The promoter of miR-3151 was methylated in 5/7 (71%) CLL cell lines, 30/98 (31%) diagnostic primary samples, but not normal controls. Methylation of miR-3151 correlated inversely with expression. Treatment with 5-Aza-2′-deoxycytidine led to promoter demethylation and miR-3151 re-expression. Luciferase assay confirmed MAP-kinase activating death domain (MADD) and phosphoinositide-3-kinase, regulatory subunit 2 (PIK3R2) as direct targets of miR-3151. Moreover, restoration of miR-3151 resulted in inhibition of cellular proliferation and enhanced apoptosis, repression of MADD and PIK3R2, downregulation of MEK/ERK and PI3K/AKT signaling, and repression of MCL1. Lastly, miR-3151 methylation was significantly associated with methylation of miR-203 and miR-34b/c in primary CLL samples. Therefore, this study showed that miR-3151 is a tumor suppressive miRNA frequently hypermethylated and hence silenced in CLL. miR-3151 silencing by DNA methylation protected CLL cells from apoptosis through over-expression of its direct targets MADD and PIK3R2, hence constitutive activation of MEK/ERK and PI3K/AKT signaling respectively, and consequently over-expression of MCL1.
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Subhash S, Andersson PO, Kosalai ST, Kanduri C, Kanduri M. Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clin Epigenetics 2016; 8:106. [PMID: 27777635 PMCID: PMC5062931 DOI: 10.1186/s13148-016-0274-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
Background Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status. Results Our study identified 5800 hypermethylated and 12,570 hypomethylated CLL-specific differentially methylated genes (cllDMGs) compared to normal controls. From cllDMGs, 40 % of hypermethylated and 60 % of hypomethylated genes were mapped to noncoding RNAs. In addition, we found that the major repetitive elements such as short interspersed elements (SINE) and long interspersed elements (LINE) have a high percentage of cllDMRs (differentially methylated regions) in IGHV subgroups compared to normal controls. Finally, two novel lncRNAs (hypermethylated CRNDE and hypomethylated AC012065.7) were validated in an independent CLL sample cohort (48 samples) compared with 6 normal sorted B cell samples using quantitative pyrosequencing analysis. The methylation levels showed an inverse correlation to gene expression levels analyzed by real-time quantitative PCR. Notably, survival analysis revealed that hypermethylation of CRNDE and hypomethylation of AC012065.7 correlated with an inferior outcome. Conclusions Thus, our comprehensive methylation analysis by MBD-Seq provided novel hyper and hypomethylated long noncoding RNAs, repetitive elements, along with protein coding genes as potential epigenetic-based CLL-signature genes involved in disease pathogenesis and prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0274-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden ; Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, S-413 45 Gothenburg, Sweden
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Enhanced miR-9 promotes laryngocarcinoma cell survival via down-regulating PTEN. Biomed Pharmacother 2016; 84:608-613. [PMID: 27694005 DOI: 10.1016/j.biopha.2016.09.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in gene regulation during laryngocarcinoma. MiR-9 is a potential oncomiR, but its function in laryngocarcinoma is not known. The aim of this study is to investigate the roles of miR-9 in laryngocarcinoma. We found miR-9 expression was higher in laryngocarcinoma tissues compared with their normal controls, so did the laryngocarcinoma cells. Cellular function of miR-9 indicated that miR-9 restoration in laryngocarcinoma cells could promote cell proliferation and metastasis. Phosphatase and tensin homolog (PTEN) was predicted as a target gene of miR-9 and verified using luciferase reporter assay. PTEN expression was down-regulated in the laryngocarcinoma cells with miR-9 overexpression. We also found that miR-9 expression was negatively associated with PTEN expression in laryngocarcinoma tissues.
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Piletič K, Kunej T. MicroRNA epigenetic signatures in human disease. Arch Toxicol 2016; 90:2405-19. [DOI: 10.1007/s00204-016-1815-7] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/04/2016] [Indexed: 01/27/2023]
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Mansouri L, Papakonstantinou N, Ntoufa S, Stamatopoulos K, Rosenquist R. NF-κB activation in chronic lymphocytic leukemia: A point of convergence of external triggers and intrinsic lesions. Semin Cancer Biol 2016; 39:40-8. [PMID: 27491692 DOI: 10.1016/j.semcancer.2016.07.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 07/30/2016] [Indexed: 02/08/2023]
Abstract
The nuclear factor-κB (NF-κB) pathway is constitutively activated in chronic lymphocytic leukemia (CLL) patients, and hence plays a major role in disease development and evolution. In contrast to many other mature B-cell lymphomas, only a few recurrently mutated genes involved in canonical or non-canonical NF-κB activation have been identified in CLL (i.e. BIRC3, MYD88 and NFKBIE mutations) and often at a low frequency. On the other hand, CLL B cells seem 'addicted' to the tumor microenvironment for their survival and proliferation, which is primarily mediated by interaction through a number of cell surface receptors, e.g. the B-cell receptor (BcR), Toll-like receptors and CD40, that in turn activate downstream NF-κB. The importance of cell-extrinsic triggering for CLL pathophysiology was recently also highlighted by the clinical efficacy of novel drugs targeting microenvironmental interactions through the inhibition of BcR signaling. In other words, CLL can be considered a prototype disease for studying the intricate interplay between external triggers and intrinsic aberrations and their combined impact on disease evolution. In this review, we will discuss the current understanding of mechanisms underlying NF-κB deregulation in CLL, including micro-environmental, genetic and epigenetic events, and summarize data generated in murine models resembling human CLL. Finally, we will also discuss different strategies undertaken to intervene with the NF-κB pathway and its upstream mediators.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nikos Papakonstantinou
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Stavroula Ntoufa
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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