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Peng L, Tu Y, Huang L, Li Y, Fu X, Chen X. DAESTB: inferring associations of small molecule-miRNA via a scalable tree boosting model based on deep autoencoder. Brief Bioinform 2022; 23:6827720. [PMID: 36377749 DOI: 10.1093/bib/bbac478] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) are closely related to a variety of human diseases, not only regulating gene expression, but also having an important role in human life activities and being viable targets of small molecule drugs for disease treatment. Current computational techniques to predict the potential associations between small molecule and miRNA are not that accurate. Here, we proposed a new computational method based on a deep autoencoder and a scalable tree boosting model (DAESTB), to predict associations between small molecule and miRNA. First, we constructed a high-dimensional feature matrix by integrating small molecule-small molecule similarity, miRNA-miRNA similarity and known small molecule-miRNA associations. Second, we reduced feature dimensionality on the integrated matrix using a deep autoencoder to obtain the potential feature representation of each small molecule-miRNA pair. Finally, a scalable tree boosting model is used to predict small molecule and miRNA potential associations. The experiments on two datasets demonstrated the superiority of DAESTB over various state-of-the-art methods. DAESTB achieved the best AUC value. Furthermore, in three case studies, a large number of predicted associations by DAESTB are confirmed with the public accessed literature. We envision that DAESTB could serve as a useful biological model for predicting potential small molecule-miRNA associations.
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Affiliation(s)
- Li Peng
- College of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.,Hunan Key Laboratory for Service computing and Novel Software Technology
| | - Yuan Tu
- College of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, 10084, China.,The Future Laboratory, Tsinghua University, Beijing, 10084, China
| | - Yang Li
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, 411105, China
| | - Xiangzheng Fu
- College of Information Science and Engineering, Hunan University, Changsha, 410082, Hunan, China
| | - Xiang Chen
- College of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
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Pan G, Luo Z, Tang R. WITHDRAWN: Genetic polymorphisms and promoter methylation of miR-9-3 in the modulation of breast cancer risk in a Chinese population. Clin Breast Cancer 2021. [DOI: 10.1016/j.clbc.2021.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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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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4
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Coêlho MC, Queiroz IC, Viana JMC, de Aquino SG, Persuhn DC, de Oliveira NFP. miR-9-1 gene methylation and DNMT3B (rs2424913) polymorphism may contribute to periodontitis. J Appl Oral Sci 2020; 28:e20190583. [PMID: 32267380 PMCID: PMC7137733 DOI: 10.1590/1678-7757-2019-0583] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/11/2019] [Accepted: 11/27/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Genetic and epigenetic changes have been associated with periodontitis in various genes; however, little is known about genes involved in epigenetic mechanisms and in oxidative stress. OBJECTIVE This study aims to investigate the association of polymorphisms C677T in MTHFR (rs1801133) and -149C→T in DNMT3B (rs2424913), as well as the methylation profiles of MTHFR, miR-9-1, miR-9-3, SOD1, and CAT with periodontitis. The association between polymorphisms and DNA methylation profiles was also analyzed. METHODOLOGY The population studied was composed of 100 nonsmokers of both sexes, divided into healthy and periodontitis groups. Genomic DNA was extracted from the epithelial buccal cells, which were collected through a mouthwash. Polymorphism analysis was performed through polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), while methylation-specific PCR (MSP) or combined bisulfite restriction analysis techniques were applied for methylation analysis. RESULTS For DNMT3B, the T allele and the TT genotype were detected more frequently in the periodontitis group, as well as the methylated profile on the miR-9-1 promoter region. There was also a tendency towards promoter region methylation on the CAT sequence of individuals with periodontal disease. CONCLUSION The polymorphism -149C→T in DNMT3B (rs2424913) and the methylated profile of the miR-9-1 promoter region are associated with periodontitis.
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Affiliation(s)
- Marina Castro Coêlho
- Universidade Federal da ParaíbaCentro de Ciências da SaúdePrograma de Pós Graduação em OdontologiaJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, Paraíba, Brasil.
| | - Ingrid Costa Queiroz
- Universidade Federal da ParaíbaCentro de Ciências da SaúdeJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências da Saúde, João Pessoa, Paraíba, Brasil.
| | - José Maria Chagas Viana
- Universidade Federal da ParaíbaCentro de Ciências da SaúdePrograma de Pós Graduação em OdontologiaJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, Paraíba, Brasil.
| | - Sabrina Garcia de Aquino
- Universidade Federal da ParaíbaCentro de Ciências da SaúdePrograma de Pós Graduação em OdontologiaJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, Paraíba, Brasil.
- Universidade Federal da ParaíbaCentro de Ciências da SaúdeDepartamento de Odontologia Clínica e SocialJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências da Saúde, Departamento de Odontologia Clínica e Social, João Pessoa, Paraíba, Brasil.
| | - Darlene Camati Persuhn
- Universidade Federal da ParaíbaCentro de Ciências Exatas e da NaturezaDepartamento de Biologia MolecularJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências Exatas e da Natureza, Departamento de Biologia Molecular, João Pessoa, Paraíba, Brasil.
| | - Naila Francis Paulo de Oliveira
- Universidade Federal da ParaíbaCentro de Ciências da SaúdePrograma de Pós Graduação em OdontologiaJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, Paraíba, Brasil.
- Universidade Federal da ParaíbaCentro de Ciências Exatas e da NaturezaDepartamento de Biologia MolecularJoão PessoaParaíbaBrasilUniversidade Federal da Paraíba, Centro de Ciências Exatas e da Natureza, Departamento de Biologia Molecular, João Pessoa, Paraíba, Brasil.
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Khafaei M, Rezaie E, Mohammadi A, Shahnazi Gerdehsang P, Ghavidel S, Kadkhoda S, Zorrieh Zahra A, Forouzanfar N, Arabameri H, Tavallaie M. miR-9: From function to therapeutic potential in cancer. J Cell Physiol 2019; 234:14651-14665. [PMID: 30693512 DOI: 10.1002/jcp.28210] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Malignant neoplasms are regarded as the main cause of death around the world; hence, many research studies were conducted to further perceive molecular mechanisms, treatment, and cancer prognosis. Cancer is known as a major factor for health-related problems in the world. The main challenges associated with these diseases are prompt diagnosis, disease remission classification and treatment status forecast. Therefore, progressing in such areas by developing new and optimized methods with the help of minimally invasive biological markers such as circular microRNAs (miRNAs) can be considered important. miRNA interactions with target genes have specified their role in development, apoptosis, differentiation, and proliferation and also, confirm direct miRNA function in cancer. Different miRNAs expression levels in various types of malignant neoplasms have been observed to be associated with prognosis of various carcinomas. miR-9 seems to implement opposite practices in different tissues or under various cancer incidences by influencing different genes. Aberrant miR-9 levels have been observed in many cancer types. Therefore, we intended to investigate the precise role of miR-9 in patients with malignant neoplasms. To this end, in this study, we attempted to examine different studies to clarify the overall role of miR-9 as a prognostic marker in several human tumors. The presented data in this study can help us to find the novel therapeutic avenues for treatment of human cancers.
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Affiliation(s)
- Mostafa Khafaei
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
| | - Ehsan Rezaie
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, Tehran, Iran
| | - Ali Mohammadi
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
| | | | - Sara Ghavidel
- Department Cell and Molecular Biology, Tonekabon Branch, Islamic Azad University, Tehran, Iran
| | - Sepideh Kadkhoda
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Atieh Zorrieh Zahra
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Narjes Forouzanfar
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Arabameri
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
| | - Mahmood Tavallaie
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
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Qi J, Shi LY, Wu Y, Shen XJ, Yuan J, Jin CJ, Cong H, Ju SQ. Epigenetic silencing of miR-335 induces migration by targeting insulin-like growth factor-1 receptor in multiple myeloma. Leuk Lymphoma 2019; 60:3188-3198. [PMID: 31190579 DOI: 10.1080/10428194.2019.1627534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiple myeloma (MM) is a common hematological malignancy and remains incurable. MiRNA-335 is a classic tumor suppressor, yet its expression pattern and biological role in MM is unclear. The aim of the present study was to determine the expression pattern, biological role, and mechanism of miR-335 in MM. In this study, we found that miR-335 expression was decreased in MM. The promoter of miR-335 was also hypermethylated in MM. It was found that over-expression of miR-335 or 5-azacytidine treatment suppressed migration of MM cells and down-regulated the expression of IGF-1R. MiR-335 thus acts as a metastatic suppressor by targeting IGF-1R in MM. Moreover, aberrant promoter hyper-methylation is critical for miR-335 silencing in MM. We also found that miR-335 assisted in predicting both the prognosis and progression of disease in MM patients. Observations might offer a new complementary diagnostic and therapeutic target in MM.
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Affiliation(s)
- Jing Qi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Lin-Ying Shi
- Medical School of Nantong University, Nantong, Jiangsu Province, China
| | - Yin Wu
- Medical School of Nantong University, Nantong, Jiangsu Province, China
| | - Xian-Juan Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Jie Yuan
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Chun-Jing Jin
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Hui Cong
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Shao-Qing Ju
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
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7
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Han B, Zheng Y, Wang L, Wang H, Du J, Ye F, Sun T, Zhang L. A novel microRNA signature predicts vascular invasion in hepatocellular carcinoma. J Cell Physiol 2019; 234:20859-20868. [PMID: 30997686 DOI: 10.1002/jcp.28690] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 12/14/2022]
Abstract
Vascular invasion (VI) in hepatocellular carcinoma (HCC) is an important clinical parameter to predict survival. In this study, we collected microRNA (miRNA) expression data from HCC patients using The Cancer Genome Atlas database and identified a novel miRNA signature associated with VI. First, we categorized HCC patients into groups with or without VI (VI+ and VI-). We identified three miRNAs (miRNA-210, miRNA-10b, and miRNA-9-1) that were associated with VI according to a Kaplan-Meier analysis. This three-miRNA signature exhibited good predictive ability for VI in patients with HCC according to a receiver operating characteristic curve analysis at 1, 3, and 5 years. Patients with HCC with a high risk score exhibited a trend toward worse outcomes as determined by multivariable Cox regression and stratified analyses. This three-miRNA signature provides an accurate prediction of VI and can be used as an independent prognostic indicator for predicting VI in HCC patients.
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Affiliation(s)
- Bing Han
- Department of GICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yujia Zheng
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Le Wang
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haixu Wang
- Department of GICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaxin Du
- Department of GICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fanglei Ye
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tongwen Sun
- Department of GICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lianfeng Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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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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Factors Regulating microRNA Expression and Function in Multiple Myeloma. Noncoding RNA 2019; 5:ncrna5010009. [PMID: 30654527 PMCID: PMC6468559 DOI: 10.3390/ncrna5010009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/13/2019] [Accepted: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
Intensive research has been undertaken during the last decade to identify the implication of microRNAs (miRNAs) in the pathogenesis of multiple myeloma (MM). The expression profiling of miRNAs in MM has provided relevant information, demonstrating different patterns of miRNA expression depending on the genetic abnormalities of MM and a key role of some miRNAs regulating critical genes associated with MM pathogenesis. However, the underlying causes of abnormal expression of miRNAs in myeloma cells remain mainly elusive. The final expression of the mature miRNAs is subject to multiple regulation mechanisms, such as copy number alterations, CpG methylation or transcription factors, together with impairment in miRNA biogenesis and differences in availability of the mRNA target sequence. In this review, we summarize the available knowledge about the factors involved in the regulation of miRNA expression and functionality in MM.
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Zhu B, Chen H, Zhang X, Pan Y, Jing R, Shen L, Wang X, Ju S, Jin C, Cong H. Serum miR-30d as a novel biomarker for multiple myeloma and its antitumor role in U266 cells through the targeting of the MTDH/PI3K/Akt signaling pathway. Int J Oncol 2018; 53:2131-2144. [PMID: 30132507 DOI: 10.3892/ijo.2018.4532] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/18/2018] [Indexed: 11/05/2022] Open
Abstract
Multiple myeloma (MM) is a hematological tumor and is characterized by the infiltration of malignant clonal plasma cells (PCs) in bone marrow. MicroRNAs (miRNAs or miRs) have been reported to play an important role in the genesis and progression of MM. However, little is known about the clinical diagnostic value and biological functions of miR-30d in MM. In this study, to investigate the role of miR-30d in MM, we used reverse transcription-quantitative polymerase chain reaction quantitative (RT-qPCR) to detect the relative expression level of miR-30d in the serum of 81 patients with primary MM and 78 healthy donors (HDs). The biological functions of miR-30d were then assessed by CCK-8 assay, flow cytometric analysis of apoptosis and western blot (WB) analysis in U266 cells. Moreover, the confirmation of the target gene of miR-30d was conducted by luciferase reporter assay. Our results indicated that miR-30d expression was significantly downregulated in the serum of patients with primary MM compared with that of the HDs and that it was significantly associated with several clinical indicators of MM. Further cell functional analyses using the U266 cells revealed that miR-30d functions as a tumor suppressor gene in MM by inhibiting cell viability and promoting cell apoptosis. Moreover, miR-30d was confirmed to directly bind to the 3'UTR of its target gene, metadherin (MTDH) and inhibit the activation of the downstream PI3K/Akt signaling pathway. On the whole, the findings of this study indicate that the serum expression level of miR-30d is of great significance to the diagnosis and treatment monitoring of patients with MM. Moreover, miR-30d carries out its antitumor role in U266 cells through the inhibition of the activation of the PI3K/Akt signaling pathway by negatively regulating MTDH, which reveals its potential for use as a therapeutic target for MM.
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Affiliation(s)
- Bingying Zhu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Hongmei Chen
- VIP ward, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xiaofen Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yafang Pan
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Lei Shen
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xudong Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Chunjing Jin
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Hui Cong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
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11
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Zhu B, Ju S, Chu H, Shen X, Zhang Y, Luo X, Cong H. The potential function of microRNAs as biomarkers and therapeutic targets in multiple myeloma. Oncol Lett 2018; 15:6094-6106. [PMID: 29731841 PMCID: PMC5920744 DOI: 10.3892/ol.2018.8157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/10/2018] [Indexed: 12/30/2022] Open
Abstract
Multiple myeloma (MM), accounting for ~1% of all types of human cancer and 13% of all hematological malignancies, is characterized by the malignant proliferation of monoclonal plasma cells (PCs) in the bone marrow. MM leads to end stage organ impairment, including bone lesions, renal dysfunction, hypercalcemia and anemia. So far, the specific pathogenesis of MM remains unclear and no early-stage sensitive biomarker of MM has been well characterized. Furthermore, treating MM is difficult, as the majority of patients eventually relapse or become refractory following treatment using presently available methods. To date, a number of studies have demonstrated that microRNAs (miRNAs) may serve crucial functions in the progression of numerous cancers, including MM. During the tumorigenesis and pathogenesis of MM, there are multiple carcinogenic events that involve the pernicious transformation from normal to malignant PCs. miRNAs, as oncogenes or tumor suppressors, regulate MM progression-related signaling pathways. In the present review, the up-to-date preliminary basic studies and associated clinical works on the underlying mechanisms of aberrant miRNA profiling in MM have been summarized, including an evaluation of its value as a potential biomarker and a novel therapeutic strategy for MM.
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Affiliation(s)
- Bingying Zhu
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Shaoqing Ju
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Haidan Chu
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xianjuan Shen
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Yan Zhang
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xi Luo
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Hui Cong
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
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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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13
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Epigenetics and MicroRNAs in Cancer. Int J Mol Sci 2018; 19:ijms19020459. [PMID: 29401683 PMCID: PMC5855681 DOI: 10.3390/ijms19020459] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
The ability to reprogram the transcriptional circuitry by remodeling the three-dimensional structure of the genome is exploited by cancer cells to promote tumorigenesis. This reprogramming occurs because of hereditable chromatin chemical modifications and the consequent formation of RNA-protein-DNA complexes that represent the principal actors of the epigenetic phenomena. In this regard, the deregulation of a transcribed non-coding RNA may be both cause and consequence of a cancer-related epigenetic alteration. This review summarizes recent findings that implicate microRNAs in the aberrant epigenetic regulation of cancer cells.
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14
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Liang J, Yang F, Zhao L, Bi C, Cai B. Physiological and pathological implications of 5-hydroxymethylcytosine in diseases. Oncotarget 2018; 7:48813-48831. [PMID: 27183914 PMCID: PMC5217052 DOI: 10.18632/oncotarget.9281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/19/2016] [Indexed: 12/11/2022] Open
Abstract
Gene expression is the prerequisite of proteins. Diverse stimuli result in alteration of gene expression profile by base substitution for quite a long time. However, during the past decades, accumulating studies proved that bases modification is involved in this process. CpG islands (CGIs) are DNA fragments enriched in CpG repeats which mostly locate in promoters. They are frequently modified, methylated in most conditions, thereby suggesting a role of methylation in profiling gene expression. DNA methylation occurs in many conditions, such as cancer, embryogenesis, nervous system diseases etc. Recently, 5-hydroxymethylcytosine (5hmC), the product of 5-methylcytosine (5mC) demethylation, is emerging as a novel demethylation marker in many disorders. Consistently, conversion of 5mC to 5hmC has been proved in many studies. Here, we reviewed recent studies concerning demethylation via 5hmC conversion in several conditions and progress of therapeutics-associated with it in clinic. We aimed to unveil its physiological and pathological significance in diseases and to provide insight into its clinical application potential.
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Affiliation(s)
- Jing Liang
- Department of Pharmacology, Harbin Medical University (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | - Fan Yang
- Department of Pharmacology, Harbin Medical University (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | - Liang Zhao
- Department of Pharmacology, Harbin Medical University (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | - Chongwei Bi
- Department of Pharmacology, Harbin Medical University (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | - Benzhi Cai
- Department of Pharmacology, Harbin Medical University (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China.,Institute of Clinical Pharmacy and Medicine, Academics of Medical Sciences of Heilongjiang Province, Harbin, China
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15
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Amodio N, D'Aquila P, Passarino G, Tassone P, Bellizzi D. Epigenetic modifications in multiple myeloma: recent advances on the role of DNA and histone methylation. Expert Opin Ther Targets 2017; 21:91-101. [PMID: 27892767 DOI: 10.1080/14728222.2016.1266339] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Multiple Myeloma (MM) is a clonal late B-cell disorder accounting for about 13% of hematological cancers and 1% of all neoplastic diseases. Recent studies on the molecular pathogenesis and biology of MM have highlighted a complex epigenomic landscape contributing to MM onset, prognosis and high individual variability. Areas covered: We describe here the current knowledge on epigenetic events characterizing MM initiation and progression, focusing on the role of DNA and histone methylation and on the most promising epi-therapeutic approaches targeting the methylation pathway. Expert opinion: Data published so far indicate that alterations of the epigenetic framework, which include aberrant global or gene/non-coding RNA specific methylation profiles, feature prominently in the pathobiology of MM. Indeed, the aberrant expression of components of the epigenetic machinery as well as the reversibility of the epigenetic marks make this pathway druggable, providing the basis for the design of epigenetic therapies against this still fatal malignancy.
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Affiliation(s)
- Nicola Amodio
- a Department of Experimental and Clinical Medicine , Magna Graecia University , Catanzaro , Italy
| | - Patrizia D'Aquila
- b Department of Biology, Ecology and Earth Sciences , University of Calabria , Rende , Italy
| | - Giuseppe Passarino
- b Department of Biology, Ecology and Earth Sciences , University of Calabria , Rende , Italy
| | - Pierfrancesco Tassone
- a Department of Experimental and Clinical Medicine , Magna Graecia University , Catanzaro , Italy.,c Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology , Temple University , Philadelphia , PA , US
| | - Dina Bellizzi
- b Department of Biology, Ecology and Earth Sciences , University of Calabria , Rende , Italy
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16
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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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17
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Liu Y, Liu WB, Liu KJ, Ao L, Cao J, Zhong JL, Liu JY. Overexpression of miR-26b-5p regulates the cell cycle by targeting CCND2 in GC-2 cells under exposure to extremely low frequency electromagnetic fields. Cell Cycle 2016; 15:357-67. [PMID: 26637059 DOI: 10.1080/15384101.2015.1120924] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The increasing prevalence of extremely low frequency electromagnetic fields (ELF-EMFs) exposure has raised considerable public concern regarding the potential hazardous effects of ELF-EMFs on male reproductive function. Increasing evidence indicates that miRNAs are necessary for spermatogenesis and male fertility. However, the regulation of miRNA expression and the roles of miRNAs in response to ELF-EMFs remain unclear. In our study, mouse spermatocyte-derived GC-2 cells were intermittently exposed to a 50 Hz ELF-EMF for 72 h (5 min on/10 min off) at magnetic field intensities of 1 mT, 2 mT and 3 mT. MiR-26b-5p was differentially expressed in response to different magnetic field intensities of ELF-EMFs. The host gene CTDSP1 showed an unmethylation status in GC-2 cells at different magnetic field intensities of ELF-EMF exposure. MiR-26b-5p had no significant, obvious influence on the cell viability, apoptosis or cell cycle of GC-2 cells. However, the overexpression of miR-26b-5p significantly decreased the percentage of G0/G1 phase cells and slightly increased the percentage of S phase cells compared to the sham group that was exposed to a 50 Hz ELF-EMF. Computational algorithms identified Cyclin D2 (CCND2) as a direct target of miR-26b-5p. MiR-26b-5p and a 50 Hz ELF-EMF altered the expression of CCND2 at both the mRNA and protein levels. Overexpressed miR-26b-5p in GC-2 cells can change the mRNA expression of CCND2 following 50 Hz ELF-EMF at 3 mT. These findings demonstrate that miR-26b-5p could serve as a potential biomarker following 50 Hz ELF-EMF exposure, and miR-26b-5p-CCND2-mediated cell cycle regulation might play a pivotal role in the biological effects of ELF-EMFs.
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Affiliation(s)
- Yong Liu
- a College of Bioengineering, Chongqing University , Chongqing , China.,b Institute of Toxicology, College of Preventive Medicine, Third Military Medical University , Chongqing , China
| | - Wen-Bin Liu
- b Institute of Toxicology, College of Preventive Medicine, Third Military Medical University , Chongqing , China
| | - Kai-Jun Liu
- b Institute of Toxicology, College of Preventive Medicine, Third Military Medical University , Chongqing , China
| | - Lin Ao
- b Institute of Toxicology, College of Preventive Medicine, Third Military Medical University , Chongqing , China
| | - Jia Cao
- b Institute of Toxicology, College of Preventive Medicine, Third Military Medical University , Chongqing , China
| | - Julia Li Zhong
- a College of Bioengineering, Chongqing University , Chongqing , China
| | - Jin-Yi Liu
- b Institute of Toxicology, College of Preventive Medicine, Third Military Medical University , Chongqing , China
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18
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Wong KY, Li Z, Zhang X, Leung GKK, Chan GCF, Chim CS. Epigenetic silencing of a long non-coding RNA KIAA0495 in multiple myeloma. Mol Cancer 2015; 14:175. [PMID: 26410378 PMCID: PMC4583761 DOI: 10.1186/s12943-015-0444-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/10/2015] [Indexed: 11/15/2022] Open
Abstract
In multiple myeloma, a long non-coding RNA, KIAA0495 (alias PDAM/TP73-AS1), had been found progressively downregulated from normal plasma cell to benign monoclonal gammopathy of undetermined significance to symptomatic myeloma. Herein, by methylation-specific PCR, the putative KIAA0495 promoter was found unmethylated in all healthy controls (N = 14) but methylated in 50 % of myeloma cell lines (N = 10). KIAA0495 methylation was shown inversely correlated with KIAA0495 expression. However, KIAA0495 methylation was detected in none of both primary myeloma samples at diagnosis (N = 61) and at relapse/progression (N = 16). Collectively, despite frequently methylated in cell lines, KIAA0495 methylation appeared unimportant in the pathogenesis or progression of myeloma.
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Affiliation(s)
- Kwan Yeung Wong
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong.
| | - Zhenhai Li
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong.
| | - Xiaoqin Zhang
- Department of Surgery, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong.
| | - Gilberto Ka Kit Leung
- Department of Surgery, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong.
| | - Godfrey Chi-Fung Chan
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, 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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