1
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Azizi E, Mofarahe ZS, Naji M. MicroRNAs, small regulatory elements with significant effects on human implantation: a review. J Assist Reprod Genet 2023; 40:697-717. [PMID: 36723761 PMCID: PMC10224887 DOI: 10.1007/s10815-023-02735-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
Embryo implantation is a critical process for achieving a successful pregnancy and live birth. The proper implantation must have a synchronized interaction between blastocyst and a receptive endometrium. Many genes are involved in the modulation of precise molecular events during implantation. MicroRNAs (miRNAs) have been extensively reported as gene regulatory molecules on post-transcriptional levels involved in various biological processes such as gametogenesis, embryogenesis, and the quality of sperm, oocyte, and embryos. A plethora of evidence has demonstrated critical roles for miRNAs in regulating genes involved in the implantation process; hence, dysregulation of miRNAs could be associated with significant impairments in implantation, such as recurrent implantation failure. In addition to the indispensable role of miRNAs in the intracellular control of gene expression, they can also be secreted into extracellular fluid and circulation. Therefore, miRNAs in body fluids and blood may be exploited as non-invasive diagnostic biomarkers for different pathological and physiological conditions. Recently, several studies have focused on the discovery of miRNAs function in the implantation process by appraising miRNAs and their target genes in human embryos, endometrial tissue, and cell culture models. Moreover, it was revealed that there could be a significant association between endometrial receptivity or implantation status and the expression of miRNAs in human body fluids, reinforcing their role as non-invasive biomarkers. In the current work, we reviewed the studies concerning the role of intracellular and extracellular miRNAs in human implantation and the influence of their dysregulation on implantation disorders.
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Affiliation(s)
- Elham Azizi
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Shams Mofarahe
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Naji
- Urology and Nephrology Research Center (UNRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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2
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Wang JZ, Nassiri F, Aldape K, von Deimling A, Sahm F. The Epigenetic Landscape of Meningiomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1416:175-188. [PMID: 37432627 DOI: 10.1007/978-3-031-29750-2_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Epigenetic changes have been found to be increasingly important in tumor development and progression. These alterations can be present in tumors such as meningiomas in the absence of any gene mutations and alter gene expression without affecting the sequence of the DNA itself. Some examples of these alterations that have been studied in meningiomas include DNA methylation, microRNA interaction, histone packaging, and chromatin restructuring. In this chapter we will describe in detail each of these mechanisms of epigenetic modification in meningiomas and their prognostic significance.
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Affiliation(s)
- Justin Z Wang
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada
| | - Farshad Nassiri
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada.
| | - Kenneth Aldape
- Laboratory of Pathology, Center Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andreas von Deimling
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
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3
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Zhan J, Liu Z, Liu R, Zhu JJ, Zhang J. Near-Infrared-Light-Mediated DNA-Logic Nanomachine for Bioorthogonal Cascade Imaging of Endogenous Interconnected MicroRNAs and Metal Ions. Anal Chem 2022; 94:16622-16631. [DOI: 10.1021/acs.analchem.2c02577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jiayin Zhan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zheng Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ran Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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4
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Jałbrzykowska K, Chrzanowska A, Roszkowski P, Struga M. The New Face of a Well-Known Antibiotic: A Review of the Anticancer Activity of Enoxacin and Its Derivatives. Cancers (Basel) 2022; 14:cancers14133056. [PMID: 35804828 PMCID: PMC9264829 DOI: 10.3390/cancers14133056] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Enoxacin is a second-generation quinolone with promising anticancer activity. In contrast to other members of the quinolone group, it exhibits an extraordinary cytotoxic mechanism of action. Enoxacin enhances RNA interference and promotes microRNA processing, as well as the production of free radicals. Interestingly, apart from its proapoptotic, cell cycle arresting and cytostatic effects, enoxacin manifests a limitation of cancer invasiveness. The underlying mechanisms are the competitive inhibition of vacuolar H+-ATPase subunits and c-Jun N-terminal kinase signaling pathway suppression. The newly synthesized enoxacin derivatives have shown a magnified cytotoxic effect with an emphasis on prooxidative, proapoptotic and microRNA interference actions. The mentioned mechanisms seem to contribute to a safer, more selective and more effective anticancer therapy. Abstract Enoxacin as a second-generation synthetic quinolone is known for its antibacterial action; however, in recent years there have been studies focusing on its anticancer potential. Interestingly, it turns out that compared to other fluoroquinolones, enoxacin exhibits uncommon cytotoxic properties. Besides its influence on apoptosis, the cell cycle and cell growth, it exhibits a regulatory action on microRNA biogenesis. It was revealed that the molecular targets of the enoxacin-mediated inhibition of osteoclastogenesis are vacuolar H+-ATPase subunits and the c-Jun N-terminal kinase signaling pathway, causing a decrease in cell invasiveness. Interestingly, the prooxidative nature of the subjected fluoroquinolone enhanced the cytotoxic effect. Crucial for the anticancer activity were the carboxyl group at the third carbon atom, fluorine at the seventh carbon atom and nitrogen at the eighth position of naphyridine. Modifications of the parent drug improved the induction of oxidative stress, cell cycle arrest and the dysregulation of microRNA. The inhibition of V-ATPase–microfilament binding was also observed. Enoxacin strongly affected various cancer but not normal cells, excluding keratinocytes, which suffered from phototoxicity. It seems to be an underestimated anticancer drug with pleiotropic action. Furthermore, its usage as a safe antibiotic with well-known pharmacokinetics and selectivity will enhance the development of anticancer treatment strategies. This review covers articles published within the years 2000–2021, with a strong focus on the recent years (2016–2021). However, some canonical papers published in twentieth century are also mentioned.
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Affiliation(s)
- Karolina Jałbrzykowska
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warszawa, Poland;
| | - Alicja Chrzanowska
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warszawa, Poland;
- Correspondence: (A.C.); (M.S.); Tel.: +48-22-5720693 (A.C. & M.S.)
| | - Piotr Roszkowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Marta Struga
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warszawa, Poland;
- Correspondence: (A.C.); (M.S.); Tel.: +48-22-5720693 (A.C. & M.S.)
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5
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Liang C, Huang M, Li T, Li L, Sussman H, Dai Y, Siemann DW, Xie M, Tang X. Towards an integrative understanding of cancer mechanobiology: calcium, YAP, and microRNA under biophysical forces. SOFT MATTER 2022; 18:1112-1148. [PMID: 35089300 DOI: 10.1039/d1sm01618k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An increasing number of studies have demonstrated the significant roles of the interplay between microenvironmental mechanics in tissues and biochemical-genetic activities in resident tumor cells at different stages of tumor progression. Mediated by molecular mechano-sensors or -transducers, biomechanical cues in tissue microenvironments are transmitted into the tumor cells and regulate biochemical responses and gene expression through mechanotransduction processes. However, the molecular interplay between the mechanotransduction processes and intracellular biochemical signaling pathways remains elusive. This paper reviews the recent advances in understanding the crosstalk between biomechanical cues and three critical biochemical effectors during tumor progression: calcium ions (Ca2+), yes-associated protein (YAP), and microRNAs (miRNAs). We address the molecular mechanisms underpinning the interplay between the mechanotransduction pathways and each of the three effectors. Furthermore, we discuss the functional interactions among the three effectors in the context of soft matter and mechanobiology. We conclude by proposing future directions on studying the tumor mechanobiology that can employ Ca2+, YAP, and miRNAs as novel strategies for cancer mechanotheraputics. This framework has the potential to bring insights into the development of novel next-generation cancer therapies to suppress and treat tumors.
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Affiliation(s)
- Chenyu Liang
- Department of Mechanical & Aerospace Engineering, Herbert Wertheim College of Engineering (HWCOE), Gainesville, FL, 32611, USA.
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
| | - Miao Huang
- Department of Mechanical & Aerospace Engineering, Herbert Wertheim College of Engineering (HWCOE), Gainesville, FL, 32611, USA.
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
| | - Tianqi Li
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), Gainesville, FL, 32611, USA.
| | - Lu Li
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), Gainesville, FL, 32611, USA.
| | - Hayley Sussman
- Department of Radiation Oncology, COM, Gainesville, FL, 32611, USA
| | - Yao Dai
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- UF Genetics Institute (UFGI), University of Florida (UF), Gainesville, FL, 32611, USA
| | - Dietmar W Siemann
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- UF Genetics Institute (UFGI), University of Florida (UF), Gainesville, FL, 32611, USA
| | - Mingyi Xie
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), Gainesville, FL, 32611, USA.
- Department of Biomedical Engineering, College of Engineering (COE), University of Delaware (UD), Newark, DE, 19716, USA
| | - Xin Tang
- Department of Mechanical & Aerospace Engineering, Herbert Wertheim College of Engineering (HWCOE), Gainesville, FL, 32611, USA.
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
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6
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Rezaei H, Motovali-Bashi M, Khalilian S. Identification of Novel miRNAs in the F8 Gene Via Bioinformatics Tools. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2700. [PMID: 34435059 PMCID: PMC8358171 DOI: 10.30498/ijb.2021.2700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background: Hemophilia A is an X-linked bleeding disorder resulting in a deficiency of plasma clotting factor VIII and caused by mutations in the FVIII gene (F8 gene).
MicroRNAs (miRNAs) in body fluids are promising biomarker candidates for Hemophilia A, due to their stability in body fluids and accessibility by non- or minimally-invasive procedures.
Therefore; Advances in miRNA analysis methods resulted in a wide range of publications on miRNAs as putative biomarkers. Objective: Here we tried to scan the F8 gene region to predict a novel miRNA and identify it as a regulator of the F8 gene. Materials and Methods: To this aim, the ability to express novel miRNAs in F8 locus was assessed via reliable bioinformatics databases such as SSCprofiler, RNAfold, miREval, FOMmiR, MaturBayes,
miRFIND, UCSC genome browser, Deep Sequencing, and miRBase. Results: Data analysis from the relevant databases offers one stem-loop structure that is predicted to express a novel miRNA Conclusions: The diagnosis of Hemophilia A with the help of these types of biomarkers is a non-invasive procedure that has been demonstrated to have a significant role in the early diagnosis of the disease.
Hopefully, the proposed candidate sequence will be confirmed in vitro and become a non-invasive biomarker in the near future
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Affiliation(s)
- Halimeh Rezaei
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Iran
| | - Majid Motovali-Bashi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Iran
| | - Sheyda Khalilian
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Iran
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7
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Heydarzadeh S, Ranjbar M, Karimi F, Seif F, Alivand MR. Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. Cell Biosci 2021; 11:43. [PMID: 33632341 PMCID: PMC7905430 DOI: 10.1186/s13578-021-00552-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-derived structures play impressive roles in various biological processes. So dysregulation of miRNAs can lead to different human diseases. Recent studies have extended our comprehension of the control of miRNA function and features. Here, we overview some remarkable miRNA properties that have potential implications for the miRNA functions, including different variants of a miRNA called isomiRs, miRNA arm selection/arm switching, and the effect of these factors on miRNA target selection. Besides, we review some aspects of miRNA interactions such as the interaction between epigenetics and miRNA (different miRNAs and their related processing enzymes are epigenetically regulated by multiple DNA methylation enzymes. moreover, DNA methylation could be controlled by diverse mechanisms related to miRNAs), direct and indirect crosstalk between miRNA and lnc (Long Non-Coding) RNAs as a further approach to conduct intercellular regulation called "competing endogenous RNA" (ceRNA) that is involved in the pathogenesis of different diseases, and the interaction of miRNA activities and some Xeno-infectious (virus/bacteria/parasite) factors, which result in modulation of the pathogenesis of infections. This review provides some related studies to a better understanding of miRNA involvement mechanisms and overcoming the complexity of related diseases that may be applicable and useful to prognostic, diagnostic, therapeutic purposes and personalized medicine in the future.
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Affiliation(s)
- Samaneh Heydarzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Ranjbar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Farhad Seif
- Department of Immunology and Allergy, Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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8
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Felicetti T, Cecchetti V, Manfroni G. Modulating microRNA Processing: Enoxacin, the Progenitor of a New Class of Drugs. J Med Chem 2020; 63:12275-12289. [PMID: 32672457 PMCID: PMC8009507 DOI: 10.1021/acs.jmedchem.0c00510] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Indexed: 12/16/2022]
Abstract
The RNA interference (RNAi) process encompasses the cellular mechanisms by which short-noncoding RNAs posttranscriptionally modulate gene expression. First discovered in 1998, today RNAi represents the foundation underlying complex biological mechanisms that are dysregulated in many diseases. MicroRNAs are effector molecules of gene silencing in RNAi, and their modulation can lead to a wide response in cells. Enoxacin was reported as the first and unique small-molecule enhancer of microRNA (SMER) maturation. Herein, the biological activity of enoxacin as SMER is discussed to shed light on its innovative mode of action, its potential in treating different diseases, and the feasibility of using enoxacin as a chemical template for inspiring medicinal chemists. We debate its mechanism of action at the molecular level and the possible impact on future ligand and/or structure-guided chemical optimizations, as well as opportunities and drawbacks associated with the development of quinolones such as SMERs.
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Affiliation(s)
- Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
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9
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Domingues C, Alvarez-Lorenzo C, Concheiro A, Veiga F, Figueiras A. Nanotheranostic Pluronic-Like Polymeric Micelles: Shedding Light into the Dark Shadows of Tumors. Mol Pharm 2019; 16:4757-4774. [DOI: 10.1021/acs.molpharmaceut.9b00945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cátia Domingues
- Faculty of Pharmacy, University of Coimbra, Coimbra 3000-295, Portugal
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Coimbra 3004-504, Portugal
- CIMAGO, Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra 3004-531, Portugal
| | - Carmen Alvarez-Lorenzo
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Angel Concheiro
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Francisco Veiga
- Faculty of Pharmacy, University of Coimbra, Coimbra 3000-295, Portugal
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Coimbra 3004-504, Portugal
| | - Ana Figueiras
- Faculty of Pharmacy, University of Coimbra, Coimbra 3000-295, Portugal
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Coimbra 3004-504, Portugal
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10
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The MicroRNA Family Both in Normal Development and in Different Diseases: The miR-17-92 Cluster. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9450240. [PMID: 30854399 PMCID: PMC6378081 DOI: 10.1155/2019/9450240] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/27/2018] [Accepted: 01/13/2019] [Indexed: 01/29/2023]
Abstract
An increasing number of research studies over recent years have focused on the function of microRNA (miRNA) molecules which have unique characteristics in terms of structure and function. They represent a class of endogenous noncoding single-strand small molecules. An abundance of miRNA clusters has been found in the genomes of various organisms often located in a polycistron. The miR-17-92 family is among the most famous miRNAs and has been identified as an oncogene. The functions of this cluster, together with the seven individual molecules that it comprises, are most related to cancers, so it would not be surprising that they are considered to have involvement in the development of tumors. The miR-17-92 cluster is therefore expected not only to be a tumor marker, but also to perform an important role in the early diagnosis of those diseases and possibly also be a target for tumor biotherapy. The miR-17-92 cluster affects the development of disease by regulating many related cellular processes and multiple target genes. Interestingly, it also has important roles that cannot be ignored in disease of the nervous system and circulation and modulates the growth and development of bone. Therefore, it provides new opportunities for disease prevention, clinical diagnosis, prognosis, and targeted therapy. Here we review the role of the miR-17-92 cluster that has received little attention in relation to neurological diseases, cardiac diseases, and the development of bone and tumors.
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11
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Guan NN, Sun YZ, Ming Z, Li JQ, Chen X. Prediction of Potential Small Molecule-Associated MicroRNAs Using Graphlet Interaction. Front Pharmacol 2018; 9:1152. [PMID: 30374302 PMCID: PMC6196296 DOI: 10.3389/fphar.2018.01152] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/24/2018] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) have been proved to be targeted by the small molecules recently, which made using small molecules to target miRNAs become a possible therapy for human diseases. Therefore, it is very meaningful to investigate the relationships between small molecules and miRNAs, which is still yet in the newly-developing stage. In this paper, we presented a prediction model of Graphlet Interaction based inference for Small Molecule-MiRNA Association prediction (GISMMA) by combining small molecule similarity network, miRNA similarity network and known small molecule-miRNA association network. This model described the complex relationship between two small molecules or between two miRNAs using graphlet interaction which consists of 28 isomers. The association score between a small molecule and a miRNA was calculated based on counting the numbers of graphlet interaction throughout the small molecule similarity network and the miRNA similarity network, respectively. Global and two types of local leave-one-out cross validation (LOOCV) as well as five-fold cross validation were implemented in two datasets to evaluate GISMMA. For Dataset 1, the AUCs are 0.9291 for global LOOCV, 0.9505, and 0.7702 for two local LOOCVs, 0.9263 ± 0.0026 for five-fold cross validation; for Dataset 2, the AUCs are 0.8203, 0.8640, 0.6591, and 0.8554 ± 0.0063, in turn. In case study for small molecules, 5-Fluorouracil, 17β-Estradiol and 5-Aza-2'-deoxycytidine, the numbers of top 50 miRNAs predicted by GISMMA and validated to be related to these three small molecules by experimental literatures are in turn 30, 29, and 25. Based on the results from cross validations and case studies, it is easy to realize the excellent performance of GISMMA.
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Affiliation(s)
- Na-Na Guan
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Zhong Ming
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China.,National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
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12
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Memari F, Joneidi Z, Taheri B, Aval SF, Roointan A, Zarghami N. Epigenetics and Epi-miRNAs: Potential markers/therapeutics in leukemia. Biomed Pharmacother 2018; 106:1668-1677. [PMID: 30170355 DOI: 10.1016/j.biopha.2018.07.133] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 07/04/2018] [Accepted: 07/24/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic variations can play remarkable roles in different normal and abnormal situations. Such variations have been shown to have a direct role in the pathogenesis of various diseases either through inhibition of tumor suppressor genes or increasing the expression of oncogenes. Enzymes involving in epigenetic machinery are the main actors in tuning the epigenetic-based controls on gene expressions. Aberrant expression of these enzymes can trigger a big chaos in the cellular gene expression networks and finally lead to cancer progression. This situation has been shown in different types of leukemia, where high or low levels of an epigenetic enzyme are partly or highly responsible for involvement or progression of a disease. DNA hypermethylation, different histone modifications, and aberrant miRNA expressions are three main epigenetic variations, which have been shown to play a role in leukemia progression. Epigenetic based treatments now are considered as novel and effective therapies in order to decrease the abnormal epigenetic modifications in patient cells. Different epigenetic-based approaches have been developed and tested to inhibit or reverse the unusual expression of epigenetic agents in leukemia. The reciprocal behavior of miRNAs in the regulation of epigenetic modifiers, while being regulated by them, unlocks a new opportunity in order to design some epigenetic-based miRNAs able to silence or sensitize these effectors in leukemia.
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Affiliation(s)
- Fatemeh Memari
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zeinab Joneidi
- Department of Genetics and Molecular Medicine, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Behnaz Taheri
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sedigheh Fekri Aval
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Roointan
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nosratollah Zarghami
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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13
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Abstract
Genetic mosaicism arises when a zygote harbors two or more distinct genotypes, typically due to de novo, somatic mutation during embryogenesis. The clinical manifestations largely depend on the differentiation status of the mutated cell; earlier mutations target pluripotent cells and generate more widespread disease affecting multiple organ systems. If gonadal tissue is spared-as in somatic genomic mosaicism-the mutation and its effects are limited to the proband, whereas mosaicism also affecting the gametes, such as germline or gonosomal mosaicism, is transmissible. Mosaicism is easily appreciated in cutaneous disorders, as phenotypically distinct mutant cells often give rise to lesions in patterns determined by the affected cell type. Genetic investigation of cutaneous mosaic disorders has identified pathways central to disease pathogenesis, revealing novel therapeutic targets. In this review, we discuss examples of cutaneous mosaicism, approaches to gene discovery in these disorders, and insights into molecular pathobiology that have potential for clinical translation.
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Affiliation(s)
- Young H Lim
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA; .,Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Zoe Moscato
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
| | - Keith A Choate
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA; .,Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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Wang J, Xu W, Shao J, He Z, Ding Z, Huang J, Guo Q, Zou W. miR-219-5p targets CaMKIIγ to attenuate morphine tolerance in rats. Oncotarget 2018; 8:28203-28214. [PMID: 28423675 PMCID: PMC5438643 DOI: 10.18632/oncotarget.15997] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/27/2017] [Indexed: 12/27/2022] Open
Abstract
Morphine tolerance is a clinical challenge in pain management. Emerging evidence suggests that microRNA (miRNA) plays a regulatory role in the development of morphine tolerance. miR-219-5p (miR-219) targets calmodulin-dependent protein kinase II γ (CaMKIIγ) to activate central pain sensitization via N-methyl-D-aspartate (NMDA) receptor. Therefore, we hypothesized that miR-219-5p attenuates morphine tolerance by targeting CaMKIIγ. We found that the expression of miR-219-5p was decreased significantly after chronic morphine treatment. Overexpression of miR-219-5p by lentivirus injection prevents the development of morphine tolerance. CaMKIIγ, the target gene of miR-219-5p was downregulated by overexpression of miR-219-5p both in vivo and in vitro. Furthermore, we found that lentiviral-mediated miR-219-5p decreased the expression of NMDA receptor subunit 1 (NR1), leading to attenuation of morphine tolerance. Overall, the data demonstrate that miR-219-5p plays a crucial role in alleviating morphine tolerance by inhibiting the CaMKII/NMDA receptor pathway. Overexpression of miR-219-5p may be a potential strategy to ameliorate morphine tolerance.
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Affiliation(s)
- Jian Wang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wei Xu
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jiali Shao
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenghua He
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuofeng Ding
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jiangju Huang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qulian Guo
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wangyuan Zou
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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Gomes LC, Ferrão ALM, Evangelista FCG, de Almeida TD, Barbosa RC, Carvalho MDG, de Paula Sabino A. Advances in chronic lymphocytic leukemia pharmacotherapy. Biomed Pharmacother 2017; 97:349-358. [PMID: 29091884 DOI: 10.1016/j.biopha.2017.10.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/18/2017] [Accepted: 10/21/2017] [Indexed: 12/14/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a lymphoproliferative disease that affects B lymphocytes in most cases. Leukemic lymphocytes have prolonged longevity, defined by resistance to apoptosis. These cells can accumulate in peripheral blood, bone marrow, and solid lymphoid organs. CLL may be indolent or aggressive and has a range of prognostic factors such as expression of CD38 and ZAP-70, immunophenotypic and cytogenetic changes, imbalanced apoptosis proteins, and others. Although CLL has a low mortality rate, this disease is generally not considered curable until today. CLL treatment involves alkylating agents and glucocorticoids, purine analogs, monoclonal antibody therapies, and bone marrow transplantation. In recent decades, new drugs have appeared focusing on new targets and specific molecules, such as the BCR receptor, Bruton's tyrosine kinase, phosphatidylinositol 3-kinase, spleen tyrosine kinase, apoptosis proteins and microRNAs. The most appropriate treatment for CLL is one that involves in its protocol a combination of drugs according to the prognostic factors presented by each patient. In this sense, treatment individualization is essential. This article examines standard treatments for CLL and explores new treatments and potential new targets, as well as schematic protocols to understand where we are, how the treatment has evolved, and the advantages and disadvantages of new targets for CLL therapy.
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Affiliation(s)
- Lorena Caixeta Gomes
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Address: 6627, Presidente Antônio Carlos Ave, Pampulha, Zip Code 31270-901, Belo Horizonte, MG, Brazil
| | - Aline Lúcia Menezes Ferrão
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Address: 6627, Presidente Antônio Carlos Ave, Pampulha, Zip Code 31270-901, Belo Horizonte, MG, Brazil
| | - Fernanda Cristina Gontijo Evangelista
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Address: 6627, Presidente Antônio Carlos Ave, Pampulha, Zip Code 31270-901, Belo Horizonte, MG, Brazil
| | - Tâmara Dauare de Almeida
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Address: 6627, Presidente Antônio Carlos Ave, Pampulha, Zip Code 31270-901, Belo Horizonte, MG, Brazil
| | - Rayson Carvalho Barbosa
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Address: 6627, Presidente Antônio Carlos Ave, Pampulha, Zip Code 31270-901, Belo Horizonte, MG, Brazil
| | - Maria das Graças Carvalho
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Address: 6627, Presidente Antônio Carlos Ave, Pampulha, Zip Code 31270-901, Belo Horizonte, MG, Brazil
| | - Adriano de Paula Sabino
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Address: 6627, Presidente Antônio Carlos Ave, Pampulha, Zip Code 31270-901, Belo Horizonte, MG, Brazil.
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Grimaldi A, Zarone MR, Irace C, Zappavigna S, Lombardi A, Kawasaki H, Caraglia M, Misso G. Non-coding RNAs as a new dawn in tumor diagnosis. Semin Cell Dev Biol 2017; 78:37-50. [PMID: 28765094 DOI: 10.1016/j.semcdb.2017.07.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/12/2022]
Abstract
The current knowledge about non-coding RNAs (ncRNAs) as important regulators of gene expression in both physiological and pathological conditions, has been the main engine for the design of innovative platforms to finalize the pharmacological application of ncRNAs as either therapeutic tools or as molecular biomarkers in cancer. Biochemical alterations of cancer cells are, in fact, largely supported by ncRNA disregulation in the tumor site, which, in turn, reflects the cancer-associated specific modification of circulating ncRNA expression pattern. The aim of this review is to describe the state of the art of pre-clinical and clinical studies that analyze the involvement of miRNAs and lncRNAs in cancer-related processes, such as proliferation, invasion and metastases, giving emphasis to their functional role. A central node of our work has been also the examination of advantages and criticisms correlated with the clinical use of ncRNAs, taking into account the pressing need to refine the profiling methods aimed at identify novel diagnostic and prognostic markers and the request to optimize the delivery of such nucleic acids for a therapeutic use in an imminent future.
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Affiliation(s)
- Anna Grimaldi
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Mayra Rachele Zarone
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Carlo Irace
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Silvia Zappavigna
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Angela Lombardi
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Hiromichi Kawasaki
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy; Wakunaga Pharmaceutical Co. LTD, 4-5-36 Miyahara, Yodogawa-ku, Osaka 532-0003 Japan
| | - Michele Caraglia
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
| | - Gabriella Misso
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
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17
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Meng W, Tai Y, Zhao H, Fu B, Zhang T, Liu W, Li H, Yang Y, Zhang Q, Feng Y, Chen G. Downregulation of miR-33a-5p in Hepatocellular Carcinoma: A Possible Mechanism for Chemotherapy Resistance. Med Sci Monit 2017; 23:1295-1304. [PMID: 28291769 PMCID: PMC5362191 DOI: 10.12659/msm.902692] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background Multi-drug resistance is one of the major problems limiting the efficacy of cisplatin (CDDP) in treatment of hepatocellular carcinoma (HCC), and abnormal microRNA (miRNA) expression in drug-resistant cell lines plays an important role in liver cancer chemotherapy resistance. Material/Methods We established stable Hep3B and 97L HCC cell strains resistant to CDDP, both in vitro and in vivo. A combination of microRNA microarray and RT-qPCR experiments were used to screen differentially expressed miRNAs in HCC cell strains. A CCK-8 assay was carried out to detect and calculate the survival rates and relative inhibitory rates. Oligonucleotide transfection was used to confirm the regulatory function of the miRNA in HCC drug resistance. Results The IC50 of Hep3B/CDDP(v), 97L/CDDP(v), Hep3B/CDDP(s), and 97L/CDDP(s) were significantly higher than that of their parental cells. Moreover, the doubling time of drug-resistant cells increased compared with their parent cells. MiRCURYTM LNA Array (v 16.0) high-throughput tests of resistant cell models and their parent cells showed that there were 5 downregulated microRNAs in the 4 drug-resistant cell lines, and we chose hsa-miR-33a-5p as our target for further study. Oligonucleotide transfection showed that miR-33a-5p overexpression increased the cisplatin sensitivity of Hep3B/CDDP(v) and 97L/CDDP(v) drug-resistant cells and reduced their resistance. Additionally, inhibition of miR-33a-5p expression reduced cisplatin sensitivity in Hep3B and 97L and increased their drug resistance. Conclusions This study confirmed that the most downregulated microRNA, miR-33a-5p, can mediate the cisplatin resistance of HCC cells, providing a new and feasible direction for research into combatting liver cancer chemotherapy resistance.
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Affiliation(s)
- Wei Meng
- Department of Hepatic Surgery and Liver Transplantation Center of The Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangzhou, Guangdong, China (mainland)
| | - Yan Tai
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Hui Zhao
- Department of Hepatic Surgery and Liver transplantation Center of The Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangzhou, Guangdong, China (mainland)
| | - Binsheng Fu
- Department of Hepatic Surgery and Liver transplantation Center of The Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangzhou, Guangdong, China (mainland)
| | - Tong Zhang
- Department of Hepatic Surgery and Liver transplantation Center of The Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangzhou, Guangdong, China (mainland)
| | - Wei Liu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Hua Li
- Department of Hepatic Surgery and Liver transplantation Center of The Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangzhou, Guangdong, China (mainland)
| | - Yang Yang
- Department of Hepatic Surgery and Liver transplantation Center of The Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangzhou, Guangdong, China (mainland).,Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland).,Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Qi Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland).,Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Yuliang Feng
- Jackson Laboratory-Genomic Medicine, Farmington, CT, USA
| | - Guihua Chen
- Department of Hepatic Surgery and Liver transplantation Center of The Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University; Organ Transplantation Research Center of Guangdong Province, Guangzhou, Guangdong, China (mainland).,Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland).,Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
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18
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Monroig-Bosque PDC, Rivera CA, Calin GA. MicroRNAs in cancer therapeutics: "from the bench to the bedside". Expert Opin Biol Ther 2016; 15:1381-5. [PMID: 26372796 DOI: 10.1517/14712598.2015.1074999] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) are non-coding RNA transcripts that regulate physiological processes by targeting proteins directly. Their involvement in research has been robust, and evidence of their regulative functions has granted them the title: master regulators of the human genome. In cancer, they are considered important therapeutic agents, due to the fact that their aberrant expression contributes to disease development, progression, metastasis, therapeutic response and patient overall survival. This has endeavored fields of biomedical sciences to invest in developing and exploiting miRNA-based therapeutics thoroughly. Herein we highlight relevant ongoing/open clinical trials involving miRNAs and cancer.
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Affiliation(s)
- Paloma del C Monroig-Bosque
- a 1 The University of Texas MD Anderson Cancer Center, Department of Experimental Therapeutics , Houston, TX, USA .,b 2 University of Puerto Rico School of Medicine, Department of Medicine , San Juan, PR, USA
| | - Carlos A Rivera
- a 1 The University of Texas MD Anderson Cancer Center, Department of Experimental Therapeutics , Houston, TX, USA .,b 2 University of Puerto Rico School of Medicine, Department of Medicine , San Juan, PR, USA
| | - George A Calin
- a 1 The University of Texas MD Anderson Cancer Center, Department of Experimental Therapeutics , Houston, TX, USA .,c 3 The University of Texas MD Anderson Cancer Center, Center for RNA Interference and Non-Coding RNAs , Houston, TX, USA
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19
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Sager M, Yeat NC, Pajaro-Van der Stadt S, Lin C, Ren Q, Lin J. Transcriptomics in cancer diagnostics: developments in technology, clinical research and commercialization. Expert Rev Mol Diagn 2015; 15:1589-603. [PMID: 26565429 DOI: 10.1586/14737159.2015.1105133] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transcriptomic technologies are evolving to diagnose cancer earlier and more accurately to provide greater predictive and prognostic utility to oncologists and patients. Digital techniques such as RNA sequencing are replacing still-imaging techniques to provide more detailed analysis of the transcriptome and aberrant expression that causes oncogenesis, while companion diagnostics are developing to determine the likely effectiveness of targeted treatments. This article examines recent advancements in molecular profiling research and technology as applied to cancer diagnosis, clinical applications and predictions for the future of personalized medicine in oncology.
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Affiliation(s)
- Monica Sager
- a College of Arts and Sciences , Washington University in St. Louis , St. Louis , MO , USA.,b Rare Genomics Institute , Bethesda , MD , USA
| | - Nai Chien Yeat
- b Rare Genomics Institute , Bethesda , MD , USA.,c School of Medicine , Washington University in St. Louis , St. Louis , MO , USA
| | - Stefan Pajaro-Van der Stadt
- a College of Arts and Sciences , Washington University in St. Louis , St. Louis , MO , USA.,b Rare Genomics Institute , Bethesda , MD , USA
| | - Charlotte Lin
- b Rare Genomics Institute , Bethesda , MD , USA.,c School of Medicine , Washington University in St. Louis , St. Louis , MO , USA
| | - Qiuyin Ren
- b Rare Genomics Institute , Bethesda , MD , USA.,d Whiting School of Engineering , Johns Hopkins University , Baltimore , MD , USA
| | - Jimmy Lin
- b Rare Genomics Institute , Bethesda , MD , USA
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Epigenetics of Meningiomas. BIOMED RESEARCH INTERNATIONAL 2015; 2015:532451. [PMID: 26101774 PMCID: PMC4458517 DOI: 10.1155/2015/532451] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/14/2014] [Indexed: 12/20/2022]
Abstract
Meningiomas account for one-third of all adult central nervous system tumours and are divided into three WHO grades. In contrast to the relatively well characterized genetic alterations, our current understanding of epigenetic modifications involved in the meningioma-genesis and progression is rather incomplete. Contrary to genetic alterations, epigenetic changes do not alter the primary DNA sequence and their reversible nature serves as an excellent basis for prevention and development of novel personalised tumour therapies. Indeed, growing body of evidence suggests that disturbed epigenetic regulation plays a key role in the pathogenesis of meningiomas. Altered DNA methylation, microRNA expression, histone, and chromatin modifications are frequently noted in meningiomas bearing prognostic and therapeutic relevance. In this review we provide an overview on recently identified epigenetic alterations in meningiomas and discuss their role in tumour initiation, progression, and recurrence.
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Shahjahani M, Mohammadiasl J, Noroozi F, Seghatoleslami M, Shahrabi S, Saba F, Saki N. Molecular basis of chronic lymphocytic leukemia diagnosis and prognosis. Cell Oncol (Dordr) 2015; 38:93-109. [PMID: 25563586 DOI: 10.1007/s13402-014-0215-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUNDS Chronic lymphocytic leukemia (CLL) is the most common type of leukemia in adults and is characterized by a clonal accumulation of mature apoptosis-resistant neoplastic cells. It is also a heterogeneous disease with a variable clinical outcome. Here, we present a review of currently known (epi)genetic alterations that are related to the etiology, progression and chemo-refractoriness of CLL. Relevant literature was identified through a PubMed search (1994-2014) of English-language papers using the terms CLL, signaling pathway, cytogenetic abnormality, somatic mutation, epigenetic alteration and micro-RNA. RESULTS CLL is characterized by the presence of gross chromosomal abnormalities, epigenetic alterations, micro-RNA expression alterations, immunoglobulin heavy chain gene mutations and other genetic lesions. The expression of unmutated immunoglobulin heavy chain variable region (IGHV) genes, ZAP-70 and CD38 proteins, the occurrence of chromosomal abnormalities such as 17p and 11q deletions and mutations of the NOTCH1, SF3B1 and BIRC3 genes have been associated with a poor prognosis. In addition, mutations in tumor suppressor genes, such as TP53 and ATM, have been associated with refractoriness to conventional chemotherapeutic agents. Micro-RNA expression alterations and aberrant methylation patterns in genes that are specifically deregulated in CLL, including the BCL-2, TCL1 and ZAP-70 genes, have also been encountered and linked to distinct clinical parameters. CONCLUSIONS Specific chromosomal abnormalities and gene mutations may serve as diagnostic and prognostic indicators for disease progression and survival. The identification of these anomalies by state-of-the-art molecular (cyto)genetic techniques such as fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), single nucleotide polymorphism (SNP) microarray-based genomic profiling and next-generation sequencing (NGS) can be of paramount help for the clinical management of these patients, including optimal treatment design. The efficacy of novel therapeutics should to be tested according to the presence of these molecular lesions in CLL patients.
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Affiliation(s)
- Mohammad Shahjahani
- Department of Hematology and Blood Banking, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Monroig PDC, Chen L, Zhang S, Calin GA. Small molecule compounds targeting miRNAs for cancer therapy. Adv Drug Deliv Rev 2015; 81:104-16. [PMID: 25239236 DOI: 10.1016/j.addr.2014.09.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/09/2014] [Accepted: 09/03/2014] [Indexed: 11/25/2022]
Abstract
One of the most fascinating discoveries in molecular oncology has been that cancer represents a disease in which genetic alterations in protein-coding, but also in non-coding genes complement each other. MicroRNAs (miRNAs) are a type of non-coding RNA (ncRNA) transcripts that can regulate gene expression primarily by disrupting messenger RNA (mRNA) translation and/or stability, or alternatively by modulating the transcription of target mRNAs. For the last decade, miRNAs have shown to be pivotal characters of every single one of the cancer hallmarks. Profiling studies have proven the significance of identifying over-expressed miRNAs (oncomiRs) causative of the activation of oncogenic pathways that lead to malignancy. Due to their crucial role in cancer, it has become a challenge to develop efficient miRNA-inhibiting strategies such as antagomiRs, locked nucleic acids or antisense oligonucleotides. However, to this date, the accessible delivery agents and their pharmacokinetic/pharmacodynamic properties are not ideal. Thus there is an urgent, unmet need to develop miRNA-based inhibitory therapeutics. Herein we present a novel therapeutic strategy that is only at the tip of the iceberg: the use of small molecule inhibitors to target specific miRNAs (SMIRs). Furthermore we describe several high-throughput techniques to screen for SMIRs both in vitro and in silico. Finally we take you through the journey that has led to discovering the handful of SMIRs that have been validated to this date.
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Lost miRNA surveillance of Notch, IGFR pathway—road to sarcomagenesis. Tumour Biol 2013; 35:483-92. [DOI: 10.1007/s13277-013-1068-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/29/2013] [Indexed: 12/16/2022] Open
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Mao Y, Mohan R, Zhang S, Tang X. MicroRNAs as pharmacological targets in diabetes. Pharmacol Res 2013; 75:37-47. [PMID: 23810798 DOI: 10.1016/j.phrs.2013.06.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 06/10/2013] [Accepted: 06/12/2013] [Indexed: 12/14/2022]
Abstract
Diabetes is characterized by high levels of blood glucose due to either the loss of insulin-producing beta-cells in the pancreas, leading to a deficiency of insulin in type 1 diabetes, or due to increased insulin resistance, leading to reduced insulin sensitivity and productivity in type 2 diabetes. There is an increasing need for new options to treat diabetes, especially type 2 diabetes at its early stages due to an ineffective control of its development in patients. Recently, a novel class of small noncoding RNAs, termed microRNAs (miRNAs), is found to play a key role as important transcriptional and posttranscriptional inhibitors of gene expression in fine-tuning the target messenger RNAs (mRNAs). miRNAs are implicated in the pathogenesis of diabetes and have become an intriguing target for therapeutic intervention. This review focuses on the dysregulated miRNAs discovered in various diabetic models and addresses the potential for miRNAs to be therapeutic targets in the treatment of diabetes.
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Affiliation(s)
- Yiping Mao
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
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