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Sumaira S, Vijayarathna S, Hemagirri M, Adnan M, Hassan MI, Patel M, Gupta R, Shanmugapriya, Chen Y, Gopinath SC, Kanwar JR, Sasidharan S. Plant bioactive compounds driven microRNAs (miRNAs): A potential source and novel strategy targeting gene and cancer therapeutics. Noncoding RNA Res 2024; 9:1140-1158. [PMID: 39022680 PMCID: PMC11250886 DOI: 10.1016/j.ncrna.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Irrespective of medical technology improvements, cancer ranks among the leading causes of mortality worldwide. Although numerous cures and treatments exist, creating alternative cancer therapies with fewer adverse side effects is vital. Since ancient times, plant bioactive compounds have already been used as a remedy to heal cancer. These plant bioactive compounds and their anticancer activity can also deregulate the microRNAs (miRNAs) in the cancerous cells. Therefore, the deregulation of miRNAs in cancer cells by plant bioactive compounds and the usage of the related miRNA could be a promising approach for cancer cure, mainly to prevent cancer and overcome chemotherapeutic side effect problems. Hence, this review highlights the function of plant bioactive compounds as an anticancer agent through the underlying mechanism that alters the miRNA expression in cancer cells, ultimately leading to apoptosis. Moreover, this review provides insight into using plant bioactive compounds -driven miRNAs as an anticancer agent to develop miRNA-based cancer gene therapy. They can be the potential resource for gene therapy and novel strategies targeting cancer therapeutics.
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Affiliation(s)
- Sahreen Sumaira
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Soundararajan Vijayarathna
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Manisekaran Hemagirri
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, P.O. Box 2440, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mitesh Patel
- Research and Development Cell and Department of Biotechnology, Parul Institute of Applied Sciences, Parul University, Vadodara, 391760, Gujarat, India
| | - Reena Gupta
- Institute of Pharmaceutical Research, Department. Pharmaceutical Research, GLA University, Mathura, India
| | - Shanmugapriya
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Yeng Chen
- Department of Oral & Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subash C.B. Gopinath
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, Perlis, Malaysia
| | - Jagat R. Kanwar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), 174001, Bilaspur, Himachal Pradesh, India
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
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2
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Vahidi S, Agah S, Mirzajani E, Asghari Gharakhyli E, Norollahi SE, Rahbar Taramsari M, Babaei K, Samadani AA. microRNAs, oxidative stress, and genotoxicity as the main inducers in the pathobiology of cancer development. Horm Mol Biol Clin Investig 2024; 45:55-73. [PMID: 38507551 DOI: 10.1515/hmbci-2023-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
Cancer is one of the most serious leading causes of death in the world. Many eclectic factors are involved in cancer progression including genetic and epigenetic alongside environmental ones. In this account, the performance and fluctuations of microRNAs are significant in cancer diagnosis and treatment, particularly as diagnostic biomarkers in oncology. So, microRNAs manage and control the gene expression after transcription by mRNA degradation, or also they can inhibit their translation. Conspicuously, these molecular structures take part in controlling the cellular, physiological and pathological functions, which many of them can accomplish as tumor inhibitors or oncogenes. Relatively, Oxidative stress is defined as the inequality between the creation of reactive oxygen species (ROS) and the body's ability to detoxify the reactive mediators or repair the resulting injury. ROS and microRNAs have been recognized as main cancer promoters and possible treatment targets. Importantly, genotoxicity has been established as the primary reason for many diseases as well as several malignancies. The procedures have no obvious link with mutagenicity and influence the organization, accuracy of the information, or fragmentation of DNA. Conclusively, mutations in these patterns can lead to carcinogenesis. In this review article, we report the impressive and practical roles of microRNAs, oxidative stress, and genotoxicity in the pathobiology of cancer development in conjunction with their importance as reliable cancer biomarkers and their association with circulating miRNA, exosomes and exosomal miRNAs, RNA remodeling, DNA methylation, and other molecular elements in oncology.
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Affiliation(s)
- Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shahram Agah
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry and Biophysics, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | | | - Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Morteza Rahbar Taramsari
- Department of Forensic Medicine, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | - Kosar Babaei
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran
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3
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Graczyk P, Dach A, Dyrka K, Pawlik A. Pathophysiology and Advances in the Therapy of Cardiomyopathy in Patients with Diabetes Mellitus. Int J Mol Sci 2024; 25:5027. [PMID: 38732253 PMCID: PMC11084712 DOI: 10.3390/ijms25095027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/19/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Diabetes mellitus (DM) is known as the first non-communicable global epidemic. It is estimated that 537 million people have DM, but the condition has been properly diagnosed in less than half of these patients. Despite numerous preventive measures, the number of DM cases is steadily increasing. The state of chronic hyperglycaemia in the body leads to numerous complications, including diabetic cardiomyopathy (DCM). A number of pathophysiological mechanisms are behind the development and progression of cardiomyopathy, including increased oxidative stress, chronic inflammation, increased synthesis of advanced glycation products and overexpression of the biosynthetic pathway of certain compounds, such as hexosamine. There is extensive research on the treatment of DCM, and there are a number of therapies that can stop the development of this complication. Among the compounds used to treat DCM are antiglycaemic drugs, hypoglycaemic drugs and drugs used to treat myocardial failure. An important element in combating DCM that should be kept in mind is a healthy lifestyle-a well-balanced diet and physical activity. There is also a group of compounds-including coenzyme Q10, antioxidants and modulators of signalling pathways and inflammatory processes, among others-that are being researched continuously, and their introduction into routine therapies is likely to result in greater control and more effective treatment of DM in the future. This paper summarises the latest recommendations for lifestyle and pharmacological treatment of cardiomyopathy in patients with DM.
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Affiliation(s)
- Patryk Graczyk
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (P.G.); (A.D.)
| | - Aleksandra Dach
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (P.G.); (A.D.)
| | - Kamil Dyrka
- Department of Pediatric Endocrinology and Rheumatology, Institute of Pediatrics, Poznan University of Medical Sciences, 60-572 Poznan, Poland;
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (P.G.); (A.D.)
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4
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Zheng H, Wang S, Li X, Hu H. A computational modeling of pri-miRNA expression. PLoS One 2024; 19:e0290768. [PMID: 38165860 PMCID: PMC10760784 DOI: 10.1371/journal.pone.0290768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/15/2023] [Indexed: 01/04/2024] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in gene regulation. Most studies focus on mature miRNAs, which leaves many unknowns about primary miRNAs (pri-miRNAs). To fill the gap, we attempted to model the expression of pri-miRNAs in 1829 primary cell types, cell lines, and tissues in this study. We demonstrated that the expression of pri-miRNAs can be modeled well by the expression of specific sets of mRNAs, which we termed their associated mRNAs. These associated mRNAs differ from their corresponding target mRNAs and are enriched with specific functions. Most associated mRNAs of a miRNA are shared across conditions, while on average, about one-fifth of the associated mRNAs are condition-specific. Our study shed new light on understanding miRNA biogenesis and general gene transcriptional regulation.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
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5
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Singh S, Sinha T, Panda AC. Regulation of microRNA by circular RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1820. [PMID: 37783567 DOI: 10.1002/wrna.1820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Circular (circ)RNAs have emerged as novel regulators of gene expression through various mechanisms. However, most publications focus on functional circRNAs regulating target gene expression by interacting with micro (mi)RNAs and acting as competing endogenous RNAs (ceRNAs). Although the theory of miRNA sponging by ceRNAs suggests the inhibition of miRNA activity, many studies are biased toward the selection of miRNAs showing a reverse expression pattern compared with circRNA expression. Although several computational tools and molecular assays have been used to predict and validate the interaction of miRNAs with circRNAs, the actual validation of functional in vivo interactions needs careful consideration of molecular experiments with specific controls. As extensive research is being performed on circRNA, many questions arise on the functional significance of circRNA-miRNA interactions. We hope the critical discussion on the criteria for selecting circRNA-miRNA pairs for functional analysis and providing standard methods for validating circRNA-miRNA interactions will advance our understanding of circRNAs as novel gene regulators. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Translation > Regulation RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
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6
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Arabkari V, Sultana A, Barua D, Webber M, Smith T, Gupta A, Gupta S. UPR-Induced miR-616 Inhibits Human Breast Cancer Cell Growth and Migration by Targeting c-MYC. Int J Mol Sci 2023; 24:13034. [PMID: 37685841 PMCID: PMC10487498 DOI: 10.3390/ijms241713034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
C/EBP homologous protein (CHOP), also known as growth arrest and DNA damage-inducible protein 153 (GADD153), belongs to the CCAAT/enhancer-binding protein (C/EBP) family. CHOP expression is induced by unfolded protein response (UPR), and sustained CHOP activation acts as a pivotal trigger for ER stress-induced apoptosis. MicroRNA-616 is located within an intron of the CHOP gene. However, the regulation of miR-616 expression during UPR and its function in breast cancer is not clearly understood. Here we show that the expression of miR-616 and CHOP (host gene of miR-616) is downregulated in human breast cancer. Both miR-5p/-3p arms of miR-616 are expressed with levels of the 5p arm higher than the 3p arm. During conditions of ER stress, the expression of miR-616-5p and miR-616-3p arms was concordantly increased primarily through the PERK pathway. Our results show that ectopic expression of miR-616 significantly suppressed cell proliferation and colony formation, whereas knockout of miR-616 increased it. We found that miR-616 represses c-MYC expression via binding sites located in its protein coding region. Furthermore, we show that miR-616 exerted growth inhibitory effects on cells by suppressing c-MYC expression. Our results establish a new role for the CHOP locus by providing evidence that miR-616 can inhibit cell proliferation by targeting c-MYC. In summary, our results suggest a dual function for the CHOP locus, where CHOP protein and miR-616 can cooperate to inhibit cancer progression.
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Affiliation(s)
- Vahid Arabkari
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, H91 TK33 Galway, Ireland; (V.A.); (A.S.); (D.B.); (M.W.)
- Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Afrin Sultana
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, H91 TK33 Galway, Ireland; (V.A.); (A.S.); (D.B.); (M.W.)
| | - David Barua
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, H91 TK33 Galway, Ireland; (V.A.); (A.S.); (D.B.); (M.W.)
| | - Mark Webber
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, H91 TK33 Galway, Ireland; (V.A.); (A.S.); (D.B.); (M.W.)
| | - Terry Smith
- Molecular Diagnostic Research Group, College of Science, University of Galway, H91 TK33 Galway, Ireland;
| | - Ananya Gupta
- Discipline of Physiology, School of Medicine, University of Galway, H91 TK33 Galway, Ireland;
| | - Sanjeev Gupta
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, H91 TK33 Galway, Ireland; (V.A.); (A.S.); (D.B.); (M.W.)
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7
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Ma N, Hou A, Pan X, Sun F, Xu X, Yu C, Lai R, Huang R, Gong L, Xie Q, Chen J, Ren J. MiR-552-3p Regulates Multiple Fibrotic and Inflammatory genes Concurrently in Hepatic Stellate Cells Improving NASH-associated Phenotypes. Int J Biol Sci 2023; 19:3456-3471. [PMID: 37496991 PMCID: PMC10367551 DOI: 10.7150/ijbs.80760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/13/2023] [Indexed: 07/28/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by hepatic steatosis, inflammation, and progressive fibrosis. Our previous study demonstrated that microRNA-552-3p (miR-552-3p) was down-regulated in the livers of patients with NASH and alleviated hepatic glycolipid metabolic disorders. However, whether miR-552-3p affects NASH progression remains unclear. In this current study, we found that hepatic miR-552-3p expression was negatively correlated with the degree of liver fibrosis and inflammation of NASH patients. Interestingly, the level of miR-552-3p was decreased during hepatic stellate cell (HSC) activation in vitro. Overexpression of miR-552-3p could not only inhibit the expression of fibrotic and inflammatory genes, but also restrain the activation of TGF-β1/Smad3 signaling pathway by down-regulating the expression of TGFBR2 and SMAD3 in HSCs, finally suppressing HSC activation. More importantly, overexpression of miR-552-3p ameliorated liver fibrosis and inflammation in two murine models: high fat/high fructose/high cholesterol diet-induced NASH model and carbon tetrachloride (CCl4)-treated liver fibrosis model. In conclusion, miR-552-3p plays a crucial role in the pathogenesis of NASH by limiting multiple fibrotic and inflammatory pathways in HSCs, which may shed light on its therapeutic potential in NASH.
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Affiliation(s)
- Ningning Ma
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
| | - Aijun Hou
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
| | - Xiangyu Pan
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Fuguang Sun
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
| | - Xiaoding Xu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Chuwei Yu
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
| | - Rongtao Lai
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Ruimin Huang
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
| | - Likun Gong
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
| | - Qing Xie
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Jing Chen
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
| | - Jin Ren
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road Beijing 100049, China
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8
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Yuan H, Ren Q, Du Y, Ma Y, Gu L, Zhou J, Tian W, Deng D. LncRNA miR663AHG represses the development of colon cancer in a miR663a-dependent manner. Cell Death Discov 2023; 9:220. [PMID: 37400477 DOI: 10.1038/s41420-023-01510-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/05/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023] Open
Abstract
The MIR663AHG gene encodes both miR663AHG and miR663a. While miR663a contributes to the defense of host cells against inflammation and inhibits colon cancer development, the biological function of lncRNA miR663AHG has not been previously reported. In this study, the subcellular localization of lncRNA miR663AHG was determined by RNA-FISH. miR663AHG and miR663a were measured by qRT-PCR. The effects of miR663AHG on the growth and metastasis of colon cancer cells were investigated in vitro and in vivo. CRISPR/Cas9, RNA pulldown, and other biological assays were used to explore the underlying mechanism of miR663AHG. We found that miR663AHG was mainly distributed in the nucleus of Caco2 and HCT116 cells and the cytoplasm of SW480 cells. The expression level of miR663AHG was positively correlated with the level of miR663a (r = 0.179, P = 0.015) and significantly downregulated in colon cancer tissues relative to paired normal tissues from 119 patients (P < 0.008). Colon cancers with low miR663AHG expression were associated with advanced pTNM stage (P = 0.021), lymph metastasis (P = 0.041), and shorter overall survival (hazard ratio = 2.026; P = 0.021). Experimentally, miR663AHG inhibited colon cancer cell proliferation, migration, and invasion. The growth of xenografts from RKO cells overexpressing miR663AHG was slower than that of xenografts from vector control cells in BALB/c nude mice (P = 0.007). Interestingly, either RNA-interfering or resveratrol-inducing expression changes of miR663AHG or miR663a can trigger negative feedback regulation of transcription of the MIR663AHG gene. Mechanistically, miR663AHG could bind to miR663a and its precursor pre-miR663a, and prevent the degradation of miR663a target mRNAs. Disruption of the negative feedback by knockout of the MIR663AHG promoter, exon-1, and pri-miR663A-coding sequence entirely blocked these effects of miR663AHG, which was restored in cells transfected with miR663a expression vector in rescue experiment. In conclusion, miR663AHG functions as a tumor suppressor that inhibits the development of colon cancer through its cis-binding to miR663a/pre-miR663a. The cross talk between miR663AHG and miR663a expression may play dominant roles in maintaining the functions of miR663AHG in colon cancer development.
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Affiliation(s)
- Hongfan Yuan
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Cancer Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
- The Department of Medical Oncology, Sichuan Cancer Hospital and Institute, Affiliated Cancer Hospital of University of Electronic and Technology of China, Chengdu, 610042, China
| | - Qianwen Ren
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Cancer Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yantao Du
- The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Yuwan Ma
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Cancer Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Cancer Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Cancer Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Wei Tian
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Cancer Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Cancer Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
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9
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Kumar P, Courtes M, Lemmers C, Le Digarcher A, Coku I, Monteil A, Hong C, Varrault A, Liu R, Wang L, Bouschet T. Functional mapping of microRNA promoters with dCas9 fused to transcriptional regulators. Front Genet 2023; 14:1147222. [PMID: 37214422 PMCID: PMC10196145 DOI: 10.3389/fgene.2023.1147222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
MicroRNAs are small non-coding RNAs that control gene expression during development, physiology, and disease. Transcription is a key factor in microRNA abundance and tissue-specific expression. Many databases predict the location of microRNA transcription start sites and promoters. However, these candidate regions require functional validation. Here, dCas9 fused to transcriptional activators or repressors - CRISPR activation (CRISPRa) and inhibition (CRISPRi)- were targeted to the candidate promoters of two intronic microRNAs, mmu-miR-335 and hsa-miR-3662, including the promoters of their respective host genes Mest and HBS1L. We report that in mouse embryonic stem cells and brain organoids, miR-335 was downregulated upon CRISPRi of its host gene Mest. Reciprocally, CRISPRa of Mest promoter upregulated miR-335. By contrast, CRISPRa of the predicted miR-335-specific promoter (located in an intron of Mest) did not affect miR-335 levels. Thus, the expression of miR-335 only depends on the promoter activity of its host gene Mest. By contrast, miR-3662 was CRISPR activatable both by the promoter of its host gene HBS1L and an intronic sequence in HEK-293T cells. Thus, CRISPRa and CRISPRi are powerful tools to evaluate the relevance of endogenous regulatory sequences involved in microRNA transcription in defined cell types.
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Affiliation(s)
- Pradeep Kumar
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mathilde Courtes
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Céline Lemmers
- Plateforme de Vectorologie de Montpellier (PVM), BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Ilda Coku
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Arnaud Monteil
- Plateforme de Vectorologie de Montpellier (PVM), BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Charles Hong
- Vanderbilt University School of Medicine Nashville, Nashville, TN, United States
| | - Annie Varrault
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Runhua Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Lizhong Wang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
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Loh HY, Norman BP, Lai KS, Cheng WH, Nik Abd Rahman NMA, Mohamed Alitheen NB, Osman MA. Post-Transcriptional Regulatory Crosstalk between MicroRNAs and Canonical TGF-β/BMP Signalling Cascades on Osteoblast Lineage: A Comprehensive Review. Int J Mol Sci 2023; 24:ijms24076423. [PMID: 37047394 PMCID: PMC10094338 DOI: 10.3390/ijms24076423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 04/14/2023] Open
Abstract
MicroRNAs (miRNAs) are a family of small, single-stranded, and non-protein coding RNAs about 19 to 22 nucleotides in length, that have been reported to have important roles in the control of bone development. MiRNAs have a strong influence on osteoblast differentiation through stages of lineage commitment and maturation, as well as via controlling the activities of osteogenic signal transduction pathways. Generally, miRNAs may modulate cell stemness, proliferation, differentiation, and apoptosis by binding the 3'-untranslated regions (3'-UTRs) of the target genes, which then can subsequently undergo messenger RNA (mRNA) degradation or protein translational repression. MiRNAs manage the gene expression in osteogenic differentiation by regulating multiple signalling cascades and essential transcription factors, including the transforming growth factor-beta (TGF-β)/bone morphogenic protein (BMP), Wingless/Int-1(Wnt)/β-catenin, Notch, and Hedgehog signalling pathways; the Runt-related transcription factor 2 (RUNX2); and osterix (Osx). This shows that miRNAs are essential in regulating diverse osteoblast cell functions. TGF-βs and BMPs transduce signals and exert diverse functions in osteoblastogenesis, skeletal development and bone formation, bone homeostasis, and diseases. Herein, we highlighted the current state of in vitro and in vivo research describing miRNA regulation on the canonical TGF-β/BMP signalling, their effects on osteoblast linage, and understand their mechanism of action for the development of possible therapeutics. In this review, particular attention and comprehensive database searches are focused on related works published between the years 2000 to 2022, using the resources from PubMed, Google Scholar, Scopus, and Web of Science.
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Affiliation(s)
- Hui-Yi Loh
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Brendan P Norman
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Wan-Hee Cheng
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Putra Nilai, Nilai 71800, Negeri Sembilan, Malaysia
| | - Nik Mohd Afizan Nik Abd Rahman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Noorjahan Banu Mohamed Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Mohd Azuraidi Osman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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A Data-Mining Approach to Identify NF-kB-Responsive microRNAs in Tissues Involved in Inflammatory Processes: Potential Relevance in Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24065123. [PMID: 36982191 PMCID: PMC10049099 DOI: 10.3390/ijms24065123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
The nuclear factor NF-kB is the master transcription factor in the inflammatory process by modulating the expression of pro-inflammatory genes. However, an additional level of complexity is the ability to promote the transcriptional activation of post-transcriptional modulators of gene expression as non-coding RNA (i.e., miRNAs). While NF-kB’s role in inflammation-associated gene expression has been extensively investigated, the interplay between NF-kB and genes coding for miRNAs still deserves investigation. To identify miRNAs with potential NF-kB binding sites in their transcription start site, we predicted miRNA promoters by an in silico analysis using the PROmiRNA software, which allowed us to score the genomic region’s propensity to be miRNA cis-regulatory elements. A list of 722 human miRNAs was generated, of which 399 were expressed in at least one tissue involved in the inflammatory processes. The selection of “high-confidence” hairpins in miRbase identified 68 mature miRNAs, most of them previously identified as inflammamiRs. The identification of targeted pathways/diseases highlighted their involvement in the most common age-related diseases. Overall, our results reinforce the hypothesis that persistent activation of NF-kB could unbalance the transcription of specific inflammamiRNAs. The identification of such miRNAs could be of diagnostic/prognostic/therapeutic relevance for the most common inflammatory-related and age-related diseases.
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Sousa-Filho CPB, Silva V, Bolin AP, Rocha ALS, Otton R. Green tea actions on miRNAs expression – An update. Chem Biol Interact 2023; 378:110465. [PMID: 37004950 DOI: 10.1016/j.cbi.2023.110465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/17/2023] [Accepted: 03/28/2023] [Indexed: 04/01/2023]
Abstract
Compounds derived from plants have been widely studied in the context of metabolic diseases and associated clinical conditions. In this regard, although the effects of Camellia sinensis plant, from which various types of teas, such as green tea, originate, have been vastly reported in the literature, the mechanisms underlying these effects remain elusive. A deep search of the literature showed that green tea's action in different cells, tissues, and diseases is an open field in the research of microRNAs (miRNAs). miRNAs are important communicator molecules between cells in different tissues implicated in diverse cellular pathways. They have emerged as an important linkage between physiology and pathophysiology, raising the issue of polyphenols can act also by changing miRNA expression. miRNAs are short, non-coding endogenous RNA, which silence the gene functions by targeting messenger RNA (mRNA) through degradation or translation repression. Therefore, the aim of this review is to present the studies that show the main compounds of green tea modulating the expression of miRNAs in inflammation, adipose tissue, skeletal muscle, and liver. We provide an overview of a few studies that have tried to demonstrate the role of miRNAs associated with the beneficial effects of compounds from green tea. We have emphasized that there is still a considerable gap in the literature investigating the role and likely involvement of miRNAs in the extensive beneficial health effects of green tea compounds already described, indicating miRNAs as potential polyphenols' mediators with a promising field to be investigated.
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Affiliation(s)
| | - Victoria Silva
- Interdisciplinary Post-graduate Program in Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
| | - Anaysa Paola Bolin
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | | | - Rosemari Otton
- Interdisciplinary Post-graduate Program in Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil.
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13
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Zhan J, Jin K, Ding N, Zhou Y, Hu G, Yuan S, Xie R, Wen Z, Chen C, Li H, Wang DW. Positive feedback loop of miR-320 and CD36 regulates the hyperglycemic memory-induced diabetic diastolic cardiac dysfunction. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:122-138. [PMID: 36618264 PMCID: PMC9813582 DOI: 10.1016/j.omtn.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Intensive glycemic control is insufficient for reducing the risk of heart failure among patients with diabetes mellitus (DM). While the "hyperglycemic memory" phenomenon is well documented, little is known about its underlying mechanisms. In this study, a type 1 DM model was established in C57BL/6 mice using streptozotocin (STZ). Leptin receptor-deficient (db/db) mice were used as a model of type 2 DM. A type 9 adeno-associated virus was used to overexpress or knock down miR-320 in vivo. Diastolic dysfunction was observed in the type 1 DM mice with elevated miR-320 expression. However, glycemic control using insulin failed to reverse diastolic dysfunction. miR-320 knockdown protected against STZ-induced diastolic dysfunction. Similar results were observed in the type 2 DM mice. In vitro, we found that miR-320 promoted CD36 expression, which in turn induced further miR-320 expression. CD36 was rapidly induced by hyperglycemia at protein level compared with the much slower induction of miR-320, suggesting a positive feedback loop of CD36/miR-320 with CD36 protein induction as the initial triggering event. In conclusion, in DM-induced cardiac injury, miR-320 and CD36 mutually enhance each other's expression, leading to a positive feedback loop and a sustained hyperlipidemic state in the heart.
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Affiliation(s)
- Jiabing Zhan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Kunying Jin
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Nan Ding
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Yufei Zhou
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Guo Hu
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Shuai Yuan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Rong Xie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Zheng Wen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Chen Chen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China,Corresponding author: Chen Chen, Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, 1095# Jiefang Ave., Wuhan 430030, China.
| | - Huaping Li
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China,Corresponding author: Huaping Li, Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China.
| | - Dao Wen Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China,Corresponding author: Dao Wen Wang, Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China.
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Sugawara T, Kawamoto Y, Kawasaki T, Umezawa A, Akutsu H. A single allele of the hsa-miR-302/367 cluster maintains human pluripotent stem cells. Regen Ther 2022; 21:37-45. [PMID: 35702483 PMCID: PMC9162946 DOI: 10.1016/j.reth.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/13/2022] [Accepted: 05/15/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction In a diploid organism, two alleles from a single genetic locus are expressed to generate a normal phenotype. Heterozygous deleterious mutation causes a reduction of functional proteins to a half dose and insufficient amounts of functional proteins can occur to generate an in–normal phenotype, namely haploinsufficiency. Heterozygous deleterious mutation of microRNAs (miRs), non-coding RNAs that regulate the expression level of target transcripts, is still not well understood. The hsa-miR-302/367 cluster is the most abundant and specifically up-regulated miR cluster in human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) and plays an important role in the maintenance of pluripotency. Methods We targeted the hsa-miR-302/367 region via a Cas9 nuclease complex with guide RNA and replaced that region with green fluorescent protein (GFP). Using a homologous donor, consisting of left and right arms and GFP, we confirmed deletion of the hsa-miR-302/367 cluster by homologous recombination without cellular destruction by microscopy. We sub-cloned GFP-positive colonies and checked the genotype of each sub-clone by genomic PCR. We then analyzed the pluripotency of heterozygous knockout cells with a hsa-miR-302/367 cluster by assessing cell proliferation ratio, morphology, and undifferentiated marker gene expression. We also used an embryoid body formation assay and transplanted wild-type and heterozygous knockout cells into immune-deficient mice. Furthermore, to analyze the lineage-specific differentiation potential of heterozygous knockout cells, we differentiated both wild-type and heterozygous knockout cells into neural stem cells. Results Here, we show that the half dose of mature miRs from the hsa-miR-302/367 cluster loci was sufficient for the continued self-renewal of hiPSCs. All GFP-positive clones were revealed to be heterozygous knockout cells, suggesting hsa-miR-302/367 cluster homozygous knockout cells were not maintained. The cell proliferation ratio, morphology, and expression of undifferentiated marker genes were comparable between wild-type and heterozygous knockout of undifferentiated human iPSCs. In addition, we found that heterozygous knockout human iPSCs have the capacity to differentiate into three germ layers, including neural stem cells. Conclusions Taken together, a single allele of the hsa-miR-302/367 cluster expresses a sufficient amount of miRs to maintain the pluripotent properties of human stem cells. hsa-miR-302/367 cluster was deleted with CRISPR/Cas9 in human pluripotent stem cells. Homozygous hsa-miR-302/367 knockout cell was not generated.
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Affiliation(s)
| | | | | | | | - Hidenori Akutsu
- Corresponding author. Department of Reproductive Medicine, Center for Regenerative Medicine, National Center for Child Health and Development (NCCHD), Okura 2-10-1, Setagaya, Tokyo, 157-8535, Japan. Tel: +81-3-5494-7047, Fax: +81-3-5494-7048.
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15
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Azimi Sanavi M, Mahdavian F, Dorosti N, Karami N, Karami S, Khatami SH, Vakili O, Taheri-Anganeh M, Karima S, Movahedpour A. A review of highly sensitive electrochemical genosensors for microRNA detection: A novel diagnostic platform for neurodegenerative diseases diagnostics. Biotechnol Appl Biochem 2022. [PMID: 36445196 DOI: 10.1002/bab.2419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
The significant role of microRNAs in regulating gene expression and in disease tracking has handed the possibility of robust and accurate diagnosis of various diseases. Measurement of these biomarkers has also had a significant impact on the preparation of natural samples. Discovery of miRNAs is a major challenge due to their small size in the real sample and their short length, which is generally measured by complex and expensive methods. Electrochemical nanobiosensors have made significant progress in this field. Due to the delicate nature of nerve tissue repair and the significance of rapid-fire feature of neurodegenerative conditions, these biosensors can be reliably promising. This review presents advances in the field of neurodegenerative diseases diagnostics. At the same time, there are still numerous openings in this field that are a bright prospect for researchers in the rapid-fire opinion of neurological diseases and indeed nerve tissue repair.
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Affiliation(s)
- Mehrnoosh Azimi Sanavi
- Department of Biochemistry and Genetics, Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Farzaneh Mahdavian
- Department of Medical Biotechnology, Faculty of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Nafiseh Dorosti
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Sari, Iran
| | - Neda Karami
- TU Wien, Institute of Solid State Electronics, Vienna, Austria
| | - Sajedeh Karami
- Department of Chemistry, Shiraz University, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Saeed Karima
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Norouzi M, Bakhtiarizadeh MR, Salehi A. Investigation of the transability of dietary small non-coding RNAs to animals. Front Genet 2022; 13:933709. [PMID: 36134021 PMCID: PMC9483711 DOI: 10.3389/fgene.2022.933709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Our daily diet not only provides essential nutrients needed for survival and growth but also supplies bioactive ingredients to promote health and prevent disease. Recent studies have shown that exogenous microRNAs (miRNAs), xenomiRs, may enter the consumer’s body through dietary intake and regulate gene expression. This fascinating phenomenon suggests that xenomiRs can act as a new class of bioactive substances associated with mammalian systems. In contrast, several studies have failed to detect xenomiRs in consumers and reported that the observed diet-derived miRNAs in the previous studies can be related to the false positive effects of experiments. This discrepancy can be attributed to the potential artifacts related to the process of experiments, small sample size, and inefficient bioinformatics pipeline. Since this hypothesis is not generally accepted yet, more studies are required. Here, a stringent and reliable bioinformatics pipeline was used to analyze 133 miRNA sequencing data from seven different studies to investigate this phenomenon. Generally, our results do not support the transfer of diet-derived miRNAs into the animal/human tissues in every situation. Briefly, xenomiRs were absent from most samples, and also, their expressions were very low in the samples where they were present, which is unlikely to be sufficient to regulate cell transcripts. Furthermore, this study showed that the possibility of miRNAs being absorbed through animals’ diets and thus influencing gene expression during specific periods of biological development is not inconceivable. In this context, our results were in agreement with the theory of the transfer of small RNAs under certain conditions and periods as xenomiRs were found in colostrum which may modulate infants’ immune systems via post-transcriptional regulation. These findings provide evidence for the selective absorption of diet-derived small RNAs, which need to be investigated in future studies to shed light on the mechanisms underlying the transference of diet-derived miRNAs.
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Affiliation(s)
- Milad Norouzi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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17
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Ambrose JM, Anand DA, Kullappan M, Hussain S, James KM, Sreekandan RN, Suga SSD, Kamaraj D, Raghavan VPV, Mohan SK. A Computational approach to screen, predict and annotate human and chimpanzee PHEX intronic miRNAs, their gene targets, and regulatory interaction networks. Comput Biol Chem 2022; 98:107673. [DOI: 10.1016/j.compbiolchem.2022.107673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/22/2021] [Accepted: 03/27/2022] [Indexed: 11/28/2022]
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18
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Saiyed AN, Vasavada AR, Johar SRK. Recent trends in miRNA therapeutics and the application of plant miRNA for prevention and treatment of human diseases. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2022; 8:24. [PMID: 35382490 PMCID: PMC8972743 DOI: 10.1186/s43094-022-00413-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/21/2022] [Indexed: 02/17/2023] Open
Abstract
Background Researchers now have a new avenue to investigate when it comes to miRNA-based therapeutics. miRNAs have the potential to be valuable biomarkers for disease detection. Variations in miRNA levels may be able to predict changes in normal physiological processes. At the epigenetic level, miRNA has been identified as a promising candidate for distinguishing and treating various diseases and defects. Main body In recent pharmacology, plants miRNA-based drugs have demonstrated a potential role in drug therapeutics. The purpose of this review paper is to discuss miRNA-based therapeutics, the role of miRNA in pharmacoepigenetics modulations, plant miRNA inter-kingdom regulation, and the therapeutic value and application of plant miRNA for cross-kingdom approaches. Target prediction and complementarity with host genes, as well as cross-kingdom gene interactions with plant miRNAs, are also revealed by bioinformatics research. We also show how plant miRNA can be transmitted from one species to another by crossing kingdom boundaries in this review. Despite several unidentified barriers to plant miRNA cross-transfer, plant miRNA-based gene regulation in trans-kingdom gene regulation may soon be valued as a possible approach in plant-based drug therapeutics. Conclusion This review summarised the biochemical synthesis of miRNAs, pharmacoepigenetics, drug therapeutics and miRNA transkingdom transfer.
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Affiliation(s)
- Atiyabanu N. Saiyed
- Department of Cell and Molecular Biology, Iladevi Cataract and IOL Research Centre, Ahmedabad, Gujarat India
- Ph.D. scholar of Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Abhay R. Vasavada
- Department of Cell and Molecular Biology, Iladevi Cataract and IOL Research Centre, Ahmedabad, Gujarat India
| | - S. R. Kaid Johar
- Department of Zoology, BMTC, Human Genetics, USSC, Gujarat University, Ahmedabad, Gujarat India
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Hao Y, Li X. Deacetylated-poly-N-acetylglucosamine-folic Acid as a Nanocarrier for Delivering miR-196a Inhibitor to Anticancer Activity. Balkan Med J 2022; 39:55-65. [PMID: 35330543 PMCID: PMC8941238 DOI: 10.4274/balkanmedj.galenos.2021.2021-8-62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs of 17-22 nucleotides in length with a critical function in posttranscriptional gene regulation. These master regulators are themselves subject to regulation both transcriptionally and posttranscriptionally. Recently, miRNA function has been shown to be modulated by exogenous RNA molecules that function as miRNA sponges. Interestingly, endogenous transcripts such as transcribed pseudogenes, long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and mRNAs may serve as natural miRNA sponges. These transcripts, which bind to miRNAs and competitively sequester them away from their targets, are naturally existing endogenous miRNA sponges, called competing endogenous RNAs (ceRNAs). Here we present a historical background of miRNAs, exogenous and endogenous miRNA sponges as well as some examples of endogenous miRNA sponges involved in regulatory mechanisms associated with various diseases, developmental stages, and other cellular processes.
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Affiliation(s)
- Ayşe Hale Alkan
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Bünyamin Akgül
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey.
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21
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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22
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Liu B, Shyr Y, Liu Q. Pan-Cancer Analysis Reveals Common and Specific Relationships between Intragenic miRNAs and Their Host Genes. Biomedicines 2021; 9:1263. [PMID: 34572448 PMCID: PMC8471046 DOI: 10.3390/biomedicines9091263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous non-coding RNAs that play important roles in regulating gene expression. Most miRNAs are located within or close to genes (host). miRNAs and their host genes have either coordinated or independent transcription. We performed a comprehensive investigation on co-transcriptional patterns of miRNAs and host genes based on 4707 patients across 21 cancer types. We found that only 11.6% of miRNA-host pairs were co-transcribed consistently and strongly across cancer types. Most miRNA-host pairs showed a strong coexpression only in some specific cancer types, demonstrating a high heterogenous pattern. For two particular types of intergenic miRNAs, readthrough and divergent miRNAs, readthrough miRNAs showed higher coexpression with their host genes than divergent ones. miRNAs located within non-coding genes had tighter co-transcription with their hosts than those located within protein-coding genes, especially exonic and junction miRNAs. A few precursor miRNAs changed their dominate form between 5' and 3' strands in different cancer types, including miR-486, miR-99b, let-7e, miR-125a, let-7g, miR-339, miR-26a, miR-16, and miR-218, whereas only two miRNAs with multiple host genes switched their co-transcriptional partner in different cancer types (miR-219a-1 with SLC39A7/HSD17B8 and miR-3615 with RAB37/SLC9A3R1). miRNAs generated from distinct precursors (such as miR-125b from miR-125b-1 or miR-125b-2) were more likely to have cancer-dependent main contributors. miRNAs and hosts were less co-expressed in KIRC than other cancer types, possibly due to its frequent VHL mutations. Our findings shed new light on miRNA biogenesis and cancer diagnosis and treatments.
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Affiliation(s)
- Baohong Liu
- Key Laboratory of Veterinary Parasitology of Gansu Province, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Sriram V, Lee JY. Calcium phosphate-polymeric nanoparticle system for co-delivery of microRNA-21 inhibitor and doxorubicin. Colloids Surf B Biointerfaces 2021; 208:112061. [PMID: 34492599 DOI: 10.1016/j.colsurfb.2021.112061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 08/13/2021] [Accepted: 08/21/2021] [Indexed: 12/15/2022]
Abstract
Targeted combination therapy has shown promise to achieve maximum therapeutic efficacy by overcoming drug resistance. MicroRNA-21 (miR-21) is frequently overexpressed in various cancer types including breast and non-small cell lung cancer and its functions can be inhibited by miR inhibitor (miR-21i). A combination of miR-21i and a chemo drug, doxorubicin (Dox), can provide synergistic effects. Here, we developed a calcium phosphate (CaP)-coated nanoparticle (NP) formulation to co-deliver miR-21i along with Dox. This NP design can be used to deliver the two agents with different physiochemical properties. The NP formulation was optimized for particle size, polydispersity, Dox loading, and miR-21i loading. The NP formulation was confirmed to downregulate miR-21 levels and upregulate tumor suppressor gene levels. The cytotoxic efficacy of the combined miR-21i and Dox-containing NPs was found to be higher than that of Dox. Therefore, the CaP-coated hybrid lipid-polymeric NPs hold potential for the delivery of miR-21i and Dox.
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Affiliation(s)
- Vishnu Sriram
- Chemical Engineering Program, Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221-0012, United States
| | - Joo-Youp Lee
- Chemical Engineering Program, Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221-0012, United States.
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De Paolis V, Lorefice E, Orecchini E, Carissimi C, Laudadio I, Fulci V. Epitranscriptomics: A New Layer of microRNA Regulation in Cancer. Cancers (Basel) 2021; 13:3372. [PMID: 34282776 PMCID: PMC8268402 DOI: 10.3390/cancers13133372] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are pervasive regulators of gene expression at the post-transcriptional level in metazoan, playing key roles in several physiological and pathological processes. Accordingly, these small non-coding RNAs are also involved in cancer development and progression. Furthermore, miRNAs represent valuable diagnostic and prognostic biomarkers in malignancies. In the last twenty years, the role of RNA modifications in fine-tuning gene expressions at several levels has been unraveled. All RNA species may undergo post-transcriptional modifications, collectively referred to as epitranscriptomic modifications, which, in many instances, affect RNA molecule properties. miRNAs are not an exception, in this respect, and they have been shown to undergo several post-transcriptional modifications. In this review, we will summarize the recent findings concerning miRNA epitranscriptomic modifications, focusing on their potential role in cancer development and progression.
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Affiliation(s)
| | | | | | - Claudia Carissimi
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
| | - Ilaria Laudadio
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
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He G, Pang R, Han J, Jia J, Ding Z, Bi W, Yu J, Chen L, Zhang J, Sun Y. TINCR inhibits the proliferation and invasion of laryngeal squamous cell carcinoma by regulating miR-210/BTG2. BMC Cancer 2021; 21:753. [PMID: 34187411 PMCID: PMC8243464 DOI: 10.1186/s12885-021-08513-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
Background Terminal differentiation-induced ncRNA (TINCR) plays an essential role in epidermal differentiation and is involved in the development of various cancers. Methods qPCR was used to detect the expression level of TINCR in tissues and cell lines of laryngeal squamous cell carcinoma (LSCC). The potential targets of TINCR were predicted by the bioinformation website. The expression of miR-210 and BTG2 genes were detected by qPCR, and the protein levels of BTG2 and Ki-67 were evaluated by western blot. CCK-8 assay, scratch test, and transwell chamber were used to evaluate the proliferation, invasion, and metastasis ability of LSCC cells. The relationships among TINCR, miR-210, and BTG2 were investigated by bioinformatics software and luciferase reporter assay. The in vivo function of TINCR was accessed on survival rate and tumor growth in nude mice. Results We used qRT-PCR to detect the expression of TINCR in laryngeal squamous cell carcinoma (LSCC) tissues and cells and found significantly lower levels in cancer tissues compared with adjacent tissues. Additionally, patients with high TINCR expression had a better prognosis. TINCR overexpression was observed to inhibit the proliferation and invasion of LSCC cells. TINCR was shown to exert its antiproliferation and invasion effects by adsorbing miR-210, which significantly promoted the proliferation and invasion of laryngeal squamous cells. Overexpression of miR-210 was determined to reverse the tumour-suppressive effects of TINCR. BTG2 (anti-proliferation factor 2) was identified as the target gene of miR-210, and BTG2 overexpression inhibited the proliferation and invasion of LSCC cells. BTG2 knockdown relieved the inhibitory effects of TINCR on the proliferation and invasion of LSCC. Finally, TINCR upregulation slowed xenograft tumour growth in nude mice and significantly increased survival compared with control mice. Conclusion The results of this study suggest that TINCR inhibits the proliferation and invasion of LSCC by regulating the miR-210/BTG2 pathway, participates in cell cycle regulation, and may become a target for the treatment of LSCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08513-0.
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Affiliation(s)
- Guoqing He
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University, No. 246 Xuefu Road, Harbin, 150086, China
| | - Rui Pang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China
| | - Jihua Han
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China
| | - Jinliang Jia
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China
| | - Zhaoming Ding
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China
| | - Wen Bi
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China
| | - Jiawei Yu
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China
| | - Lili Chen
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China
| | - Jiewu Zhang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No.150 Haping Road, Harbin, 150081, China.
| | - Yanan Sun
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University, No. 246 Xuefu Road, Harbin, 150086, China.
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Abstract
MicroRNAs orchestrate the tight regulation of numerous cellular processes and the deregulation in their activities has been implicated in many diseases, including diabetes and cancer. There is an increasing amount of epidemiological evidence associating diabetes, particularly type 2 diabetes mellitus, to an elevated risk of various cancer types, including breast cancer. However, little is yet known about the underlying molecular mechanisms and even less about the role miRNAs play in driving the tumorigenic potential of the cell signaling underlying diabetes pathogenesis. This article reviews the role of miRNA in bridging the diabetes–breast cancer association by discussing specific miRNAs that are implicated in diabetes and breast cancer and highlighting the overlap between the disease-specific regulatory miRNA networks to identify a 20-miRNA signature that is common to both diseases. Potential therapeutic targeting of these molecular players may help to alleviate the socioeconomic burden on public health that is imposed by the type 2 diabetes mellitus (T2DM)–breast cancer association.
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27
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Liu H, Xiu Y, Zhang Q, Xu Y, Wan Q, Tao L. Silencing microRNA‑29b‑3p expression protects human trabecular meshwork cells against oxidative injury via upregulation of RNF138 to activate the ERK pathway. Int J Mol Med 2021; 47:101. [PMID: 33907817 PMCID: PMC8054636 DOI: 10.3892/ijmm.2021.4934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/26/2021] [Indexed: 12/25/2022] Open
Abstract
In recent years, the potential involvement of numerous microRNAs (miRNAs) in glaucoma has been widely reported. However, the role of microRNA-29b-3p (miR-29b-3p) in the pathogenesis of glaucoma remains unknown. This study aimed to explore the biological role and regulatory mechanism of miR-29b-3p in the oxidative injury of human trabecular meshwork (HTM) cells induced by H2O2 stimulation. By establishing a glaucoma rat model, the effects of miR-29-3p in glaucoma were detected in vivo. Our findings demonstrated that miR-29b-3p was upregulated in a glaucoma model and antagomiR-29b-3p alleviated the symptoms of glaucoma. In vitro assays revealed that miR-29b-3p expression was significantly upregulated in HTM cells with H2O2 stimulation. Knockdown of miR-29b-3p alleviated H2O2-induced oxidative injury in HTM cells by promoting cell viability, and inhibiting cell apoptosis, reactive oxygen species generation and extracellular matrix production. Subsequently, it was found that E3 ubiquitin-protein ligase RNF138 (RNF138) was a downstream target of miR-29b-3p. RNF138 expression was downregulated in HTM cells with H2O2 stimulation. RNF138 knockdown significantly rescued the protective effect of miR-29b-3p inhibitor on HTM cells under oxidative injury. Additionally, miR-29b-3p silencing activated the ERK pathway via upregulating RNF138. Collectively, silencing of miR-29b-3p protected HTM cells against oxidative injury by upregulation of RNF138 to activate the ERK pathway.
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Affiliation(s)
- Heting Liu
- Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Yanghui Xiu
- Eye Institute and Xiamen Eye Center, Affiliated Xiamen University, Xiamen, Fujian 361000, P.R. China
| | - Qing Zhang
- Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Yuxin Xu
- Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Qianqian Wan
- Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Liming Tao
- Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
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de Sousa MAP, de Athayde FRF, Maldonado MBC, de Lima AO, Fortes MRS, Lopes FL. Single nucleotide polymorphisms affect miRNA target prediction in bovine. PLoS One 2021; 16:e0249406. [PMID: 33882076 PMCID: PMC8059806 DOI: 10.1371/journal.pone.0249406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) can have significant effects on phenotypic characteristics in cattle. MicroRNAs (miRNAs) are small, non-coding RNAs that act as post-transcriptional regulators by binding them to target mRNAs. In the present study, we scanned ~56 million SNPs against 1,064 bovine miRNA sequences and analyzed, in silico, their possible effects on target binding prediction, primary miRNA formation, association with QTL regions and the evolutionary conservation for each SNP locus. Following target prediction, we show that 71.6% of miRNA predicted targets were altered as a consequence of SNPs located within the seed region of the mature miRNAs. Next, we identified variations in the Minimum Free Energy (MFE), which represents the capacity to alter molecule stability and, consequently, miRNA maturation. A total of 48.6% of the sequences analyzed showed values within those previously reported as sufficient to alter miRNA maturation. We have also found 131 SNPs in 46 miRNAs, with altered target prediction, occurring in QTL regions. Lastly, analysis of evolutionary conservation scores for each SNP locus suggested that they have a conserved biological function through the evolutionary process. Our results suggest that SNPs in microRNAs have the potential to affect bovine phenotypes and could be of great value for genetic improvement studies, as well as production.
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Affiliation(s)
- Marco Antônio Perpétuo de Sousa
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Flavia Regina Florêncio de Athayde
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Marina Rufino S. Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Flavia Lombardi Lopes
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
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Kwak JS, Kim KH. Effect of miR-155 on type I interferon response in Epithelioma papulosum cyprini cells. FISH & SHELLFISH IMMUNOLOGY 2021; 111:1-5. [PMID: 33460718 DOI: 10.1016/j.fsi.2021.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/27/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
MicroRNA-155 (miRNA-155) is known to play an important role in the regulation of innate and adaptive immune responses in mammals. However, no information is available on the role of miRNA-155 in relation to type I interferon (IFN) responses in fish cells. In the present study, we found that the protein inhibitor of activated STAT 4a (PIAS4a) gene of fathead minnow (Pimephales promelas) was a target of miR-155, which was verified by the inhibitory activity of miR-155 in the expression of reporter gene harboring 3'UTR of PIAS4a of EPC cells. Furthermore, cells over-expressing miR-155 showed a significantly higher type I IFN response after polyinosinic-polycytidylic acid (poly I:C) stimulation, suggesting the targeting of PIAS4a in EPC cells by miR-155 can be a cause of the up-regulation of type I IFN, and miR-155 can act as an antiviral factor. However, as the targeting PIAS4a might not be the sole cause of the type I IFN up-regulation by miR-155, further studies on the uncovering of miR-155 target genes that are involved in type I IFN responses in fish are required.
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Affiliation(s)
- Jun Soung Kwak
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea
| | - Ki Hong Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea.
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Cha M, Zheng H, Talukder A, Barham C, Li X, Hu H. A two-stream convolutional neural network for microRNA transcription start site feature integration and identification. Sci Rep 2021; 11:5625. [PMID: 33707582 PMCID: PMC7952457 DOI: 10.1038/s41598-021-85173-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/24/2021] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in post-transcriptional gene regulation and phenotype development. Understanding the regulation of miRNA genes is critical to understand gene regulation. One of the challenges to study miRNA gene regulation is the lack of condition-specific annotation of miRNA transcription start sites (TSSs). Unlike protein-coding genes, miRNA TSSs can be tens of thousands of nucleotides away from the precursor miRNAs and they are hard to be detected by conventional RNA-Seq experiments. A number of studies have been attempted to computationally predict miRNA TSSs. However, high-resolution condition-specific miRNA TSS prediction remains a challenging problem. Recently, deep learning models have been successfully applied to various bioinformatics problems but have not been effectively created for condition-specific miRNA TSS prediction. Here we created a two-stream deep learning model called D-miRT for computational prediction of condition-specific miRNA TSSs ( http://hulab.ucf.edu/research/projects/DmiRT/ ). D-miRT is a natural fit for the integration of low-resolution epigenetic features (DNase-Seq and histone modification data) and high-resolution sequence features. Compared with alternative computational models on different sets of training data, D-miRT outperformed all baseline models and demonstrated high accuracy for condition-specific miRNA TSS prediction tasks. Comparing with the most recent approaches on cell-specific miRNA TSS identification using cell lines that were unseen to the model training processes, D-miRT also showed superior performance.
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Affiliation(s)
- Mingyu Cha
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Amlan Talukder
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Clayton Barham
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, USA.
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL, USA.
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Transcriptome analysis of arterial and venous circulating miRNAs during hypertension. Sci Rep 2021; 11:3469. [PMID: 33568719 PMCID: PMC7875986 DOI: 10.1038/s41598-021-82979-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 01/04/2021] [Indexed: 11/18/2022] Open
Abstract
Most current circulating miRNA biomarkers are derived from peripheral venous blood, whereas miRNA deregulation in arterial blood in disease conditions has been largely ignored. To explore whether peripheral venous blood miRNAs could represent a bona fide specific miRNA deregulation pattern, we selected hypertension, a disease that is particularly associated with vessels, as the model. Circulating miRNA profiles of arterial and venous blood from spontaneously hypertensive (SHR) rats and their corresponding controls (i.e., WKY rats) were investigated by next-generation miRNA sequencing. Little miRNAs were observed between arterial and venous circulating miRNAs in WKY rats. Interestingly, this number was enhanced in SHR hypertensive rats. Bioinformatical analysis of disease association, enriched target genes and the regulatory transcription factors of these differentially expressed miRNAs implied a potential functional link with cardiovascular disease-related functions. Comparisons between arterial and venous miRNAs in hypertension-versus-control conditions also revealed prominent disease association of circulating miRNAs and their target genes in arteries but not in veins. Moreover, a young non-hypertensive animal model in SHR background (i.e. JSHR) was used as a second control for SHR. Additional transcriptomic analysis and droplet digital PCR validation of arterial and venous deregulated miRNAs among SHR and its two controls (WKY, JSHR) revealed a noticeable consensus of artery-deregulated miRNAs in hypertension and two novel arterial circulating signatures (miR-455-3p and miR-140-3p) of hypertension. These results suggest the necessity of re-evaluating the efficacy of certain venous miRNAs identified in previous studies as potential biomarkers in cardiovascular diseases or a wider disease spectrum.
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32
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Nan K, Pei JP, Fan LH, Zhang YK, Zhang X, Liu K, Shi ZB, Dang XQ, Wang KZ. Resveratrol prevents steroid-induced osteonecrosis of the femoral head via miR-146a modulation. Ann N Y Acad Sci 2021; 1503:23-37. [PMID: 33454992 DOI: 10.1111/nyas.14555] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/13/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022]
Abstract
The purpose of this study was to investigate the possible use of resveratrol (Res) to reverse abnormal osteogenesis/osteoclastogenesis activity that occurs during femoral head osteonecrosis and to explore the detailed mechanisms. Application of Res to bone marrow-derived mesenchymal stem cells in vitro promoted survival, inhibited apoptosis, and downregulated expression of reactive oxygen species expression. Moreover, Res application was associated with elevated microRNA-146a (miR-146a) expression, osteogenic differentiation, and suppressed osteoclastic differentiation, which were markedly reversed by miR-146a inhibitor. Histopathological observations and micro-computed tomography scanning results indicated that the Res-treated group had lower incidence of osteonecrosis and better bone microstructure than the untreated group. Res inhibited osteoclastogenesis through altering the levels of sirtuin1 (Sirt1), nuclear transcription factor-κB (NF-κB), and receptor activator of NF-κB ligand (RANKL). Simultaneously, Res treatment improved bone formation and increased β-catenin and runt-related transcription factor 2 (Runt2) expression levels, while reducing forkhead box class O (FOXO) family protein levels. The results of our study suggest that Res prevents steroid-induced osteonecrosis by upregulating miR-146a, and thereby stabilizes osteogenesis/osteoclastogenesis homeostasis via Wnt/FOXO and Sirt1/NF-κB pathways.
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Affiliation(s)
- Kai Nan
- Department of Orthopaedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, People's Republic of China
| | - Jun-Peng Pei
- Department of Orthopaedics, Wuhan General Hospital of Guangzhou Command, Wuhan, People's Republic of China
| | - Li-Hong Fan
- Department of Orthopaedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, People's Republic of China
| | - Yuan-Kai Zhang
- Department of Orthopaedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, People's Republic of China
| | - Xin Zhang
- Department of Orthopaedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, People's Republic of China
| | - Kang Liu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Zhi-Bin Shi
- Department of Orthopaedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, People's Republic of China
| | - Xiao-Qian Dang
- Department of Orthopaedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, People's Republic of China
| | - Kun-Zheng Wang
- Department of Orthopaedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, People's Republic of China
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Zhang D, Yamaguchi S, Zhang X, Yang B, Kurooka N, Sugawara R, Albuayjan HHH, Nakatsuka A, Eguchi J, Hiyama TY, Kamiya A, Wada J. Upregulation of Mir342 in Diet-Induced Obesity Mouse and the Hypothalamic Appetite Control. Front Endocrinol (Lausanne) 2021; 12:727915. [PMID: 34526970 PMCID: PMC8437242 DOI: 10.3389/fendo.2021.727915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/10/2021] [Indexed: 12/21/2022] Open
Abstract
In obesity and type 2 diabetes, numerous genes are differentially expressed, and microRNAs are involved in transcriptional regulation of target mRNAs, but miRNAs critically involved in the appetite control are not known. Here, we identified upregulation of miR-342-3p and its host gene Evl in brain and adipose tissues in C57BL/6 mice fed with high fat-high sucrose (HFHS) chow by RNA sequencing. Mir342 (-/-) mice fed with HFHS chow were protected from obesity and diabetes. The hypothalamic arcuate nucleus neurons co-express Mir342 and EVL. The percentage of activated NPY+pSTAT3+ neurons were reduced, while POMC+pSTAT3+ neurons increased in Mir342 (-/-) mice, and they demonstrated the reduction of food intake and amelioration of metabolic phenotypes. Snap25 was identified as a major target gene of miR-342-3p and the reduced expression of Snap25 may link to functional impairment hypothalamic neurons and excess of food intake. The inhibition of miR-342-3p may be a potential candidate for miRNA-based therapy.
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Affiliation(s)
- Dongxiao Zhang
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Satoshi Yamaguchi
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Xinhao Zhang
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Boxuan Yang
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naoko Kurooka
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Ryosuke Sugawara
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Haya Hamed H. Albuayjan
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Atsuko Nakatsuka
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Jun Eguchi
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takeshi Y. Hiyama
- Department of Cellular Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Atsunori Kamiya
- Department of Cellular Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- *Correspondence: Jun Wada,
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Li Y, Li C, Liu S, Yang J, Shi L, Yao Y. The associations and roles of microRNA single-nucleotide polymorphisms in cervical cancer. Int J Med Sci 2021; 18:2347-2354. [PMID: 33967611 PMCID: PMC8100648 DOI: 10.7150/ijms.57990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/26/2021] [Indexed: 11/05/2022] Open
Abstract
Cervical cancer is one of the fourth most common gynecological malignancies and has been identified as the fourth leading cause of cancer death in women worldwide. MicroRNAs (miRNAs) are single-stranded sequences of noncoding RNAs that are approximately 22-24 nucleotides in length. They modulate posttranscriptional mRNA expression and play critical roles in cervical cancer. Single nucleotide polymorphisms (SNPs) in miRNA genes may alter miRNA expression and maturation and have been associated with various cancers. This review mainly focuses on the roles of SNPs in miRNA genes in the development of cervical cancer and summarizes the research progress of miRNA SNPs in cervical cancer and their molecular regulation mechanisms.
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Affiliation(s)
- Yaheng Li
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Chuanyin Li
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Shuyuan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Jia Yang
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Li Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Yufeng Yao
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
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Ahn YH, Ko YH. Diagnostic and Therapeutic Implications of microRNAs in Non-Small Cell Lung Cancer. Int J Mol Sci 2020; 21:E8782. [PMID: 33233641 PMCID: PMC7699705 DOI: 10.3390/ijms21228782] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
microRNAs (miRNAs), endogenous suppressors of target mRNAs, are deeply involved in every step of non-small cell lung cancer (NSCLC) development, from tumor initiation to progression and metastasis. They play roles in cell proliferation, apoptosis, angiogenesis, epithelial-to-mesenchymal transition, migration, invasion, and metastatic colonization, as well as immunosuppression. Due to their versatility, numerous attempts have been made to use miRNAs for clinical applications. miRNAs can be used as cancer subtype classifiers, diagnostic markers, drug-response predictors, prognostic markers, and therapeutic targets in NSCLC. Many challenges remain ahead of their actual clinical application; however, when achieved, the use of miRNAs in the clinic is expected to enable great progress in the diagnosis and treatment of patients with NSCLC.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Biomarkers, Pharmacological/analysis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Carcinoma, Non-Small-Cell Lung/diagnosis
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Cell Line, Tumor
- Cell Movement/drug effects
- Cell Proliferation/drug effects
- Epithelial-Mesenchymal Transition/drug effects
- Epithelial-Mesenchymal Transition/genetics
- Epithelial-Mesenchymal Transition/immunology
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/diagnosis
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lymphatic Metastasis
- MicroRNAs/agonists
- MicroRNAs/antagonists & inhibitors
- MicroRNAs/genetics
- MicroRNAs/immunology
- Neovascularization, Pathologic/diagnosis
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/immunology
- Prognosis
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Signal Transduction
- Tumor Escape/drug effects
- Tumor Escape/genetics
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Affiliation(s)
- Young-Ho Ahn
- Department of Molecular Medicine, College of Medicine, Ewha Womans University, Seoul 07804, Korea
- Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Yoon Ho Ko
- Division of Oncology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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Keewan E, Naser SA. MiR-146a rs2910164 G > C polymorphism modulates Notch-1/IL-6 signaling during infection: a possible risk factor for Crohn's disease. Gut Pathog 2020; 12:48. [PMID: 33072191 PMCID: PMC7557229 DOI: 10.1186/s13099-020-00387-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MiR-146a, an effector mediator, targets Notch-1 and regulates the innate and adaptive immune systems response. Recently, we reported that Notch-1 signaling plays a key role in macrophage polarization and response during infection. We employed Mycobacterium avium paratuberculosis (MAP) infection in Crohn's disease (CD) as a model to demonstrate the role of Notch-1/IL-6 signaling on MCL-1 based apoptosis and intracellular MAP infection and persistence. This study was designed to investigate the impact of polymorphisms in miR146a on the immune response and infection in our MAP-CD model. METHODS We determined the incidence of miR-146a rs2910164 G > C in 42 blood samples from clinical CD patients and controls. We also measured the effect of rs2910164 on expression of Notch-1 and IL-6, and plasma IL-6 protein levels in our study group. Finally, we analyzed the blood samples for MAP DNA and studied any correlation with miR-146a polymorphism. Samples were analyzed for statistical significance using unpaired tow-tailed t-test, unpaired two-tailed z-score and odds ratio. P < 0.05 considered significant. RESULTS MiR-146a rs2910164 GC was detected at a higher incidence in CD (52.6%) compared to healthy controls (21.7%) rs2910164 GC Heterozygous polymorphism upregulated Notch-1 and IL-6, by 0.9 and 1.7-fold, respectively. As expected, MAP infection was detected more in CD samples (63%) compared to healthy controls (9%). Surprisingly, MAP infection was detected at a higher rate in samples with rs2910164 GC (67%) compared to samples with normal genotype (33%). CONCLUSIONS The data clearly associates miR-146a rs2910164 GC with an overactive immune response and increases the risk to acquire infection. The study is even more relevant now in our efforts to understand susceptibility to SARS-CoV-2 infection and the development of COVID-19. This study suggests that genetic variations among COVID-19 patients may predict who is at a higher risk of acquiring infection, developing exacerbating symptoms, and possibly death. A high scale study with more clinical samples from different disease groups is planned.
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Affiliation(s)
- Esra’a Keewan
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4110 Libra drive, Orlando, FL 32816 USA
| | - Saleh A. Naser
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4110 Libra drive, Orlando, FL 32816 USA
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Modulation of telomerase expression and function by miRNAs: Anti-cancer potential. Life Sci 2020; 259:118387. [PMID: 32890603 DOI: 10.1016/j.lfs.2020.118387] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 12/11/2022]
Abstract
Telomerase is a nucleoprotein reverse transcriptase that maintains the telomere, a protective structure at the ends of the chromosome, and is active in cancer cells, stem cells, and fetal cells. Telomerase immortalizes cancer cells and induces unlimited cell division by preventing telomere shortening. Immortalized cancer cells have unlimited proliferative potential due to telomerase activity that causes tumorigenesis and malignancy. Therefore, telomerase can be a lucrative anti-cancer target. The regulation of catalytic subunit of telomerase (TERT) determines the extent of telomerase activity. miRNAs, as an endogenous regulator of gene expression, can control telomerase activity by targeting TERT mRNA. miRNAs that have a decreasing effect on TERT translation mediate modulation of telomerase activity in cancer cells by binding to TERT mRNA and regulating TERT translation. In this review, we provide an update on miRNAs that influence telomerase activity by regulation of TERT translation.
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Identification and Validation of Circulating Micrornas as Prognostic Biomarkers in Pancreatic Ductal Adenocarcinoma Patients Undergoing Surgical Resection. J Clin Med 2020; 9:jcm9082440. [PMID: 32751582 PMCID: PMC7464450 DOI: 10.3390/jcm9082440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal and aggressive cancers with a less than 6% five-year survival rate. Circulating microRNAs (miRNAs) are emerging as a useful tool for non-invasive diagnosis and prognosis estimation in the various cancer types, including PDAC. Our study aimed to evaluate whether miRNAs in the pre-operative blood plasma specimen have the potential to predict the prognosis of PDAC patients. In total, 112 PDAC patients planned for surgical resection were enrolled in our prospective study. To identify prognostic miRNAs, we used small RNA sequencing in 24 plasma samples of PDAC patients with poor prognosis (overall survival (OS) < 16 months) and 24 plasma samples of PDAC patients with a good prognosis (OS > 20 months). qPCR validation of selected miRNA candidates was performed in the independent cohort of PDAC patients (n = 64). In the discovery phase of the study, we identified 44 miRNAs with significantly different levels in the plasma samples of the group of good and poor prognosis patients. Among these miRNAs, 23 showed lower levels, and 21 showed higher levels in plasma specimens from PDAC patients with poor prognosis. Eleven miRNAs were selected for the validation, but only miR-99a-5p and miR-365a-3p were confirmed to have significantly lower levels and miR-200c-3p higher levels in plasma samples of poor prognosis cases. Using the combination of these 3-miRNA levels, we were able to identify the patients with poor prognosis with sensitivity 85% and specificity 80% (Area Under the Curve = 0.890). Overall, 3-miRNA prognostic score associated with OS was identified in the pre-operative blood plasma samples of PDAC patients undergoing surgical resection. Following further independent validations, the detection of these miRNA may enable identification of PDAC patients who have no survival benefit from the surgical treatment, which is associated with the high morbidity rates.
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Uray K, Major E, Lontay B. MicroRNA Regulatory Pathways in the Control of the Actin-Myosin Cytoskeleton. Cells 2020; 9:E1649. [PMID: 32660059 PMCID: PMC7408560 DOI: 10.3390/cells9071649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are key modulators of post-transcriptional gene regulation in a plethora of processes, including actin-myosin cytoskeleton dynamics. Recent evidence points to the widespread effects of miRNAs on actin-myosin cytoskeleton dynamics, either directly on the expression of actin and myosin genes or indirectly on the diverse signaling cascades modulating cytoskeletal arrangement. Furthermore, studies from various human models indicate that miRNAs contribute to the development of various human disorders. The potentially huge impact of miRNA-based mechanisms on cytoskeletal elements is just starting to be recognized. In this review, we summarize recent knowledge about the importance of microRNA modulation of the actin-myosin cytoskeleton affecting physiological processes, including cardiovascular function, hematopoiesis, podocyte physiology, and osteogenesis.
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Affiliation(s)
- Karen Uray
- Correspondence: (K.U.); (B.L.); Tel.: +36-52-412345 (K.U. & B.L.)
| | | | - Beata Lontay
- Correspondence: (K.U.); (B.L.); Tel.: +36-52-412345 (K.U. & B.L.)
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Verma HK, Ratre YK, Mazzone P, Laurino S, Bhaskar LVKS. Micro RNA facilitated chemoresistance in gastric cancer: a novel biomarkers and potential therapeutics. ALEXANDRIA JOURNAL OF MEDICINE 2020. [DOI: 10.1080/20905068.2020.1779992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Henu Kumar Verma
- Developmental and Stem Cell Biology Laboratory, Institute of Experimental Endocrinology and Oncology CNR, Naples, Italy
- Section of Stem Cell and Development, Istituto di Ricerche Genetiche “Gaetano Salvatore” Biogem, Ariano Irpino, Italy
| | | | - Pellegrino Mazzone
- Section of Stem Cell and Development, Istituto di Ricerche Genetiche “Gaetano Salvatore” Biogem, Ariano Irpino, Italy
| | - Simona Laurino
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture, Italy
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Gablo NA, Prochazka V, Kala Z, Slaby O, Kiss I. Cell-free microRNAs as Non-invasive Diagnostic and Prognostic Bio- markers in Pancreatic Cancer. Curr Genomics 2020; 20:569-580. [PMID: 32581645 PMCID: PMC7290054 DOI: 10.2174/1389202921666191217095017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/01/2019] [Accepted: 12/01/2019] [Indexed: 12/22/2022] Open
Abstract
Pancreatic cancer (PaC) is one of the most lethal cancers, with an increasing global incidence rate. Unfavorable prognosis largely results from associated difficulties in early diagnosis and the absence of prognostic and predictive biomarkers that would enable an individualized therapeutic approach. In fact, PaC prognosis has not improved for years, even though much efforts and resources have been devoted to PaC research, and the multimodal management of PaC patients has been used in clinical practice. It is thus imperative to develop optimal biomarkers, which would increase diagnostic precision and improve the post-diagnostic management of PaC patients. Current trends in biomarker research envisage the unique opportunity of cell-free microRNAs (miRNAs) present in circulation to become a convenient, non-invasive tool for accurate diagnosis, prognosis and prediction of response to treatment. This review analyzes studies focused on cell-free miRNAs in PaC. The studies provide solid evidence that miRNAs are detectable in serum, blood plasma, saliva, urine, and stool, and that they present easy-to-acquire biomarkers with strong diagnostic, prognostic and predictive potential.
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Affiliation(s)
- Natalia A Gablo
- 1Central European Institute of Technology, Masaryk University, Brno, Czech Republic; 2Department of Surgery, Institutions shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; 3Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vladimir Prochazka
- 1Central European Institute of Technology, Masaryk University, Brno, Czech Republic; 2Department of Surgery, Institutions shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; 3Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Zdenek Kala
- 1Central European Institute of Technology, Masaryk University, Brno, Czech Republic; 2Department of Surgery, Institutions shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; 3Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ondrej Slaby
- 1Central European Institute of Technology, Masaryk University, Brno, Czech Republic; 2Department of Surgery, Institutions shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; 3Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Igor Kiss
- 1Central European Institute of Technology, Masaryk University, Brno, Czech Republic; 2Department of Surgery, Institutions shared with the Faculty Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; 3Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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Najminejad H, Farhadihosseinabadi B, Dabaghian M, Dezhkam A, Rigi Yousofabadi E, Najminejad R, Abdollahpour-Alitappeh M, Karimi MH, Bagheri N, Mahi-Birjand M, Ghasemi N, Mazaheri M, Kalantar SM, Seifalian A, Sheikhha MH. Key Regulatory miRNAs and their Interplay with Mechanosensing and Mechanotransduction Signaling Pathways in Breast Cancer Progression. Mol Cancer Res 2020; 18:1113-1128. [PMID: 32430354 DOI: 10.1158/1541-7786.mcr-19-1229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/14/2020] [Accepted: 05/15/2020] [Indexed: 11/16/2022]
Abstract
According to the WHO, breast cancer is the most common cancer in women worldwide. Identification of underlying mechanisms in breast cancer progression is the main concerns of researches. The mechanical forces within the tumor microenvironment, in addition to biochemical stimuli such as different growth factors and cytokines, activate signaling cascades, resulting in various changes in cancer cell physiology. Cancer cell proliferation, invasiveness, migration, and, even, resistance to cancer therapeutic agents are changed due to activation of mechanotransduction signaling. The mechanotransduction signaling is frequently dysregulated in breast cancer, indicating its important role in cancer cell features. So far, a variety of experimental investigations have been conducted to determine the main regulators of the mechanotransduction signaling. Currently, the role of miRNAs has been well-defined in the cancer process through advances in molecular-based approaches. miRNAs are small groups of RNAs (∼22 nucleotides) that contribute to various biological events in cells. The central role of miRNAs in the regulation of various mediators involved in the mechanotransduction signaling has been well clarified over the last decade. Unbalanced expression of miRNAs is associated with different pathologic conditions. Overexpression and downregulation of certain miRNAs were found to be along with dysregulation of mechanotransduction signaling effectors. This study aimed to critically review the role of miRNAs in the regulation of mediators involved in the mechanosensing pathways and clarify how the cross-talk between miRNAs and their targets affect the cell behavior and physiology of breast cancer cells.
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Affiliation(s)
- Hamid Najminejad
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Behrouz Farhadihosseinabadi
- Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Neuroscience Research Center (NRC), Iran University of Medical Sciences, Tehran, Iran
| | - Mehran Dabaghian
- Research and Development Department, Razi Vaccine and serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Asiyeh Dezhkam
- Department of Midwifery, School of Nursing and Midwifery, Iranshahr University of Medical Sciences, Iranshahr, Iran
| | | | - Reza Najminejad
- Department of Internal Medicine, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | | | | | - Nader Bagheri
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Motahareh Mahi-Birjand
- Infectious Disease Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Nasrin Ghasemi
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahta Mazaheri
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyed Mehdi Kalantar
- Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Alexander Seifalian
- Nanotechnology & Regenerative Medicine Commercialization Centre (Ltd), The London BioScience Innovation Centre, London, United Kingdom.
| | - Mohammad Hasan Sheikhha
- Genetics and Biotechnology Lab, Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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Ren X, Lin S, Kong T, Gong Y, Ma H, Zheng H, Zhang Y, Li S. The miRNAs profiling revealed by high-throughput sequencing upon WSSV infection in mud crab Scylla paramamosain. FISH & SHELLFISH IMMUNOLOGY 2020; 100:427-435. [PMID: 32147373 DOI: 10.1016/j.fsi.2020.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
microRNAs (miRNAs) are known to regulate various immune functions by silencing the target genes in both vertebrates and invertebrates. However, in mud crab Scylla paramamosain, the role of miRNAs during the response to virus invasion remains unclear. To investigate the roles of miRNAs in S. paramamosain during virus infection, the mud crab was challenged with white spot syndrome virus (WSSV) and then subjected to the transcriptional analysis at different conditions. The results of high-throughput sequencing revealed that 940,379 and 1,306,023 high-quality mappable reads were detected in the hemocyte of normal and WSSV-infected mud crabs, respectively. Besides, the total number of 261 unique miRNAs were identified. Among them, 131 miRNAs were specifically expressed in the hemocytes of normal mud crabs, 46 miRNAs were specifically transcribed in those of WSSV-infected individuals, the other 84 miRNAs were expressed in both normal and WSSV-infected individuals. Furthermore, a number of 152 (89 down-regulated and 63 up-regulated) miRNAs were found to be differentially expressed in the WSSV-infected hemocytes, normalized to the controls. The identified miRNAs were subjected to GO analysis and target gene prediction and the results suggested that the differentially regulated miRNAs were mainly correlated with the changes of the immune responses of the hemocytes, including phagocytosis, melanism, and apoptosis as well. Taken together, the results demonstrated that the expressed miRNAs during the virus infection were mainly involved in the regulation of immunological pathways in mud crabs. Our findings not only enrich the understanding of the functions of miRNAs in the innate immune system but also provide some novel potential targets for the prevention of WSSV infection in crustaceans.
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Affiliation(s)
- Xin Ren
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shanmeng Lin
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Tongtong Kong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yi Gong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Institute of Marine Sciences, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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Bedi K, Paulsen MT, Wilson TE, Ljungman M. Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing. NAR Genom Bioinform 2020; 2:lqz014. [PMID: 31709421 PMCID: PMC6824518 DOI: 10.1093/nargab/lqz014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/07/2019] [Accepted: 10/26/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are key contributors to gene regulatory networks. Because miRNAs are processed from RNA polymerase II transcripts, insight into miRNA regulation requires a comprehensive understanding of the regulation of primary miRNA transcripts. We used Bru-seq nascent RNA sequencing and hidden Markov model segmentation to map primary miRNA transcription units (TUs) across 32 human cell lines, allowing us to describe TUs encompassing 1443 miRNAs from miRBase and 438 from MirGeneDB. We identified TUs for 61 miRNAs with an unknown CAGE TSS signal for MirGeneDB miRNAs. Many primary transcripts containing miRNA sequences failed to generate mature miRNAs, suggesting that miRNA biosynthesis is under both transcriptional and post-transcriptional control. In addition to constitutive and cell-type specific TU expression regulated by differential promoter usage, miRNA synthesis can be regulated by transcription past polyadenylation sites (transcriptional read through) and promoter divergent transcription (PROMPTs). We identified 197 miRNA TUs with novel promoters, 97 with transcriptional read-throughs and 3 miRNA TUs that resemble PROMPTs in at least one cell line. The miRNA TU annotation data resource described here reveals a greater complexity in miRNA regulation than previously known and provides a framework for identifying cell-type specific differences in miRNA transcription in cancer and cell transition states.
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Affiliation(s)
- Karan Bedi
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Behl T, Kumar C, Makkar R, Gupta A, Sachdeva M. Intercalating the Role of MicroRNAs in Cancer: As Enemy or Protector. Asian Pac J Cancer Prev 2020; 21:593-598. [PMID: 32212783 PMCID: PMC7437313 DOI: 10.31557/apjcp.2020.21.3.593] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Indexed: 12/18/2022] Open
Abstract
Objective: The transformation in cells at genetic levels stimulatesthe proliferation of cancer. The current review highlights the role of miRNA in management of cancer by altering processes of body at cellular levels. Methods: A deep research on the literature available till date for miRNA in cancer was conducted using various medical sites like PubMed, MEDLINE from internet and data was collected. The articles were majorly preferred in English language. Results: The development of normal cells into cancerous cells is a multivalent procedure highlighting numerous responsible factors. During the progression of cancer, the role of oncogene and tumor suppressor genes outshines at different levels of tumorogenesis. Metastasis poses highest threat in cancer progression and fabricates obstacles to clinicians and researchers in preventing formation of tumor on secondary sites. The mesenchymal-epithelial transition (MET) and epithelial mesenchymal transition (EMT) induce dissemination and ultimately progression of cancer. Conclusion: A comprehensive knowledge of the altered genes and the mechanism by which they induce formation of tumor is essential as they contribute in proliferating cancer at various stages, aggravating clinical symptoms. Hence miRNAs can be efficiently employed as an emerging treatment therapy for cancer.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Chanchal Kumar
- Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rashita Makkar
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Amit Gupta
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
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Wang S, Talukder A, Cha M, Li X, Hu H. Computational annotation of miRNA transcription start sites. Brief Bioinform 2020; 22:380-392. [PMID: 32003428 PMCID: PMC7820843 DOI: 10.1093/bib/bbz178] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/13/2019] [Accepted: 12/29/2019] [Indexed: 12/26/2022] Open
Abstract
Motivation MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in gene regulation and phenotype development. The identification of miRNA transcription start sites (TSSs) is critical to understand the functional roles of miRNA genes and their transcriptional regulation. Unlike protein-coding genes, miRNA TSSs are not directly detectable from conventional RNA-Seq experiments due to miRNA-specific process of biogenesis. In the past decade, large-scale genome-wide TSS-Seq and transcription activation marker profiling data have become available, based on which, many computational methods have been developed. These methods have greatly advanced genome-wide miRNA TSS annotation. Results In this study, we summarized recent computational methods and their results on miRNA TSS annotation. We collected and performed a comparative analysis of miRNA TSS annotations from 14 representative studies. We further compiled a robust set of miRNA TSSs (RSmirT) that are supported by multiple studies. Integrative genomic and epigenomic data analysis on RSmirT revealed the genomic and epigenomic features of miRNA TSSs as well as their relations to protein-coding and long non-coding genes. Contact xiaoman@mail.ucf.edu, haihu@cs.ucf.edu
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Affiliation(s)
- Saidi Wang
- Computer Science, University of Central Florida, Orlando, FL-32816, US
| | - Amlan Talukder
- Computer Science, University of Central Florida, Orlando, FL-32816, US
| | - Mingyu Cha
- Computer Science, University of Central Florida, Orlando, FL-32816, US
| | - Xiaoman Li
- Burnett School of Biomedical Science, University of Central Florida, Orlando, FL-32816, US
| | - Haiyan Hu
- Computer Science, University of Central Florida, Orlando, FL-32816, US
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48
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Chen G, Zhang M, Zhu J, Chen F, Yu D, Zhang A, He J, Hua W, Duan P. Common genetic variants in pre-microRNAs are associated with cervical cancer susceptibility in southern Chinese women. J Cancer 2020; 11:2133-2138. [PMID: 32127940 PMCID: PMC7052933 DOI: 10.7150/jca.39636] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cervical cancer is a commonly diagnosed cancer among females. Polymorphisms in pre-microRNAs have been demonstrated to play critical roles in cancer. However, the roles of pre-microRNA polymorphisms in the aetiology of cervical cancer have not been well documented. We genotyped eight pre-microRNA polymorphisms in 290 cervical cancer patients and 445 cancer-free female controls using quantitative polymerase chain reaction with TaqMan probes. To estimate the association between pre-microRNA polymorphisms and the risk of cervical cancer, an unconditional logistic regression model was used to calculate the odds ratio (OR) and 95% confidence interval (CI), adjusting for age, menopause, delivery, and abortion. We found that the pre-miR-137 rs1625579 T > G polymorphism was associated with a significant decrease in cervical cancer risk (TG/GG versus TT: adjusted OR (AOR) = 0.47, 95% CI = 0.27-0.81; TG versus TT: AOR = 0.56, 95% CI = 0.34-0.91). We also observed a significant association between the pre-miR-27a rs895819 T > C polymorphism and decreased cervical cancer risk (TC/CC versus TT: AOR = 0.65, 95% CI = 0.44-0.96). Stratified analysis further demonstrated that the pre-miR-137 rs1625579 T > C and pre-miR-27a rs895819 T > C polymorphisms significantly reduced the risk of cervical cancer susceptibility in patients younger than 49 years, those who experienced fewer abortions, and clinical stage I patients. Moreover, the pre-miR-137 rs1625579 T > G polymorphism showed protective effects in premenopausal women, squamous cell carcinoma patients, and patients with unclassified types of pathologies; the pre-miR-27a rs895819 T > C polymorphism was also associated with a decreased risk in patients older than 49 years, menopausal women, and women who had experienced vaginal pregnancies. The pre-miR-137 rs1625579 T > G and pre-miR-27a rs895819 T > C polymorphisms may provide protective effects against susceptibility to cervical cancer risk.
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Affiliation(s)
- Guange Chen
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Mingyao Zhang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jiawei Zhu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Feng Chen
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Danyang Yu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Anqi Zhang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Wenfeng Hua
- Department of Laboratory Medicine and Central Laboratories, Guangdong Second Provincial General Hospital, Guangzhou 510317, Guangdong, China
- ✉ Corresponding authors: Ping Duan, Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Western Road, Wenzhou 325027, Zhejiang, China, ; or Wenfeng Hua, Department of Laboratory Medicine and Central Laboratories, Guangdong Second Provincial General Hospital, Guangzhou 510317, Guangdong, China,
| | - Ping Duan
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
- ✉ Corresponding authors: Ping Duan, Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Western Road, Wenzhou 325027, Zhejiang, China, ; or Wenfeng Hua, Department of Laboratory Medicine and Central Laboratories, Guangdong Second Provincial General Hospital, Guangzhou 510317, Guangdong, China,
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49
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Dong Y, Lin Y, Gao X, Zhao Y, Wan Z, Wang H, Wei M, Chen X, Qin W, Yang G, Liu L. Targeted blocking of miR328 lysosomal degradation with alkalized exosomes sensitizes the chronic leukemia cells to imatinib. Appl Microbiol Biotechnol 2019; 103:9569-9582. [PMID: 31701195 DOI: 10.1007/s00253-019-10127-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 02/05/2023]
Abstract
Imatinib resistance remains the biggest hurdle for the treatment of chronic myeloid leukemia (CML), with the underlying mechanisms not fully understood. In this study, we found that miR328 significantly and strikingly decreased among other miRNA candidates during the induction of imatinib resistance. Overexpression of miR328 sensitized resistant cells to imatinib via post-transcriptionally decreasing ABCG2 expression, while miR328 knockdown conferred imatinib resistance in parental K562 cells. Moreover, miR328 was found selectively degraded in the lysosomes of K562R cells, as inhibition of lysosome with chloroquine restored miR328 expression and increased sensitivity to imatinib. Moreover, delivery of alkalized exosomes increased endogenous miR328 expression. Compared with the corresponding controls, the alkalized exosomes with or without miR328 sensitized the chronic leukemia cells to imatinib. Taken together, our study has revealed that lysosomal clearance of miR328 in imatinib-resistant cells at least partially contributes to the drug resistance, while delivery of alkalized exosomes would sensitize the chromic leukemia cells to imatinib.
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Affiliation(s)
- Yan Dong
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Yao Lin
- Department of Stomatology, the Second Affiliated hospital, Shantou University Medical College, Shantou, China
| | - Xiaotong Gao
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Yingxin Zhao
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Zhuo Wan
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Haotian Wang
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Mengying Wei
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Changlexi Road NO.169th, Xi'an, 710032, China
| | - Xutao Chen
- Department of Implantation, School of Stomatology, Fourth Military Medical University, Xi'an, China
| | - Weiwei Qin
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China
| | - Guodong Yang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Changlexi Road NO.169th, Xi'an, 710032, China.
| | - Li Liu
- Department of Hematology, Tangdu Hospital, Fourth Military Medical University, Xinsi Road NO. 569th, Xi'an, 710038, China.
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50
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Pan P, Weisenberger DJ, Zheng S, Wolf M, Hwang DG, Rose-Nussbaumer JR, Jurkunas UV, Chan MF. Aberrant DNA methylation of miRNAs in Fuchs endothelial corneal dystrophy. Sci Rep 2019; 9:16385. [PMID: 31705138 PMCID: PMC6841734 DOI: 10.1038/s41598-019-52727-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Homeostatic maintenance of corneal endothelial cells is essential for maintenance of corneal deturgescence and transparency. In Fuchs endothelial corneal dystrophy (FECD), an accelerated loss and dysfunction of endothelial cells leads to progressively severe visual impairment. An abnormal accumulation of extracellular matrix (ECM) is a distinctive hallmark of the disease, however the molecular pathogenic mechanisms underlying this phenomenon are not fully understood. Here, we investigate genome-wide and sequence-specific DNA methylation changes of miRNA genes in corneal endothelial samples from FECD patients. We discover that miRNA gene promoters are frequent targets of aberrant DNA methylation in FECD. More specifically, miR-199B is extensively hypermethylated and its mature transcript miR-199b-5p was previously found to be almost completely silenced in FECD. Furthermore, we find that miR-199b-5p directly and negatively regulates Snai1 and ZEB1, two zinc finger transcription factors that lead to increased ECM deposition in FECD. Taken together, these findings suggest a novel epigenetic regulatory mechanism of matrix protein production by corneal endothelial cells in which miR-199B hypermethylation leads to miR-199b-5p downregulation and thereby the increased expression of its target genes, including Snai1 and ZEB1. Our results support miR-199b-5p as a potential therapeutic target to prevent or slow down the progression of FECD disease.
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Affiliation(s)
- Peipei Pan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Siyu Zheng
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Marie Wolf
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - David G Hwang
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA.,Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Jennifer R Rose-Nussbaumer
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA.,Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Ula V Jurkunas
- Department of Ophthalmology, Harvard Medical School, and Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA, USA
| | - Matilda F Chan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA. .,Francis I. Proctor Foundation, University of California, San Francisco, CA, USA.
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