1
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Maruhashi K, Kashima H, Miyano S, Park H. Meta graphical lasso: uncovering hidden interactions among latent mechanisms. Sci Rep 2024; 14:18105. [PMID: 39103384 DOI: 10.1038/s41598-024-68959-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024] Open
Abstract
In complex systems, it's crucial to uncover latent mechanisms and their context-dependent relationships. This is especially true in medical research, where identifying unknown cancer mechanisms and their impact on phenomena like drug resistance is vital. Directly observing these mechanisms is challenging due to measurement complexities, leading to an approach that infers latent mechanisms from observed variable distributions. Despite machine learning advancements enabling sophisticated generative models, their black-box nature complicates the interpretation of complex latent mechanisms. A promising method for understanding these mechanisms involves estimating latent factors through linear projection, though there's no assurance that inferences made under specific conditions will remain valid across contexts. We propose a novel solution, suggesting data, even from systems appearing complex, can often be explained by sparse dependencies among a few common latent factors, regardless of the situation. This simplification allows for modeling that yields significant insights across diverse fields. We demonstrate this with datasets from finance, where we capture societal trends from stock price movements, and medicine, where we uncover new insights into cancer drug resistance through gene expression analysis.
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Affiliation(s)
- Koji Maruhashi
- Fujitsu Research, 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki, 2118588, Kanagawa, Japan.
| | | | - Satoru Miyano
- M &D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan
| | - Heewon Park
- M &D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, 2, Bomun-ro 34da-gil, Seongbuk-gu, Seoul, 02844, Republic of Korea.
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2
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Guan YJ, Yu CQ, Li LP, You ZH, Wei MM, Wang XF, Yang C, Guo LX. MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules. BMC Bioinformatics 2024; 25:6. [PMID: 38166644 PMCID: PMC10763044 DOI: 10.1186/s12859-023-05629-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
According to the expression of miRNA in pathological processes, miRNAs can be divided into oncogenes or tumor suppressors. Prediction of the regulation relations between miRNAs and small molecules (SMs) becomes a vital goal for miRNA-target therapy. But traditional biological approaches are laborious and expensive. Thus, there is an urgent need to develop a computational model. In this study, we proposed a computational model to predict whether the regulatory relationship between miRNAs and SMs is up-regulated or down-regulated. Specifically, we first use the Large-scale Information Network Embedding (LINE) algorithm to construct the node features from the self-similarity networks, then use the General Attributed Multiplex Heterogeneous Network Embedding (GATNE) algorithm to extract the topological information from the attribute network, and finally utilize the Light Gradient Boosting Machine (LightGBM) algorithm to predict the regulatory relationship between miRNAs and SMs. In the fivefold cross-validation experiment, the average accuracies of the proposed model on the SM2miR dataset reached 79.59% and 80.37% for up-regulation pairs and down-regulation pairs, respectively. In addition, we compared our model with another published model. Moreover, in the case study for 5-FU, 7 of 10 candidate miRNAs are confirmed by related literature. Therefore, we believe that our model can promote the research of miRNA-targeted therapy.
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Affiliation(s)
- Yong-Jian Guan
- School of Information Engineering, Xijing University, Xi'an, China
| | - Chang-Qing Yu
- School of Information Engineering, Xijing University, Xi'an, China.
| | - Li-Ping Li
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, China.
- College of Agriculture and Forestry, Longdong University, Qingyang, China.
| | - Zhu-Hong You
- School of Computer Science, North-Western Polytechnical University, Xi'an, China
| | - Meng-Meng Wei
- School of Information Engineering, Xijing University, Xi'an, China
| | - Xin-Fei Wang
- School of Information Engineering, Xijing University, Xi'an, China
| | - Chen Yang
- School of Information Engineering, Xijing University, Xi'an, China
| | - Lu-Xiang Guo
- School of Information Engineering, Xijing University, Xi'an, China
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3
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Rafiq M, Dandare A, Javed A, Liaquat A, Raja AA, Awan HM, Khan MJ, Naeem A. Competing Endogenous RNA Regulatory Networks of hsa_circ_0126672 in Pathophysiology of Coronary Heart Disease. Genes (Basel) 2023; 14:genes14030550. [PMID: 36980823 PMCID: PMC10047999 DOI: 10.3390/genes14030550] [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: 12/28/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Coronary heart disease (CHD) is a global health concern, and its molecular origin is not fully elucidated. Dysregulation of ncRNAs has been linked to many metabolic and infectious diseases. This study aimed to explore the role of circRNAs in the pathogenesis of CHD and predicted a candidate circRNA that could be targeted for therapeutic approaches to the disease. circRNAs associated with CHD were identified and CHD gene expression profiles were obtained, and analyzed with GEO2R. In addition, differentially expressed miRNA target genes (miR-DEGs) were identified and subjected to functional enrichment analysis. Networks of circRNA/miRNA/mRNA and the miRNA/affected pathways were constructed. Furthermore, a miRNA/mRNA homology study was performed. We identified that hsa_circ_0126672 was strongly associated with the CHD pathology by competing for endogenous RNA (ceRNA) mechanisms. hsa_circ_0126672 characteristically sponges miR-145-5p, miR-186-5p, miR-548c-3p, miR-7-5p, miR-495-3p, miR-203a-3p, and miR-21. Up-regulation of has_circ_0126672 affected various CHD-related cellular functions, such as atherosclerosis, JAK/STAT, and Apelin signaling pathways. Our results also revealed a perfect and stable interaction for the hybrid of miR-145-5p with NOS1 and RPS6KB1. Finally, miR-145-5p had the highest degree of interaction with the validated small molecules. Henchashsa_circ_0126672 and target miRNAs, notably miR-145-5p, could be good candidates for the diagnosis and therapeutic approaches to CHD.
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Affiliation(s)
- Muhammad Rafiq
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad 45550, Pakistan
| | - Abdullahi Dandare
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Usmanu Danfodiyo University Sokoto, Sokoto P.M.B 2346, Nigeria
| | - Arham Javed
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad 45550, Pakistan
| | - Afrose Liaquat
- Department of Biochemistry, Shifa College of Medicine, Shifa Tameer-e-Millat University, Islamabad 45550, Pakistan
| | - Afraz Ahmad Raja
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Hassaan Mehboob Awan
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Correspondence: (M.J.K.); (A.N.); Tel.: +92-519-049-6140 (M.J.K)
| | - Aisha Naeem
- Health Research Governance Department, Ministry of Public Health, Doha P.O. Box 42, Qatar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Correspondence: (M.J.K.); (A.N.); Tel.: +92-519-049-6140 (M.J.K)
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4
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Nutraceutical-Based Nanoformulations for Breast and Ovarian Cancer Treatment. Int J Mol Sci 2022; 23:ijms231912032. [PMID: 36233349 PMCID: PMC9569679 DOI: 10.3390/ijms231912032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Different strategies have been investigated for a more satisfactory treatment of advanced breast cancer, including the adjuvant use of omega-3 polyunsaturated fatty acids (PUFAs). These nutritional compounds have been shown to possess potent anti-inflammatory and antiangiogenic activities, the capacity to affect transduction pathways/receptors involved in cell growth and to reprogram tumor microenvironment. Omega-3 PUFA-containing nanoformulations designed for drug delivery in breast cancer were shown to potentiate the effects of enclosed drugs, enhance drug delivery to target sites, and minimize drug-induced side effects. We have critically analyzed here the results of the most recent studies investigating the effects of omega-3 PUFA-containing nanoformulations in breast cancer. The anti-neoplastic efficacy of omega-3 PUFAs has also been convincingly demonstrated by using preclinical in vivo models of ovarian cancer. The results obtained are critically analyzed here and seem to provide a sufficient rationale to move to still lacking interventional clinical trials, as well as to evaluate possible advantages of enclosing omega-3 PUFAs to drug-delivery nanosystems for ovarian cancer. Future perspectives in this area are also provided.
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Yu F, Li B, Sun J, Qi J, De Wilde RL, Torres-de la Roche LA, Li C, Ahmad S, Shi W, Li X, Chen Z. PSRR: A Web Server for Predicting the Regulation of miRNAs Expression by Small Molecules. Front Mol Biosci 2022; 9:817294. [PMID: 35386297 PMCID: PMC8979021 DOI: 10.3389/fmolb.2022.817294] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
Background: MicroRNAs (miRNAs) play key roles in a variety of pathological processes by interacting with their specific target mRNAs for translation repression and may function as oncogenes (oncomiRs) or tumor suppressors (TSmiRs). Therefore, a web server that could predict the regulation relations between miRNAs and small molecules is expected to achieve implications for identifying potential therapeutic targets for anti-tumor drug development. Methods: Upon obtaining positive/known small molecule-miRNA regulation pairs from SM2miR, we generated a multitude of high-quality negative/unknown pairs by leveraging similarities between the small molecule structures. Using the pool of the positive and negative pairs, we created the Dataset1 and Dataset2 datasets specific to up-regulation and down-regulation pairs, respectively. Manifold machine learning algorithms were then employed to construct models of predicting up-regulation and down-regulation pairs on the training portion of pairs in Dataset1 and Dataset2, respectively. Prediction abilities of the resulting models were further examined by discovering potential small molecules to regulate oncogenic miRNAs identified from miRNA sequencing data of endometrial carcinoma samples. Results: The random forest algorithm outperformed four machine-learning algorithms by achieving the highest AUC values of 0.911 for the up-regulation model and 0.896 for the down-regulation model on the testing datasets. Moreover, the down-regulation and up-regulation models yielded the accuracy values of 0.91 and 0.90 on independent validation pairs, respectively. In a case study, our model showed highly-reliable results by confirming all top 10 predicted regulation pairs as experimentally validated pairs. Finally, our predicted binding affinities of oncogenic miRNAs and small molecules bore a close resemblance to the lowest binding energy profiles using molecular docking. Predictions of the final model are freely accessible through the PSRR web server at https://rnadrug.shinyapps.io/PSRR/. Conclusion: Our study provides a novel web server that could effectively predict the regulation of miRNAs expression by small molecules.
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Affiliation(s)
- Fanrong Yu
- Department of Obstetrics and Gynecology, Fengxian District Central Hospital, Shanghai Jiao Tong University Affiliated to Sixth People’s Hospital South Campus, Shanghai, China
| | - Bihui Li
- Department of Oncology, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Jianfeng Sun
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technical University of Munich, Freising, Germany
| | - Jing Qi
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße, Düsseldorf, Germany
| | - Rudy Leon De Wilde
- University Hospital for Gynecology, Pius-Hospital, University Medicine Oldenburg, Oldenburg, Germany
| | | | - Cheng Li
- Department of Orthopaedic Surgery, Beijing Jishuitan Hospital, Fourth Clinical College of Peking University, Beijing, China
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Wenjie Shi
- University Hospital for Gynecology, Pius-Hospital, University Medicine Oldenburg, Oldenburg, Germany
| | - Xiqing Li
- Oncology Department, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- *Correspondence: Zihao Chen, ; Xiqing Li,
| | - Zihao Chen
- University Hospital for Gynecology, Pius-Hospital, University Medicine Oldenburg, Oldenburg, Germany
- *Correspondence: Zihao Chen, ; Xiqing Li,
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Iwamoto N, Furukawa K, Endo Y, Shimizu T, Sumiyoshi R, Umeda M, Koga T, Kawashiri SY, Igawa T, Ichinose K, Tamai M, Origuchi T, Kawakami A. Methotrexate Alters the Expression of microRNA in Fibroblast-like Synovial Cells in Rheumatoid Arthritis. Int J Mol Sci 2021; 22:ijms222111561. [PMID: 34768991 PMCID: PMC8584010 DOI: 10.3390/ijms222111561] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to investigate the effect of methotrexate (MTX) on microRNA modulation in rheumatoid arthritis fibroblast-like synovial cells (RA-FLS). RA-FLS were treated with MTX for 48 h. We then performed miRNA array analysis to investigate differentially expressed miRNAs. Transfection with miR-877-3p precursor and inhibitor were used to investigate the functional role of miR-877-3p in RA-FLS. Gene ontology analysis was used to investigate the cellular processes involving miR-877-3p. The production of cytokines/chemokines was screened by multiplex cytokine/chemokine bead assay and confirmed by ELISA and quantitative real-time PCR. The migratory and proliferative activities of RA-FLS were analyzed by wound healing assay and MKI-67 expression. MTX treatment altered the expression of 13 miRNAs (seven were upregulated and six were downregulated). Among them, quantitative real-time PCR confirmed that miR-877-3p was upregulated in response to MTX (1.79 ± 0.46-fold, p < 0.05). The possible target genes of miR-877-3p in RA-FLS revealed by the microarray analysis were correlated with biological processes. The overexpression of miR-877-3p decreased the production of GM-CSF and CCL3, and the overexpression of miR-877-3p inhibited migratory and proliferative activity. MTX altered the miR-877-3p expression on RA-FLS, and this alteration of miR-877-3p attenuated the abundant production of cytokines/chemokines and proliferative property of RA-FLS.
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Affiliation(s)
- Naoki Iwamoto
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
- Correspondence: ; Tel.: +81-95-819-7260; Fax: +81-95-849-7270
| | - Kaori Furukawa
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Yushiro Endo
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Toshimasa Shimizu
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Remi Sumiyoshi
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Masataka Umeda
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Tomohiro Koga
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan
| | - Shin-ya Kawashiri
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
- Division of Advanced Preventive Medical Sciences, Department of Community Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan
| | - Takashi Igawa
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Kunihiro Ichinose
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Mami Tamai
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
| | - Tomoki Origuchi
- Department of Physical Therapy, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan;
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8102, Japan; (K.F.); (Y.E.); (T.S.); (R.S.); (M.U.); (T.K.); (S.-y.K.); (T.I.); (K.I.); (M.T.); (A.K.)
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Nasiri-Aghdam M, Garcia-Garduño TC, Jave-Suárez LF. CELF Family Proteins in Cancer: Highlights on the RNA-Binding Protein/Noncoding RNA Regulatory Axis. Int J Mol Sci 2021; 22:11056. [PMID: 34681716 PMCID: PMC8537729 DOI: 10.3390/ijms222011056] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional modifications to coding and non-coding RNAs are unquestionably a pivotal way in which human mRNA and protein diversity can influence the different phases of a transcript's life cycle. CELF (CUGBP Elav-like family) proteins are RBPs (RNA-binding proteins) with pleiotropic capabilities in RNA processing. Their responsibilities extend from alternative splicing and transcript editing in the nucleus to mRNA stability, and translation into the cytoplasm. In this way, CELF family members have been connected to global alterations in cancer proliferation and invasion, leading to their identification as potential tumor suppressors or even oncogenes. Notably, genetic variants, alternative splicing, phosphorylation, acetylation, subcellular distribution, competition with other RBPs, and ultimately lncRNAs, miRNAs, and circRNAs all impact CELF regulation. Discoveries have emerged about the control of CELF functions, particularly via noncoding RNAs, and CELF proteins have been identified as competing, antagonizing, and regulating agents of noncoding RNA biogenesis. On the other hand, CELFs are an intriguing example through which to broaden our understanding of the RBP/noncoding RNA regulatory axis. Balancing these complex pathways in cancer is undeniably pivotal and deserves further research. This review outlines some mechanisms of CELF protein regulation and their functional consequences in cancer physiology.
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Affiliation(s)
- Maryam Nasiri-Aghdam
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Texali C. Garcia-Garduño
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Ciencias Biomédicas, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Luis Felipe Jave-Suárez
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
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Chalabi-Dchar M, Fenouil T, Machon C, Vincent A, Catez F, Marcel V, Mertani HC, Saurin JC, Bouvet P, Guitton J, Venezia ND, Diaz JJ. A novel view on an old drug, 5-fluorouracil: an unexpected RNA modifier with intriguing impact on cancer cell fate. NAR Cancer 2021; 3:zcab032. [PMID: 34409299 PMCID: PMC8364333 DOI: 10.1093/narcan/zcab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/01/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
5-Fluorouracil (5-FU) is a chemotherapeutic drug widely used to treat patients with solid tumours, such as colorectal and pancreatic cancers. Colorectal cancer (CRC) is the second leading cause of cancer-related death and half of patients experience tumour recurrence. Used for over 60 years, 5-FU was long thought to exert its cytotoxic effects by altering DNA metabolism. However, 5-FU mode of action is more complex than previously anticipated since 5-FU is an extrinsic source of RNA modifications through its ability to be incorporated into most classes of RNA. In particular, a recent report highlighted that, by its integration into the most abundant RNA, namely ribosomal RNA (rRNA), 5-FU creates fluorinated active ribosomes and induces translational reprogramming. Here, we review the historical knowledge of 5-FU mode of action and discuss progress in the field of 5-FU-induced RNA modifications. The case of rRNA, the essential component of ribosome and translational activity, and the plasticity of which was recently associated with cancer, is highlighted. We propose that translational reprogramming, induced by 5-FU integration in ribosomes, contributes to 5-FU-driven cell plasticity and ultimately to relapse.
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Affiliation(s)
- Mounira Chalabi-Dchar
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Tanguy Fenouil
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Christelle Machon
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Anne Vincent
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Frédéric Catez
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Jean-Christophe Saurin
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Philippe Bouvet
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Jérôme Guitton
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Nicole Dalla Venezia
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
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Murugan B, Krishnan UM. Differently sized drug-loaded mesoporous silica nanoparticles elicit differential gene expression in MCF-7 cancer cells. Nanomedicine (Lond) 2021; 16:1017-1034. [PMID: 33970678 DOI: 10.2217/nnm-2020-0375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study investigates the effects of different sized unmodified and chemo-responsive mesoporous silica nanocarriers on MCF-7 cancer cells. Materials & methods: Unmodified and thiol-functionalized large and small-sized mesoporous MCM-41 silica nanoparticles prepared using templated sol-gel process were characterized for their physicochemical properties and in vitro and in vivo anticancer efficacy. Microarray analysis was carried out to assess their differential effect on gene expression. Results: Thiol-functionalized nanoparticles displayed chemo responsive release and greater cytotoxicity to cancer cells when compared with unmodified carriers. Microarray studies showed distinct differences in genes differentially regulated by sMCM-41and lMCM-41 carriers when compared with the free drug. Conclusion: The small chemo-responsive carrier was more effective in suppressing oncogenes and genes involved in proliferation, invasion and survival while the large carrier mainly altered membrane-associated pathways.
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Affiliation(s)
- Baranya Murugan
- Centre for Nanotechnology & Advanced Biomaterials, SASTRA Deemed-to-be University, Thanjavur, 613401, India.,School of Chemical & Biotechnology, SASTRA Deemed-to-be University, Thanjavur, 613401, India
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology & Advanced Biomaterials, SASTRA Deemed-to-be University, Thanjavur, 613401, India.,School of Chemical & Biotechnology, SASTRA Deemed-to-be University, Thanjavur, 613401, India.,School of Arts, Science & Humanities, SASTRA Deemed-to-be University, Thanjavur, 613401, India
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10
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Pal JK, Ray SS, Pal SK. Identifying Drug Resistant miRNAs Using Entropy Based Ranking. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:973-984. [PMID: 31398129 DOI: 10.1109/tcbb.2019.2933205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
MicroRNAs play an important role in controlling drug sensitivity and resistance in cancer. Identification of responsible miRNAs for drug resistance can enhance the effectiveness of treatment. A new set theoretic entropy measure (SPEM) is defined to determine the relevance and level of confidence of miRNAs in deciding their drug resistant nature. Here, a pattern is represented by a pair of values. One of them implies the degree of its belongingness (fuzzy membership) to a class and the other represents the actual class of origin (crisp membership). A measure, called granular probability, is defined that determines the confidence level of having a particular pair of membership values. The granules used to compute the said probability are formed by a histogram based method where each bin of a histogram is considered as one granule. The width and number of the bins are automatically determined by the algorithm. The set thus defined, comprising a pair of membership values and the confidence level for having them, is used for the computation of SPEM and thereby identifying the drug resistant miRNAs. The efficiency of SPEM is demonstrated extensively on six data sets. While the achieved F-score in classifying sensitive and resistant samples ranges between 0.31 & 0.50 using all the miRNAs by SVM classifier, the same score varies from 0.67 to 0.94 using only the top 1 percent drug resistant miRNAs. Superiority of the proposed method as compared to some existing ones is established in terms of F-score. The significance of the top 1 percent miRNAs in corresponding cancer is also verified by the different articles based on biological investigations. Source code of SPEM is available at http://www.jayanta.droppages.com/SPEM.html.
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11
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WM Nor WMFSB, Chung I, Said NABM. MicroRNA-548m Suppresses Cell Migration and Invasion by Targeting Aryl Hydrocarbon Receptor in Breast Cancer Cells. Oncol Res 2021; 28:615-629. [PMID: 33109304 PMCID: PMC7962940 DOI: 10.3727/096504020x16037933185170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer among women and one of the leading causes of cancer mortality worldwide, in which the most severe form happens when it metastasizes to other regions of the body. Metastasis is responsible for most treatment failures in advanced breast cancer. Epithelialmesenchymal transition (EMT) plays a significant role in promoting metastatic processes in breast cancer. MicroRNAs (miRNAs) are highly conserved endogenous short noncoding RNAs that play a role in regulating a broad range of biological processes, including cancer initiation and development, by functioning as tumor promoters or tumor suppressors. Expression of miR-548m has been found in various types of cancers, but the biological function and molecular mechanisms of miR-548m in cancers have not been fully studied. Here we demonstrated the role of miR-548m in modulating EMT in the breast cancer cell lines MDA-MB-231 and MCF-7. Expression data for primary breast cancer obtained from NCBI GEO data sets showed that miR-548m expression was downregulated in breast cancer patients compared with healthy group. We hypothesize that miR-548m acts as a tumor suppressor in breast cancer. Overexpression of miR-548m in both cell lines increased E-cadherin expression and decreased the EMT-associated transcription factors SNAI1, SNAI2, ZEB1, and ZEB2, as well as MMP9 expression. Consequently, migration and invasion capabilities of both MDA-MB-231 and MCF-7 cells were significantly inhibited in miR-548m-overexpressing cells. Analysis of 1,059 putative target genes of miR-548m revealed common pathways involving both tight junction and the mTOR signaling pathway, which has potential impacts on cell migration and invasion. Furthermore, this study identified aryl hydrocarbon receptor (AHR) as a direct target of miR-548m in breast cancer cells. Taken together, our findings suggest a novel function of miR-548m in reversing the EMT of breast cancer by reducing their migratory and invasive potentials, at least in part via targeting AHR expression.
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Affiliation(s)
- WM Farhan Syafiq B. WM Nor
- *Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- †Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Ivy Chung
- ‡Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- §University of Malaya Cancer Research Institute, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Akmarina B. M. Said
- †Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
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12
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Zheng Y, Yang Z, Jin C, Chen C, Wu N. hsa-miR-191-5p inhibits replication of human immunodeficiency virus type 1 by downregulating the expression of NUP50. Arch Virol 2021; 166:755-766. [PMID: 33420627 DOI: 10.1007/s00705-020-04899-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/13/2020] [Indexed: 01/24/2023]
Abstract
MicroRNAs (miRNAs) are important host molecules involved in human immunodeficiency virus type 1 (HIV-1) infection. Antiretroviral therapy (ART) can affect the miRNA expression profile, but differentially expressed miRNAs still remain to be identified. In this study, we used gene chips to analyze miRNA expression profiles in peripheral blood mononuclear cells from ART-naive HIV-1 patients and those receiving ART, as well as from uninfected individuals. We measured differences in miRNA expression by quantitative polymerase chain reaction (qPCR) in an expanded sample. We found significant differences in the expression of has-miR-191-5p among the three groups (P < 0.05). Furthermore, we showed that hsa-miR-191-5p has an inhibitory effect on HIV-1 replication in cell models in vitro. We identified CCR1 and NUP50 as target molecules of hsa-miR-191-5p and found that hsa-miR-191-5p inhibits the expression of CCR1 and NUP50. Knockdown of NUP50 resulted in significant inhibition of HIV-1 replication. In summary, our research shows that hsa-miR-191-5p expression is reduced in HIV-1-infected patients and acts an inhibitor of HIV-1 infection via a mechanism that may involve targeted repression of NUP50 expression.
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Affiliation(s)
- Yanghao Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | | | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Chaoyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China.
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13
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Azar MRMH, Aghazadeh H, Mohammed HN, Sara MRS, Hosseini A, Shomali N, Tamjidifar R, Tarzi S, Mansouri M, Sarand SP, Marofi F, Akbari M, Xu H, Shotorbani SS. miR-193a-5p as a promising therapeutic candidate in colorectal cancer by reducing 5-FU and Oxaliplatin chemoresistance by targeting CXCR4. Int Immunopharmacol 2021; 92:107355. [PMID: 33429333 DOI: 10.1016/j.intimp.2020.107355] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/26/2020] [Accepted: 12/26/2020] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most common causes of cancer-related deaths worldwide. The role of microRNAs (miRNAs/miRs) as small (19-25 nucleotides in length) non-coding RNA molecules that modify gene expression has been shown in several types of cancer. 5-Fluorouracil (5-FU) and oxaliplatin (Ox) are two common chemotherapeutic agents used to treat cancer. The present study aimed to evaluate the expression levels of miR-193a-5p in CRC, and its effect on the C-X-C Motif Chemokine Receptor 4 (CXCR4) target gene alone and in combination with chemotherapeutic drugs, to determine its possible role in chemoresistance. CRC tissues and adjacent non-cancerous tissue were obtained from 67 patients who had undergone surgery to determine the expression levels of miR-193a-5p and CXCR4. Subsequently, qPCR and Western blotting were performed to determine the effect of miR-193a-5p and chemotherapy drugs on CXCR4. َAlso, MTT assay, and flow cytometry was performed to determine their role in cell viability and apoptosis. Besides, the relationship between miR-193a-5p and CXCR4 with patients' clinical features was investigated. The results of the present study showed that miR-193a-5p was significantly downregulated, whereas CXCR4 was significantly upregulated in tumor tissues obtained from patients with CRC compared with the adjacent non-tumor healthy controls. In addition, the upregulation of miR-193-5p reduced the expression levels of CXCR4, particularly in combination with 5-FU and OX. Besides, using rescue experiments, the present study showed that miR-193a-5p replacement was able to suppress CXCR4-induced CRC cell proliferation by directly targeting CXCR4. Furthermore, there was a significant association between miR-193a-5p and CXCR4 with certain clinicopathological characteristics, particularly with metastasis-related features. These results suggest that miR-193a-5p serves a tumor-suppressive function in CRC and can directly target CXCR4 and decrease its mRNA and protein expression levels. Additionally, miR-193a-5p in combination with 5-FU and Ox potentiated reducing CXR4 expression, which may reveal its contribution to tumor chemoresistance. In conclusion, miR-193-5p may be applicable as a prognostic and diagnostic marker, and also serve as a therapeutic factor by reducing CXCR4 in combination with chemotherapeutic drugs.
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Affiliation(s)
| | - Hamed Aghazadeh
- Pharmaceutical Engineering Department, Faculty of Chemical Engineering, University of Tehran, Tehran 1417414418, Iran
| | | | - Mehdi Rezai Seghin Sara
- Department of Biochemistry, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran
| | - Arezoo Hosseini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran
| | - Navid Shomali
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran
| | - Rozita Tamjidifar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran; Department of Biology Ahar Branch, Islamic Azad University, Ahar 5451116714, Iran
| | - Saeed Tarzi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran; Department of Biology Ahar Branch, Islamic Azad University, Ahar 5451116714, Iran
| | - Mahmoud Mansouri
- University of Tehran, Master of Sciences in Applied Chemistry, Tehran 1417414418, Iran
| | - Sahar Pashaei Sarand
- Amirkabir University of Technology (Polytechnic of Tehran), Master of Sciences in Applied Chemistry, Tehran 441315875, Iran
| | - Faroogh Marofi
- Department of Hematology, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran
| | - Huaxi Xu
- Department of Immunology, Center of Clinical Medicine and Laboratory, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China.
| | - Siamak Sandoghchian Shotorbani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran; Department of Immunology, Center of Clinical Medicine and Laboratory, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China.
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14
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Kang T, Zhu J, Luo X, Jia W, Wu P, Cai C. Controlled Self-Assembly of a Close-Packed Gold Octahedra Array for SERS Sensing Exosomal MicroRNAs. Anal Chem 2021; 93:2519-2526. [DOI: 10.1021/acs.analchem.0c04561] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tuli Kang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Jingtian Zhu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Xiaojun Luo
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Wenyu Jia
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
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15
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Pan X, Zhang B. Identification of Stable Reference Genes for Toxicogenomic and Gene Expression Analysis. Methods Mol Biol 2021; 2326:67-94. [PMID: 34097262 DOI: 10.1007/978-1-0716-1514-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gene expression analysis has been becoming a popular method for studying gene function and response to different environmental stresses, including toxin/pollution exposure. Selection of a suitable reference gene is critically important for gene expression analysis due to that wrong reference genes will cause misleading and even wrong conclusion. A good reference gene should be a more stable reference gene, particularly during the toxicant exposure treatment and/or other investigation condition. In this chapter, a step-by-step protocol is present for primer design, reverse transcription PCR, primer efficiency and specificity test, qRT-PCR, and the strategy for identifying most stable reference genes for toxicogenomic and gene expression analysis. The detailed method for determining the primer gene specificity and primer efficiency are also presented in this chapter. Low primer efficiency will affect the fold changes during gene expression analysis; however, it does not affect the conclusion, up- or downregulation. Choosing a wrong reference gene may result in wrong conclusion.
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Affiliation(s)
- Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, USA.
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16
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Cansaran-Duman D, Tanman Ü, Yangın S, Atakol O. The comparison of miRNAs that respond to anti-breast cancer drugs and usnic acid for the treatment of breast cancer. Cytotechnology 2020; 72:10.1007/s10616-020-00430-7. [PMID: 33128199 PMCID: PMC7695759 DOI: 10.1007/s10616-020-00430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 10/14/2020] [Indexed: 02/01/2023] Open
Abstract
This study was designed to compare usnic acid with anti-breast cancer drug molecules (A-BCDM) routinely used in the treatment of breast cancer. The miRNA information of 17 anti-breast cancer drug used in breast cancer treatment was obtained from the Small Molecule-miRNA Network-Based Inferance (SMIR-NBI) tool. We had been determined common and different expressed miRNAs between 17 A-BCDM & usnic acid and were classified according to the common miRNAs to reveal molecular similarity. As a result of the bioinformatic analyzes, 20 common miRNAs were determined between 17 A-BCDM and usnic acid. The common miRNAs were analyzed with bioinformatic tolls for determining pathways and targets. The most common miRNAs for 6 of 17 A-BCDM and usnic acid were determined as miR-374a-5p and miR-26a-5p. We compared the anti-proliferative effect of usnic acid and one of the 17 A-BCDM that tamoxifen on MDA-MB-231 triple negative breast cancer cell with real-time cell analysis system. The real time PCR assay was carried out with miR-26a-5p for evaluate to expression level of MDA-MB-231 breast cancer cell and MCF-12A non-cancerous epithelial breast cell. As a result of study, usnic acid as novel candidate drug molecule showed high similarity ratio with 5-Fluorouracil, Sulindac Sulfide, Curcumin and Cisplatin A-BCDM used in treatment of breast cancer. miR-26a-5p as common response miRNA of usnic acid and tamoxifen was showed a decreased level of expression by validated qRT-PCR assay. The obtained from study, in addition to 17 A-BCDM, usnic acid has also the potential to be used as a candidate molecule in the treatment of breast cancer. Moreover, miR-26a-5p might be used as a biomarker in the treatment of breast cancer but further analysis is required.
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Affiliation(s)
| | - Ümmügülsüm Tanman
- Ankara University, Biotechnology Institute, Keçiören, Ankara, Turkey
| | - Sevcan Yangın
- Ankara University, Biotechnology Institute, Keçiören, Ankara, Turkey
| | - Orhan Atakol
- Faculty of Science, Department of Chemistry, Ankara University, Tandoğan, Ankara, Turkey
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17
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Mansoori B, Mohammadi A, Abedi-Gaballu F, Abbaspour S, Ghasabi M, Yekta R, Shirjang S, Dehghan G, Hamblin MR, Baradaran B. Hyaluronic acid-decorated liposomal nanoparticles for targeted delivery of 5-fluorouracil into HT-29 colorectal cancer cells. J Cell Physiol 2020; 235:6817-6830. [PMID: 31989649 PMCID: PMC7384933 DOI: 10.1002/jcp.29576] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022]
Abstract
The use of liposomes as drug carriers improves the therapeutic efficacy of anticancer drugs, while at the same time reducing side effects. Hyaluronic acid (HA) is recognized by the CD44 receptor, which is overexpressed in many cancer cells. In this study, we developed HA-modified liposomes encapsulating 5-fluorouracil (5-FU) and tested them against a CD44 expressing colorectal cell line (HT29) and a non-CD44 expressing hepatoma cell line. The average size of 5-FU-lipo and 5-FU-lipo-HA nanoparticles were 112 ± 28 and 144 ± 77 nm, respectively. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay showed selective cancer cell death depending on the CD44 expression in a time-dependent manner. Apoptosis assays and cell-cycle analysis indicated that G0/G1 arrest occurred. The colony formation study revealed that cells treated with 5-FU-lipo and 5-FU-lipo-HA had reduced colony formation. Quantitative reverse-transcription polymerase chain reaction study showed that the oncogenic messenger RNA and microRNA levels were significantly reduced in the 5-FU-lipo-HA-treated group, while tumor suppressors were increased in that group. We suggest that optimal targeted delivery and release of 5-FU into colorectal cancer cells, renders them susceptible to apoptosis, cell-cycle arrest, and decreased colony formation.
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Affiliation(s)
- Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Fereydoon Abedi-Gaballu
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Soheil Abbaspour
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehri Ghasabi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Yekta
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Solmaz Shirjang
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Michael R. Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Tanman Ü, Yangın S, Cansaran-Duman D. Determination of Dysregulated miRNA Expression Levels by qRT-PCR after the Application of Usnic Acid to Breast Cancer. Anticancer Agents Med Chem 2020; 20:548-558. [DOI: 10.2174/1871520619666190923163552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/24/2019] [Accepted: 07/03/2019] [Indexed: 12/30/2022]
Abstract
Background and Purpose:
Breast cancer still remains to be one of the most threatening cancer types
in women. Recent studies have allowed scientists to better investigate the potential use of natural compounds in
the treatment of breast cancers. Usnic acid is a secondary metabolite extracted from lichen species and has many
biological activities. The response of microRNAs regulated by drug molecules may provide useful diagnostic
and prognostic biomarkers, as well as potential therapeutics for breast cancers. Although the aberrant expression
of microRNAs was observed after drug treatment, the regulatory mechanisms remain partially known. Micro
RNAs (miRNAs) play an important role in gene regulation at the post-transcriptional level.
Methods:
In this study, we used quantitative Real-Time PCR (qRT-PCR) technology to demonstrate that usnic
acid significantly changes the expression profile of miRNAs.
Results:
Eleven miRNAs were significantly and differentially expressed in breast cancer cells after treatment
with usnic acid. Three miRNAs were up-regulated, while eight were down-regulated in usnic acid treated cells.
Target prediction and GO analysis revealed many target genes and their related pathways that are potentially
regulated by usnic acid regulated differentially expressed miRNAs. We found that usnic acid treatment caused
significant changes in the expression of hsa-miR-5006-5p, hsa-miR-892c-3p, hsa-miR-4430, hsa-miR-5194,
hsa-miR-3198, hsa-miR-3171, hsa-miR-933 and hsa-miR-185-3p in breast cancer cells.
Conclusions:
Usnic acid response miRNAs might play important regulatory roles in the tumorigenesis and
development of breast cancer, and they could serve as prognostic predictors for breast cancer patients.
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Affiliation(s)
- Ümmügülsüm Tanman
- Ankara University, Biotechnology Institute, System Biotechnology Advance Research Unit, Tandogan, Ankara, Turkey
| | - Sevcan Yangın
- Ankara University, Biotechnology Institute, System Biotechnology Advance Research Unit, Tandogan, Ankara, Turkey
| | - Demet Cansaran-Duman
- Ankara University, Biotechnology Institute, System Biotechnology Advance Research Unit, Tandogan, Ankara, Turkey
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19
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Feng Y, Chen X, Ding W, Ma J, Zhang B, Li X. MicroRNA-16 participates in the cell cycle alteration of HepG2 cells induced by MC-LR. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110295. [PMID: 32066005 DOI: 10.1016/j.ecoenv.2020.110295] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 05/26/2023]
Abstract
Microcystin-LR (MC-LR) is a cyclic hepatotoxin produced by cyanobacteria in freshwater, and chronic MC-LR exposure could induce human hepatitis if consumed in drinking water. In recent years, many studies have indicated that microRNAs participate in the hepatotoxicity of MC-LR. The purpose of this study was to investigate the potential function of miR-16 in the hepatocellular toxicity and cell cycle alteration induced by MC-LR in human hepatocellular carcinoma (HepG2) cells after treatment with 10 μM MC-LR. The result of flow cytometry detection showed that a low concentration of MC-LR (10 μM) failed to induce apoptosis but promoted cell cycle G1/S transition in HepG2 cells. In addition, the expression of apoptosis-related genes was suppressed after MC-LR exposure. These results confirm that MC-LR exposure at a low dose can promote the proliferation of HepG2 cells. Furthermore, we also found that microRNA-16 (miR-16) expression was suppressed in HepG2 cells following MC-LR exposure. Hence, we overexpressed miR-16 in HepG2 cells and treated them with MC-LR, and the results showed that miR-16 overexpression induced an increase in the G0/G1 phase and a decrease in the S phase cell cycle populations in HepG2 cells, suggesting that miR-16 can inhibit the cell proliferation of HepG2 cells. In conclusion, our results suggest that miR-16 may play a vital role in the cell cycle alteration of HepG2 cells after MC-LR exposure.
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Affiliation(s)
- Yiyi Feng
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Xi Chen
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Weikai Ding
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Junguo Ma
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Bangjun Zhang
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Xiaoyu Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
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20
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Kartini D, Taher A, Panigoro SS, Setiabudy R, Jusman SW, Haryana SM, Abdullah M, Rustamadji P, Purwanto DJ, Sutandyo N, Suroyo I, Siregar BH, Maruli H, Sungkar S. Effect of melatonin supplementation in combination with neoadjuvant chemotherapy to miR-210 and CD44 expression and clinical response improvement in locally advanced oral squamous cell carcinoma: a randomized controlled trial. J Egypt Natl Canc Inst 2020; 32:12. [PMID: 32372215 DOI: 10.1186/s43046-020-0021-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/31/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Squamous cell carcinoma of the oral cavity (OSCC) is the sixth most common malignancy. Surgery is mainstay treatment for oral cancers. Surgery in locally advanced OSCC presents many challenges primarily because the head and neck have critical structures that can be damaged by tumor or treatment. It is thought that neoadjuvant chemotherapy (NC) in locally advanced OSCC is able to shrink tumor size. Chemoresistancy is a problem due to hypoxic microenvironment characterized by increased expression of HIF-1α. It is also regulated by miR-210 as well as increased expression of CD44 and CD133. Melatonin has a powerful antioxidant and oncostatic effects that are expected to improve tumor hypoxia and clinical response. Fifty patients with OSCC were included and randomized. miR-210 and CD44 expression were measured before and after intervention using qRT-PCR absolute quantification, and clinical response was evaluated according to RECIST 1.1 criteria. This study aims to determine the effect of melatonin in improving the clinical response of patients with locally advanced oral squamous cell carcinoma (OSCC) after neoadjuvant chemotherapy to miR-210 and CD44 expression. RESULTS Melatonin administration reduced miR-210 levels but not significant (p = 0.767). CD44 expression also decreased in the melatonin group compared with placebo yet was not significant (p = 0.103). There was a decrease in the expression of miR-210 and CD44 followed by a decrease in the percentage of residual tumor but not significant (p = 0.114). CONCLUSION In OSCC, the addition of 20-mg melatonin to neoadjuvant chemotherapy (NC) reduced the expression of miR-210 and CD44 and decreased the percentage of tumor residue; however, no statistically significant result was observed. TRIAL REGISTRATION This study is registered to ClinicalTrials.gov under trial registration number: NCT04137627 with date of registration on October 22, 2019-retrospectively registered, accessible from: https://clinicaltrials.gov/ct2/show/NCT04137627.
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Affiliation(s)
- Diani Kartini
- Oncology Division, Department of Surgery, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, 10430, Indonesia.
| | - Akmal Taher
- Department of Urology, Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Sonar Soni Panigoro
- Oncology Division, Department of Surgery, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, 10430, Indonesia
| | - Rianto Setiabudy
- Department of Pharmacology and Therapeutics, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Sri Widia Jusman
- Department of Biochemistry and Molecular Genetics, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Murdani Abdullah
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - Primariadewi Rustamadji
- Department of Pathological Anatomy, Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Denni Joko Purwanto
- Department of Surgical Oncology, Dharmais Hospital, National Cancer Center, Jakarta, Indonesia
| | - Noorwati Sutandyo
- Department of Hematology and Medical Oncology, Dharmais Hospital, National Cancer Center, Jakarta, Indonesia
| | - Indrati Suroyo
- Department of Radiology, Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - Budi Harapan Siregar
- Oncology Division, Department of Surgery, Persahabatan General Hospital, Jakarta, Indonesia
| | - Haris Maruli
- Oncology Division, Department of Surgery, Persahabatan General Hospital, Jakarta, Indonesia
| | - Saleha Sungkar
- Department of Parasitology, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
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21
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Qiao L, Wu C, Cai Z, Wu X, Wu P, Cai C. Cascade signal amplification sensing strategy for highly specific and sensitive detection of homologous microRNAs in different molecular subtypes of breast cancer. Anal Chim Acta 2020; 1093:86-92. [PMID: 31735218 DOI: 10.1016/j.aca.2019.09.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 11/29/2022]
Abstract
Discriminative identification of homologous miRNAs in miRNA family with high specificity and sensitivity is crucial for accurate classification, diagnosis and prognosis of breast cancer. Herein, we report a reliable, sensitive, and selective assay by coupling fluorescence resonance energy transfer (FRET) with cascade signal amplification. The strategy is developed by designing two programmable DNA probes that can be triggered to shift from "off" to "on" state in a cascade hybridization reaction in the presence of target miRNA let-7a, leading to the generation of an amplified signal. The assay can detect concentrations as low as ∼3.0 pM let-7a and discriminate let-7a from other highly homologous members in the let-7 miRNA family. Moreover, it can also be used to determine let-7a levels at single-cell resolution and evaluate the drug efficacy of let-7a expression among various molecular types of breast cancer cell lines. The advantage of this assay is a combined result of signal generation and amplification triggered by target miRNA, which can satisfy an assay of analogous miRNA in a downregulated manner with high specificity. It has promising potential as a selective assay for homologous miRNAs in precision medicine.
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Affiliation(s)
- Ling Qiao
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China
| | - Chuanli Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China
| | - Zhewei Cai
- Department of Chemical and Biomolecular Engineering, Clarkson University, Potsdam, NY, 13699, United States
| | - Xingchen Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China.
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China.
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22
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Pedroza-Torres A, Romero-Córdoba SL, Justo-Garrido M, Salido-Guadarrama I, Rodríguez-Bautista R, Montaño S, Muñiz-Mendoza R, Arriaga-Canon C, Fragoso-Ontiveros V, Álvarez-Gómez RM, Hernández G, Herrera LA. MicroRNAs in Tumor Cell Metabolism: Roles and Therapeutic Opportunities. Front Oncol 2019; 9:1404. [PMID: 31921661 PMCID: PMC6917641 DOI: 10.3389/fonc.2019.01404] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022] Open
Abstract
Dysregulated metabolism is a common feature of cancer cells and is considered a hallmark of cancer. Altered tumor-metabolism confers an adaptive advantage to cancer cells to fulfill the high energetic requirements for the maintenance of high proliferation rates, similarly, reprogramming metabolism confers the ability to grow at low oxygen concentrations and to use alternative carbon sources. These phenomena result from the dysregulated expression of diverse genes, including those encoding microRNAs (miRNAs) which are involved in several metabolic and tumorigenic pathways through its post-transcriptional-regulatory activity. Further, the identification of key actionable altered miRNA has allowed to propose novel targeted therapies to modulated tumor-metabolism. In this review, we discussed the different roles of miRNAs in cancer cell metabolism and novel miRNA-based strategies designed to target the metabolic machinery in human cancer.
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Affiliation(s)
- Abraham Pedroza-Torres
- Cátedra CONACyT-Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Sandra L Romero-Córdoba
- Departamento de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Montserrat Justo-Garrido
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología - Instituto de Investigaciones Biomédicas - Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Iván Salido-Guadarrama
- Biología Computacional, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Rubén Rodríguez-Bautista
- Unidad de Oncología Torácica y Laboratorio de Medicina Personalizada, Instituto Nacional de Cancerologia, Mexico City, Mexico
| | - Sarita Montaño
- Laboratorio de Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa (FCQB-UAS), Culiacán, Mexico
| | - Rodolfo Muñiz-Mendoza
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología - Instituto de Investigaciones Biomédicas - Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | | | - Greco Hernández
- Laboratorio de Traducción y Cáncer, Unidad de Investigaciones Biomedicas en Cáncer, Instituto Nacional de Cancerolgía, Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología - Instituto de Investigaciones Biomédicas - Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
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Xie B, Becker E, Stuparevic I, Wery M, Szachnowski U, Morillon A, Primig M. The anti-cancer drug 5-fluorouracil affects cell cycle regulators and potential regulatory long non-coding RNAs in yeast. RNA Biol 2019; 16:727-741. [PMID: 30760080 PMCID: PMC6546400 DOI: 10.1080/15476286.2019.1581596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/16/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022] Open
Abstract
5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3'-5' exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work on 5-FU's cytotoxicity has been focused on mRNAs and non-coding transcripts such as rRNAs, tRNAs and snoRNAs. However, the effect of 5-FU on long non-coding RNAs (lncRNAs), which include regulatory transcripts important for cell growth and differentiation, is poorly understood. RNA profiling of synchronized 5-FU treated yeast cells and protein assays reveal that the drug specifically inhibits a set of cell cycle regulated genes involved in mitotic division, by decreasing levels of the paralogous Swi5 and Ace2 transcriptional activators. We also observe widespread accumulation of different lncRNA types in treated cells, which are typically present at high levels in a strain lacking EXOSC10/Rrp6. 5-FU responsive lncRNAs include potential regulatory antisense transcripts that form double-stranded RNAs (dsRNAs) with overlapping sense mRNAs. Some of these transcripts encode proteins important for cell growth and division, such as the transcription factor Ace2, and the RNA exosome subunit EXOSC6/Mtr3. In addition to revealing a transcriptional effect of 5-FU action via DNA binding regulators involved in cell cycle progression, our results have implications for the function of putative regulatory lncRNAs in 5-FU mediated cytotoxicity. The data raise the intriguing possibility that the drug deregulates lncRNAs/dsRNAs involved in controlling eukaryotic cell division, thereby highlighting a new class of promising therapeutical targets.
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Affiliation(s)
- Bingning Xie
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Rennes, France
| | - Emmanuelle Becker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Rennes, France
- Univ Rennes, Inria, CNRS, IRISA F-35000, Rennes, France
| | - Igor Stuparevic
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Rennes, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL UniversityCNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL UniversityCNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL UniversityCNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Rennes, France
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24
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Qu J, Chen X, Sun YZ, Zhao Y, Cai SB, Ming Z, You ZH, Li JQ. In Silico Prediction of Small Molecule-miRNA Associations Based on the HeteSim Algorithm. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:274-286. [PMID: 30654189 PMCID: PMC6348698 DOI: 10.1016/j.omtn.2018.12.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/15/2018] [Accepted: 12/04/2018] [Indexed: 01/27/2023]
Abstract
Targeting microRNAs (miRNAs) with drug small molecules (SMs) is a new treatment method for many human complex diseases. Unsurprisingly, identification of potential miRNA-SM associations is helpful for pharmaceutical engineering and disease therapy in the field of medical research. In this paper, we developed a novel computational model of HeteSim-based inference for SM-miRNA Association prediction (HSSMMA) by implementing a path-based measurement method of HeteSim on a heterogeneous network combined with known miRNA-SM associations, integrated miRNA similarity, and integrated SM similarity. Through considering paths from an SM to a miRNA in the heterogeneous network, the model can capture the semantics information under each path and predict potential miRNA-SM associations based on all the considered paths. We performed global, miRNA-fixed local and SM-fixed local leave one out cross validation (LOOCV) as well as 5-fold cross validation based on the dataset of known miRNA-SM associations to evaluate the prediction performance of our approach. The results showed that HSSMMA gained the corresponding areas under the receiver operating characteristic (ROC) curve (AUCs) of 0.9913, 0.9902, 0.7989, and 0.9910 ± 0.0004 based on dataset 1 and AUCs of 0.7401, 0.8466, 0.6149, and 0.7451 ± 0.0054 based on dataset 2, respectively. In case studies, 2 of the top 10 and 13 of the top 50 predicted potential miRNA-SM associations were confirmed by published literature. We further implemented case studies to test whether HSSMMA was effective for new SMs without any known related miRNAs. The results from cross validation and case studies showed that HSSMMA could be a useful prediction tool for the identification of potential miRNA-SM associations.
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Affiliation(s)
- Jia Qu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Shu-Bin Cai
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhong Ming
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Ürümqi 830011, China.
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
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25
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The promising role of miR-296 in human cancer. Pathol Res Pract 2018; 214:1915-1922. [DOI: 10.1016/j.prp.2018.09.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/08/2018] [Accepted: 09/28/2018] [Indexed: 12/18/2022]
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26
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Guan NN, Sun YZ, Ming Z, Li JQ, Chen X. Prediction of Potential Small Molecule-Associated MicroRNAs Using Graphlet Interaction. Front Pharmacol 2018; 9:1152. [PMID: 30374302 PMCID: PMC6196296 DOI: 10.3389/fphar.2018.01152] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/24/2018] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) have been proved to be targeted by the small molecules recently, which made using small molecules to target miRNAs become a possible therapy for human diseases. Therefore, it is very meaningful to investigate the relationships between small molecules and miRNAs, which is still yet in the newly-developing stage. In this paper, we presented a prediction model of Graphlet Interaction based inference for Small Molecule-MiRNA Association prediction (GISMMA) by combining small molecule similarity network, miRNA similarity network and known small molecule-miRNA association network. This model described the complex relationship between two small molecules or between two miRNAs using graphlet interaction which consists of 28 isomers. The association score between a small molecule and a miRNA was calculated based on counting the numbers of graphlet interaction throughout the small molecule similarity network and the miRNA similarity network, respectively. Global and two types of local leave-one-out cross validation (LOOCV) as well as five-fold cross validation were implemented in two datasets to evaluate GISMMA. For Dataset 1, the AUCs are 0.9291 for global LOOCV, 0.9505, and 0.7702 for two local LOOCVs, 0.9263 ± 0.0026 for five-fold cross validation; for Dataset 2, the AUCs are 0.8203, 0.8640, 0.6591, and 0.8554 ± 0.0063, in turn. In case study for small molecules, 5-Fluorouracil, 17β-Estradiol and 5-Aza-2'-deoxycytidine, the numbers of top 50 miRNAs predicted by GISMMA and validated to be related to these three small molecules by experimental literatures are in turn 30, 29, and 25. Based on the results from cross validations and case studies, it is easy to realize the excellent performance of GISMMA.
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Affiliation(s)
- Na-Na Guan
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Zhong Ming
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China.,National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
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27
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Luo M, Zhang Q, Xia M, Hu F, Ma Z, Chen Z, Guo AY. Differential Co-expression and Regulatory Network Analysis Uncover the Relapse Factor and Mechanism of T Cell Acute Leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:184-194. [PMID: 30195757 PMCID: PMC6023839 DOI: 10.1016/j.omtn.2018.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/02/2018] [Accepted: 05/04/2018] [Indexed: 01/17/2023]
Abstract
The pediatric T cell acute lymphoblastic leukemia (T-ALL) still remains a cancer with worst prognosis for high recurrence. Massive studies were conducted for the leukemia relapse based on diagnosis and relapse paired samples. However, the initially diagnostic samples may contain the relapse information and mechanism, which were rarely studied. In this study, we collected mRNA and microRNA (miRNA) data from initially diagnosed pediatric T-ALL samples with their relapse or remission status after treatment. Integrated differential co-expression and miRNA-transcription factor (TF)-gene regulatory network analyses were used to reveal the possible relapse mechanisms for pediatric T-ALL. We detected miR-1246/1248 and NOTCH2 served as key nodes in the relapse network, and they combined with TF WT1/SOX4/REL to form regulatory modules that influence the progress of T-ALL. A regulatory loop miR-429-MYCN-MFHAS1 was found potentially associated with the remission of T-ALL. Furthermore, we proved miR-1246/1248 combined with NOTCH2 could promote cell proliferation in the T-ALL cell line by experiments. Meanwhile, analysis based on the miRNA-drug relationships demonstrated that drugs 5-fluorouracil, ascorbate, and trastuzumab targeting miR-1246 could serve as potential supplements for the standard therapy. In conclusion, our findings revealed the potential molecular mechanisms of T-ALL relapse by the combination of co-expression and regulatory network, and they provide preliminary clues for precise treatment of T-ALL patients.
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Affiliation(s)
- Mei Luo
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qiong Zhang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mengxuan Xia
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Feifei Hu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhaowu Ma
- Laboratory of Neuronal Network and Brain Diseases Modulation, School of Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Zehua Chen
- Joint Laboratory for the Research of Pharmaceutics-Huazhong University of Science and Technology and Infinitus, Wuhan, China
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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Translational reprogramming of colorectal cancer cells induced by 5-fluorouracil through a miRNA-dependent mechanism. Oncotarget 2018; 8:46219-46233. [PMID: 28515355 PMCID: PMC5542262 DOI: 10.18632/oncotarget.17597] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/06/2017] [Indexed: 11/25/2022] Open
Abstract
5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug in colorectal cancer. Previous studies showed that 5-FU modulates RNA metabolism and mRNA expression. In addition, it has been reported that 5-FU incorporates into the RNAs constituting the translational machinery and that 5-FU affects the amount of some mRNAs associated with ribosomes. However, the impact of 5-FU on translational regulation remains unclear. Using translatome profiling, we report that a clinically relevant dose of 5-FU induces a translational reprogramming in colorectal cancer cell lines. Comparison of mRNA distribution between polysomal and non-polysomal fractions in response to 5-FU treatment using microarray quantification identified 313 genes whose translation was selectively regulated. These regulations were mostly stimulatory (91%). Among these genes, we showed that 5-FU increases the mRNA translation of HIVEP2, which encodes a transcription factor whose translation in normal condition is known to be inhibited by mir-155. In response to 5-FU, the expression of mir-155 decreases thus stimulating the translation of HIVEP2 mRNA. Interestingly, the 5-FU-induced increase in specific mRNA translation was associated with reduction of global protein synthesis. Altogether, these findings indicate that 5-FU promotes a translational reprogramming leading to the increased translation of a subset of mRNAs that involves at least for some of them, miRNA-dependent mechanisms. This study supports a still poorly evaluated role of translational control in drug response.
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Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma. Sci Rep 2018; 8:733. [PMID: 29335598 PMCID: PMC5768793 DOI: 10.1038/s41598-017-19004-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Pemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0.05) using the Genotype-Tissue Expression data and found evidence for their clinical relevance using integrated molecular profiling and lung adenocarcinoma survival data from The Cancer Genome Atlas project. We identified 39 miRNAs with significant differential expression (BH adjusted p < 0.05) in LCLs. We developed a gene expression based imputation model of drug sensitivity, quantified its prediction performance, and found a significant correlation of the imputed phenotype generated from expression data with survival time in lung adenocarcinoma patients. Differentially expressed genes (MTHFD2 and SUFU) that are putative targets of differentially expressed miRNAs also showed differential perturbation in A549 fusion lung tumor cells with further replication in A549 cells. Our study suggests pemetrexed may be used in combination with agents that target miRNAs to increase its cytotoxicity.
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30
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Eldeib MG, Kandil YI, Abdelghany TM, Mansour OA, El-Zahabi MM. Alterations of microRNAs expression in response to 5-Fluorouracil, Oxaliplatin, and Irinotecan treatment of colorectal cancer cells. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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31
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Wang S, Zhu F. Chemical composition and biological activity of staghorn sumac (Rhus typhina). Food Chem 2017; 237:431-443. [DOI: 10.1016/j.foodchem.2017.05.111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/04/2017] [Accepted: 05/22/2017] [Indexed: 12/19/2022]
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32
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Carney MC, Tarasiuk A, DiAngelo SL, Silveyra P, Podany A, Birch LL, Paul IM, Kelleher S, Hicks SD. Metabolism-related microRNAs in maternal breast milk are influenced by premature delivery. Pediatr Res 2017; 82:226-236. [PMID: 28422941 PMCID: PMC5552431 DOI: 10.1038/pr.2017.54] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/19/2017] [Indexed: 12/16/2022]
Abstract
BackgroundMaternal breast milk (MBM) is enriched in microRNAs, factors that regulate protein translation throughout the human body. MBM from mothers of term and preterm infants differs in nutrient, hormone, and bioactive-factor composition, but the microRNA differences between these groups have not been compared. We hypothesized that gestational age at delivery influences microRNA in MBM, particularly microRNAs involved in immunologic and metabolic regulation.MethodsMBM from mothers of premature infants (pMBM) obtained 3-4 weeks post delivery was compared with MBM from mothers of term infants obtained at birth (tColostrum) and 3-4 weeks post delivery (tMBM). The microRNA profile in lipid and skim fractions of each sample was evaluated with high-throughput sequencing.ResultsThe expression profiles of nine microRNAs in lipid and skim pMBM differed from those in tMBM. Gene targets of these microRNAs were functionally related to elemental metabolism and lipid biosynthesis. The microRNA profile of tColostrum was also distinct from that of pMBM, but it clustered closely with tMBM. Twenty-one microRNAs correlated with gestational age demonstrated limited relationships with method of delivery, but not other maternal-infant factors.ConclusionPremature delivery results in a unique MBM microRNA profile with metabolic targets. This suggests that preterm milk may have adaptive functions for growth in premature infants.
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Affiliation(s)
- Molly C. Carney
- Franklin and Marshall College, Lancaster, PA,Department of Pediatrics, Penn State College of Medicine, Hershey, PA
| | - Andrij Tarasiuk
- Franklin and Marshall College, Lancaster, PA,Department of Pediatrics, Penn State College of Medicine, Hershey, PA
| | - Susan L. DiAngelo
- Department of Pediatrics, Penn State College of Medicine, Hershey, PA
| | - Patricia Silveyra
- Department of Pediatrics, Penn State College of Medicine, Hershey, PA,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Abigail Podany
- Department of Surgery, Penn State College of Medicine, Hershey, PA
| | - Leann L. Birch
- Department of Foods and Nutrition, University of Georgia, Athens, GA
| | - Ian M. Paul
- Department of Pediatrics, Penn State College of Medicine, Hershey, PA,Department of Public Health Sciences, Penn State College of Medicine, Hershey PA
| | - Shannon Kelleher
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA,Department of Pharmacology, Penn State College of Medicine, Hershey, PA,Department of Surgery, Penn State College of Medicine, Hershey, PA
| | - Steven D. Hicks
- Department of Pediatrics, Penn State College of Medicine, Hershey, PA,Corresponding author: Steven D. Hicks, Penn State College of Medicine, Department of Pediatrics, Mail Code HS83, 500 University Drive, PO Box 850, Hershey, PA 17033 0850, 717 531 8006,
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Yazdi Rouholamini SE, Moghassemi S, Maharat Z, Hakamivala A, Kashanian S, Omidfar K. Effect of silibinin-loaded nano-niosomal coated with trimethyl chitosan on miRNAs expression in 2D and 3D models of T47D breast cancer cell line. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2017; 46:524-535. [DOI: 10.1080/21691401.2017.1326928] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Seyede Elmira Yazdi Rouholamini
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeid Moghassemi
- Department of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Zahra Maharat
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Susan Kashanian
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Haghnavaz N, Asghari F, Elieh Ali Komi D, Shanehbandi D, Baradaran B, Kazemi T. HER2 positivity may confer resistance to therapy with paclitaxel in breast cancer cell lines. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2017; 46:518-523. [PMID: 28509576 DOI: 10.1080/21691401.2017.1326927] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION MicroRNAs (miRNAs) are short non-coding single-stranded RNAs. Involving in post-transcriptional gene silencing, miRNAs are thought to play important roles in many cancers such as breast cancer. Paclitaxel is used widely in the treatment of breast cancer. In this study, we investigated the effect of paclitaxel treatment on the expression levels of two oncomirs (oncomiRs), miR-21 and miR-203, in breast cancer cell lines. MATERIALS AND METHODS MTT assay was performed to determine IC50 of paclitaxel for human breast cancer cell lines including MCF-7, MDA-MB-231, SKBR3 and BT-474. After RNA extraction and cDNA synthesis, the expression levels of miRNAs were then quantitatively evaluated using real-time PCR. RESULTS Our results showed that after treatment, the expression levels of both miR-21 and miR-203 were significantly increased in HER2-positive cell lines, BT-474 and SKBR3. HER2-negative cell lines, MCF-7 and MDA-MB-231, in contrast had significantly decreased expression of both assessed oncomiRs. CONCLUSION Our results showed that the expression levels of oncomiRs were increased in HER-2 positive breast cancer cells and this finding is in line with previous studies. Our findings present a probable mechanism of resistance against paclitaxel chemotherapy in HER2-positive breast cancers.
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Affiliation(s)
- Navideh Haghnavaz
- a Immunology Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Immunology, Faculty of Medicine , Tabriz University of Medical Science , Tabriz , Iran.,c Student research committee , Tabriz University of Medical Science , Tabriz , Iran
| | - Faezeh Asghari
- a Immunology Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Immunology, Faculty of Medicine , Tabriz University of Medical Science , Tabriz , Iran
| | - Daniel Elieh Ali Komi
- a Immunology Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Immunology, Faculty of Medicine , Tabriz University of Medical Science , Tabriz , Iran
| | - Dariush Shanehbandi
- b Department of Immunology, Faculty of Medicine , Tabriz University of Medical Science , Tabriz , Iran
| | - Behzad Baradaran
- a Immunology Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Immunology, Faculty of Medicine , Tabriz University of Medical Science , Tabriz , Iran
| | - Tohid Kazemi
- a Immunology Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Immunology, Faculty of Medicine , Tabriz University of Medical Science , Tabriz , Iran
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Tormo E, Pineda B, Serna E, Guijarro A, Ribas G, Fores J, Chirivella E, Climent J, Lluch A, Eroles P. MicroRNA Profile in Response to Doxorubicin Treatment in Breast Cancer. J Cell Biochem 2016; 116:2061-73. [PMID: 25802200 DOI: 10.1002/jcb.25162] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED Chemotherapy treatment is the standard in triple negative breast cancers, a cancer subgroup which lacks a specific target. The mechanisms leading to the response, as well as any markers that allow the differentiation between responder and non-responder groups prior to treatment are unknown. In parallel, miRNAs can act as oncogenes or tumor suppressors and there is evidence of their involvement in promoting resistance to anticancer drugs. Therefore we hypothesized that changes in miRNA expression after doxorubicin treatment may also be relevant in treatment response. OBJECTIVE To study miRNAs that are differentially expressed in response to doxorubicin treatment. METHODS One luminal-A and two triple negative, breast cancer cell lines were exposed to doxorubicin. Microarray analysis was performed to identify the common and differentially modified miRNAs. Genes and pathways that are theoretically regulated by these miRNAs were analyzed. RESULTS Thirteen miRNAs common to all three lines were modified, in addition to 25 that were specific to triple negative cell lines, and 69 that changed only in the luminal-A cell line. This altered expression pattern seemed to be more strongly related to the breast cancer subgroup than to the treatment. The analysis of target genes revealed that cancer related pathways were the most affected by these miRNAs, moreover many of them had been previously related to chemotherapy resistance; thus suggesting follow-up studies. Additionally, through functional assays, we showed that miR-548c-3p is implicated in doxorubicin-treated MCF-7 cell viability, suggesting a role for this miRNA in resistance.
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Affiliation(s)
- Eduardo Tormo
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Begoña Pineda
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Eva Serna
- Unidad Central de, Investigación en Medicina-INCLIVA, Universitat de Valencia, Valencia, Spain
| | - Alba Guijarro
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Gloria Ribas
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Jaume Fores
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | | | - Joan Climent
- INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Ana Lluch
- INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Hematology and Medical Oncology, Hospital Clínico Universitario de, Valencia, Spain
| | - Pilar Eroles
- INCLIVA Biomedical Research Institute, Valencia, Spain
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Wang Y, Wang L, Yin C, An B, Hao Y, Wei T, Li L, Song G. Arsenic trioxide inhibits breast cancer cell growth via microRNA-328/hERG pathway in MCF-7 cells. Mol Med Rep 2015; 12:1233-8. [PMID: 25824027 DOI: 10.3892/mmr.2015.3558] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 03/03/2015] [Indexed: 11/05/2022] Open
Abstract
Arsenic trioxide (As2O3) has been widely used in the treatment of acute promyelocytic leukemia and has been observed to exhibit therapeutic effects in various types of solid tumor. In a previous study by this group, it was shown that As2O3 induces the apoptosis of MCF-7 breast cancer cells through inhibition of the human ether-à-go-go-related gene (hERG) channel. The present study was designed to further investigate the effect of As2O3 on breast cancer cells and to examine the mechanism underlying the regulation of hERG expression. The present study confirmed that As2O3 inhibited tumor growth in vivo, following MCF-7 cell implantation into nude mice. Using computational prediction , it was identified that microRNA (miR)-328 had a binding site in the 3'-untranslated region of hERG mRNA. A luciferase activity assay demonstrated that hERG is a target gene of miR-328. Further investigation using western blot analysis and reverse transcription-quantitative polymerase chain reaction revealed that As2O3 downregulated hERG expression via upregulation of miR-328 expression in MCF-7 cells. In conclusion, As2O3 was observed to inhibit breast cancer cell growth, at least in part, through the miR-328/hERG pathway.
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Affiliation(s)
- Ying Wang
- Medical Functional Laboratory, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Leqiu Wang
- Department of Otolaryngology, Hongqi Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Changhao Yin
- Department of Neurology, Hongqi Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Baizhu An
- Department of Anatomy, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Yankun Hao
- Medical Functional Laboratory, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Tao Wei
- Medical Functional Laboratory, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Li Li
- Medical Functional Laboratory, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Gaochen Song
- Medical Functional Laboratory, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
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Wang S, Zhu F, Marcone MF. Staghorn Sumac Reduces 5-Fluorouracil-Induced Toxicity in Normal Cells. J Med Food 2015; 18:938-40. [PMID: 25621382 DOI: 10.1089/jmf.2014.0114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Edible staghorn sumac (Rhus hirta) fruit extract was applied in conjunction with chemotherapeutic drug 5-fluorouracil to promote cytotoxicity of the drugs toward human breast cancer cells MCF-7 while protecting normal cells MCF-10A from drug toxicity. Sumac extract would be a promising chemotherapeutic drug conjugate in cancer chemotherapy.
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Affiliation(s)
- Sunan Wang
- 1 Canadian Food and Wine Institute, Niagara College , Niagara-on-the-Lake, Canada
| | - Fan Zhu
- 2 School of Chemical Sciences, University of Auckland , Auckland, New Zealand
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Liu H, Qin H, Chen GX, Liang MY, Rong J, Yao JP, Wu ZK. Comparative expression profiles of microRNA in left and right atrial appendages from patients with rheumatic mitral valve disease exhibiting sinus rhythm or atrial fibrillation. J Transl Med 2014; 12:90. [PMID: 24708751 PMCID: PMC4077055 DOI: 10.1186/1479-5876-12-90] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The atrial fibrillation (AF) associated microRNAs (miRNAs) were found in the right atrium (RA) and left atrium (LA) from patients with rheumatic mitral valve disease (RMVD). However, most studies only focus on the RA; and the potential differences of AF-associated miRNAs between the RA and LA are still unknown. The aim of this study was to perform miRNA expression profiles analysis to compare the potential differences of AF-associated miRNAs in the right atrial appendages (RAA) and left atrial appendages (LAA) from RMVD patients. METHODS Samples tissues from the RAA and LAA were obtained from 18 RMVD patients (10 with AF) during mitral valve replacement surgery. From these tissues, miRNA expression profiles were created and analyzed using a human miRNA microarray. Then, the results were validated using qRT-PCR analysis for 12 selected miRNAs. Finally, potential targets of 10 validated miRNAs were predicted and their functions and potential pathways were analyzed using the miRFocus database. RESULTS In RAA, 65 AF-associated miRNAs were found and significantly dysregulated (i.e. 28 miRNAs were up-regulated and 37 were down-regulated). In LAA, 42 AF-associated miRNAs were found and significantly dysregulated (i.e. 22 miRNAs were up-regulated and 20 were down-regulated). Among these AF-associated miRNAs, 23 of them were found in both RAA and LAA, 45 of them were found only in RAA, and 19 of them were found only in LAA. Finally, 10 AF-associated miRNAs validated by qRT-PCR were similarly distributed in RAA and LAA; 3 were found in both RAA and LAA, 5 were found only in RAA, and 2 were found only in LAA. Potential miRNA targets and molecular pathways were identified. CONCLUSIONS We have found the different distributions of AF-associated miRNAs in the RAA and LAA from RMVD patients. This may reflect different miRNA mechanisms in AF between the RA and LA. These findings may provide new insights into the underlying mechanisms of AF in RMVD patients.
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Affiliation(s)
| | | | | | | | | | | | - Zhong-kai Wu
- Second Department of Cardiac Surgery, First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, China.
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Abstract
MicroRNAs (miRNAs) are a class of small, non-coding, and endogenous RNA molecules, which are evolutionarily conserved but play a significant role in regulation of protein-coding gene expression at posttranscriptional and translational levels. Strikingly, a single miRNA is able to trigger hundreds of putative target genes by incomplete or complete complementary binding to their 3' untranslated regions. Given their appearance in almost all types of tissues, miRNAs have been demonstrated to be intensively involved in normal and pathological processes of human cells. Aside from the role as invaluable biomarkers in indication of tumorigenesis and tumor progression, numerous studies have revealed the potential of miRNAs as novel targets of anticancer drugs in cancer therapy. In this review article, we focus on the summary of the latest publications on the topic of miRNA and anticancer drugs, and expect to shed light on understanding the molecular mechanisms of chemoresistance involving miRNA regulation. These pieces of evidence will eventually provide insight into the development of novel and more efficacious anticancer drugs in the future.
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Affiliation(s)
- Zhiwei Xing
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot 010050, China
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Siddeek B, Inoubli L, Lakhdari N, Rachel PB, Fussell KC, Schneider S, Mauduit C, Benahmed M. MicroRNAs as potential biomarkers in diseases and toxicology. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 764-765:46-57. [PMID: 24486656 DOI: 10.1016/j.mrgentox.2014.01.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 01/20/2014] [Accepted: 01/20/2014] [Indexed: 02/06/2023]
Abstract
MiRNAs (microRNAs) are single-stranded non-coding RNAs of approximately 21-23 nucleotides in length whose main function is to inhibit gene expression by interfering with mRNA processes. MicroRNAs suppress gene expression by affecting mRNA (messenger RNAs) stability, targeting the mRNA for degradation, or both. In this review, we have examined how microRNA expression could be altered following exposure to chemicals and how they could represent appropriate tissue and more interestingly circulating biomarkers. Among the key questions before using the microRNA for evaluation of risk toxicity, it remains still to clarify how they could be causally involved in the adverse effects and how stable their changes are.
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Affiliation(s)
- Bénazir Siddeek
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France; BASF Agro, Ecully F-69130, France
| | - Lilia Inoubli
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France
| | - Nadjem Lakhdari
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France
| | - Paul Bellon Rachel
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France
| | | | - Steffen Schneider
- BASF SE, experimental toxicology and ecology, 67056 Ludwigshafen, Germany
| | - Claire Mauduit
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France; Université Lyon 1, UFR Médecine Lyon Sud, Lyon, F-69921, France; Hospices Civils de Lyon, Hôpital Lyon Sud, laboratoire d'anatomie et de cytologie pathologiques, Pierre-Bénite, F-69495, France
| | - Mohamed Benahmed
- Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, Nice, F-06204, France; Université de Nice Sophia-Antipolis, UFR Médecine, Nice, F-06000, France; Centre Hospitalier Universitaire de Nice, Pôle Digestif, Gynécologie, Obstetrique, Centre de Reproduction, Nice, F-06202, France.
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Liu H, Chen GX, Liang MY, Qin H, Rong J, Yao JP, Wu ZK. Atrial fibrillation alters the microRNA expression profiles of the left atria of patients with mitral stenosis. BMC Cardiovasc Disord 2014; 14:10. [PMID: 24461008 PMCID: PMC3909014 DOI: 10.1186/1471-2261-14-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 01/22/2014] [Indexed: 12/22/2022] Open
Abstract
Background Structural changes of the left and right atria associated with atrial fibrillation (AF) in mitral stenosis (MS) patients are well known, and alterations in microRNA (miRNA) expression profiles of the right atria have also been investigated. However, miRNA changes in the left atria still require delineation. This study evaluated alterations in miRNA expression profiles of left atrial tissues from MS patients with AF relative to those with normal sinus rhythm (NSR). Methods Sample tissues from left atrial appendages were obtained from 12 MS patients (6 with AF) during mitral valve replacement surgery. From these tissues, miRNA expression profiles were created and analyzed using a human miRNA microarray. Results were validated via reverse-transcription and quantitative PCR for 5 selected miRNAs. Potential miRNA targets were predicted and their functions and potential pathways analyzed via the miRFocus database. Results The expression levels of 22 miRNAs differed between the AF and NSR groups. Relative to NSR patients, in those with AF the expression levels of 45% (10/22) of these miRNAs were significantly higher, while those of the balance (55%, 12/22) were significantly lower. Potential miRNA targets and molecular pathways were identified. Conclusions AF alters the miRNA expression profiles of the left atria of MS patients. These findings may be useful for the biological understanding of AF in MS patients.
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Affiliation(s)
| | | | | | | | | | | | - Zhong-kai Wu
- Second Department of Cardiac Surgery, First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou 510080, China.
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Yao Y, Chen S, Zhou X, Xie L, Chen A. 5-FU and ixabepilone modify the microRNA expression profiles in MDA-MB-453 triple-negative breast cancer cells. Oncol Lett 2013; 7:541-547. [PMID: 24396484 PMCID: PMC3881949 DOI: 10.3892/ol.2013.1697] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 10/14/2013] [Indexed: 12/20/2022] Open
Abstract
This study aimed to discover new potential mechanisms of chemotherapy with drugs used in the treatment of luminal androgen receptor (LAR)-type triple-negative breast cancer (TNBC). We examined the microRNA (miRNA) expression profiles of LAR-type TNBC in vitro, and explored the variation in miRNA expression profiles in cells when treated with the chemotherapy drugs capecitabine and ixabepilone. The present study revealed that the expression levels of the three antitumor miRNAs, miR-122a, miR-145 and miR-205, were significantly elevated in MDA-MB-453 LAR-type TNBC tumor cells treated with 5-fluorouracil together with ixabepilone. By contrast, carcinogenic miR-296 miRNA expression significantly declined, and levels of several other miRNAs such as miR-221, miR-210, miR-21 and miR-10b were also altered. The drugs may exert their effects through the regulation of miRNA expression levels, thereby providing a theoretical basis for clinical implementation of miRNA expression profiles as a diagnostic method for the early diagnosis, classification and prognosis of breast cancer.
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Affiliation(s)
- Yongshan Yao
- Third Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443003, P.R. China
| | - Shenghan Chen
- Department of Electrocardiography, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443003, P.R. China
| | - Xin Zhou
- Third Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443003, P.R. China
| | - Li Xie
- Third Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443003, P.R. China
| | - Aijun Chen
- Third Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443003, P.R. China
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Wang J, Cui Q. Specific Roles of MicroRNAs in Their Interactions with Environmental Factors. J Nucleic Acids 2012; 2012:978384. [PMID: 23209884 PMCID: PMC3502025 DOI: 10.1155/2012/978384] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/26/2012] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) have emerged as critical regulators of gene expression by modulating numerous target mRNAs expression at posttranscriptional level. Extensive studies have shown that miRNAs are critical in various important biological processes, including cell growth, proliferation, differentiation, development, and apoptosis. In terms of their importance, miRNA dysfunction has been associated with a broad range of diseases. Increased number of studies have shown that miRNAs can functionally interact with a wide spectrum of environmental factors (EFs) including drugs, industrial materials, virus and bacterial pathogens, cigarette smoking, alcohol, nutrition, sleep, exercise, stress, and radiation. More importantly, the interactions between miRNAs and EFs have been shown to play critical roles in determining abnormal phenotypes and diseases. In this paper, we propose an outline of the current knowledge about specific roles of miRNAs in their interactions with various EFs and analyze the literatures detailing miRNAs-EFs interactions in the context of various of diseases.
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Affiliation(s)
- Juan Wang
- Department of Biomedical Informatics, Peking University Health Science Center, Beijing 100191, China ; MOE Key Lab of Cardiovascular Sciences, Peking University, Beijing 100191, China ; Institute of Systems Biomedicine, Peking University, Beijing 100191, China
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Rukov JL, Shomron N. MicroRNA pharmacogenomics: post-transcriptional regulation of drug response. Trends Mol Med 2011; 17:412-23. [PMID: 21652264 DOI: 10.1016/j.molmed.2011.04.003] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/23/2011] [Accepted: 04/26/2011] [Indexed: 12/16/2022]
Abstract
The field of pharmacogenomics aims to predict which drugs will be most effective and safe for a particular individual based on their genome sequence or expression profile, thereby allowing personalized treatment. The bulk of pharmacogenomic research has focused on the role of single nucleotide polymorphisms, copy number variations or differences in gene expression levels of drug metabolizing or transporting genes and drug targets. In this review paper, we focus instead on microRNAs (miRNAs): small noncoding RNAs, prevalent in metazoans, that negatively regulate gene expression in many cellular processes. We discuss how miRNAs, by regulating the expression of pharmacogenomic-related genes, can play a pivotal role in drug efficacy and toxicity and have potential clinical implications for personalized medicine.
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Affiliation(s)
- Jakob Lewin Rukov
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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