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Liu H, Dong J, Duan Z, Xia F, Willner I, Huang F. Light-activated CRISPR-Cas12a for amplified imaging of microRNA in cell cycle phases at single-cell levels. SCIENCE ADVANCES 2024; 10:eadp6166. [PMID: 39047109 PMCID: PMC11268419 DOI: 10.1126/sciadv.adp6166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024]
Abstract
An ortho-nitrobenzyl phosphate ester-caged nucleic acid hairpin structure coupled to the CRISPR-Cas12a complex is introduced as a functional reaction module for the light-induced activation of the CRISPR-Cas12a (LAC12a) machinery toward the amplified fluorescence detection of microRNA-21 (miRNA-21). The LAC12a machinery is applied for the selective, in vitro sensing of miRNA-21 and for the intracellular imaging of miRNA-21 in different cell lines. The LAC12a system is used to image miRNA-21 in different cell cycle phases of MCF-7 cells. Moreover, the LAC12a machinery integrated in cells enables the two-photon laser confocal microscopy-assisted, light-stimulated spatiotemporal, selective activation of the CRISPR-Cas12a miRNA-21 imaging machinery at the single-cell level and the evaluation of relative expression levels of miRNA-21 at distinct cell cycle phases. The method is implemented to map the distribution of cell cycle phases in an array of single cells.
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Affiliation(s)
- Hong Liu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Jiantong Dong
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Itamar Willner
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fujian Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
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Le HT, Staelens M, Lazzari D, Chan G, Tuszyński JA. Real-Time Monitoring of the Effect of Tumour-Treating Fields on Cell Division Using Live-Cell Imaging. Cells 2022; 11:2712. [PMID: 36078119 PMCID: PMC9454843 DOI: 10.3390/cells11172712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The effects of electric fields (EFs) on various cell types have been thoroughly studied, and exhibit a well-known regulatory effect on cell processes, implicating their usage in several medical applications. While the specific effect exerted on cells is highly parameter-dependent, the majority of past research has focused primarily on low-frequency alternating fields (<1 kHz) and high-frequency fields (in the order of MHz). However, in recent years, low-intensity (1-3 V/cm) alternating EFs with intermediate frequencies (100-500 kHz) have been of topical interest as clinical treatments for cancerous tumours through their disruption of cell division and the mitotic spindle, which can lead to cell death. These aptly named tumour-treating fields (TTFields) have been approved by the FDA as a treatment modality for several cancers, such as malignant pleural mesothelioma and glioblastoma multiforme, demonstrating remarkable efficacy and a high safety profile. In this work, we report the results of in vitro experiments with HeLa and MCF-10A cells exposed to TTFields for 18 h, imaged in real time using live-cell imaging. Both studied cell lines were exposed to 100 kHz TTFields with a 1-1 duty cycle, which resulted in significant mitotic and cytokinetic arrest. In the experiments with HeLa cells, the effects of the TTFields' frequency (100 kHz vs. 200 kHz) and duty cycle (1-1 vs. 1-0) were also investigated. Notably, the anti-mitotic effect was stronger in the HeLa cells treated with 100 kHz TTFields. Additionally, it was found that single and two-directional TTFields (oriented orthogonally) exhibit a similar inhibitory effect on HeLa cell division. These results provide real-time evidence of the profound ability of TTFields to hinder the process of cell division by significantly delaying both the mitosis and cytokinesis phases of the cell cycle.
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Affiliation(s)
- Hoa T. Le
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Michael Staelens
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Davide Lazzari
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, 10129 Turin, Italy
| | - Gordon Chan
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Jack A. Tuszyński
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
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LNX1 Contributes to Cell Cycle Progression and Cisplatin Resistance. Cancers (Basel) 2021; 13:cancers13164066. [PMID: 34439220 PMCID: PMC8394373 DOI: 10.3390/cancers13164066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The ligand of numb-protein X1 (LNX1) is reported to be upregulated in various cancers, however the cellular function of LNX1 is not clearly characterized. The aim of the present study was to elucidate the regulation of LNX1 expression and clarify the role of LNX1 in cell-cycle progression and resistance to the cancer therapeutic agent, cisplatin. We found that LNX1 expression is decreased by DNA damage including cisplatin treatment and the levels of S and G2/M populations were correlated with LNX1 expression. We also showed that the upregulation of LNX1 contributes to cell-cycle progression and cisplatin resistance. Our data suggest that LNX1 is the important regulator of the cell cycle, and contributes to tumor progression. Abstract The ligand of numb-protein X1 (LNX1) acts as a proto-oncogene by inhibiting p53 stability; however, the regulation of LNX1 expression has not been investigated. In this study, we screened chemicals to identify factors that potentially regulate LNX1 expression. We found that LNX1 expression levels were decreased by DNA damage, including that by cisplatin. Upon treatment with lipopolysaccharide (LPS) and phorbol 12-myristate 13-acetate (PMA), LNX1 expression levels increased. In addition, cell-cycle progression increased upon LNX1 expression; the levels of S and G2/M populations were correlated with LNX1 expression. Moreover, in CRISPR-Cas9-mediated LNX1 knockout cells, we observed a delay in cell-cycle progression and a downregulation of genes encoding the cell-cycle markers cyclin D1 and cyclin E1. Finally, the upregulation of LNX1-activated cell-cycle progression and increased resistance to cisplatin-mediated cell death. Taken together, these results suggest that LNX1 contributes to cell-cycle progression and cisplatin resistance.
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Pham TND, Ma W, Miller D, Kazakova L, Benchimol S. Erythropoietin inhibits chemotherapy-induced cell death and promotes a senescence-like state in leukemia cells. Cell Death Dis 2019; 10:22. [PMID: 30622244 PMCID: PMC6325163 DOI: 10.1038/s41419-018-1274-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022]
Abstract
There are conflicting reports on the adverse effects of erythropoietin (EPO) for the management of cancer-associated anemia. The recognition that erythropoietin receptors (EPORs) are expressed outside the erythroid lineage and concerns that erythropoiesis-stimulating agents (ESAs) may cause tumors to grow and increase the risk of venous thromboembolism have resulted in substantially fewer cancer patients receiving ESA therapy to manage myelosuppressive chemotherapy. In this study, we found that EPO suppresses p53-dependent apoptosis induced by genotoxic (daunorubicin, doxorubicin, and γ-radiation) and non-genotoxic (nutlin-3a) agents and induces a senescence-like state in myeloid leukemia cells. EPO interferes with stress-dependent Mdm2 downregulation and leads to the destabilization of p53 protein. EPO selectively modulates the expression of p53 target genes in response to DNA damage preventing the induction of a number of noncoding RNAs (ncRNAs) previously associated with p53-dependent apoptosis. EPO also enhances the expression of the cyclin-dependent kinase inhibitor p21WAF1 and promotes recruitment of p53 to the p21 promoter. In addition, EPO antagonizes Mcl-1 protein degradation in daunorubicin-treated cells. Hence, EPO signaling targets Mcl-1 expression and the p53-Mdm2 network to promote tumor cell survival.
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Affiliation(s)
| | - Weili Ma
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
| | - David Miller
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
| | - Lidia Kazakova
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
| | - Samuel Benchimol
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada.
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Tsamou M, Martens DS, Cox B, Madhloum N, Vrijens K, Nawrot TS. Sex-specific associations between telomere length and candidate miRNA expression in placenta. J Transl Med 2018; 16:254. [PMID: 30208911 PMCID: PMC6134555 DOI: 10.1186/s12967-018-1627-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/04/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In the early-life environment, proper development of the placenta is essential for both fetal and maternal health. Telomere length at birth has been related to life expectancy. MicroRNAs (miRNAs) as potential epigenetic determinants of telomere length at birth have not been identified. In this study, we investigate whether placental miRNA expression is associated with placental telomere length at birth. METHODS We measured the expression of seven candidate miRNAs (miR-16-5p, -20a-5p, -21-5p, -34a-5p, 146a-5p, -210-3p and -222-3p) in placental tissue at birth in 203 mother-newborn (51.7% girls) pairs from the ENVIRONAGE birth cohort. We selected miRNAs known to be involved in crucial cellular processes such as inflammation, oxidative stress, cellular senescence related to aging. Placental miRNA expression and relative average placental telomere length were measured using RT-qPCR. RESULTS Both before and after adjustment for potential covariates including newborn's ethnicity, gestational age, paternal age, maternal smoking status, maternal educational status, parity, date of delivery and outdoor temperature during the 3rd trimester of pregnancy, placental miR-34a, miR-146a, miR-210 and miR-222 expression were significantly (p ≤ 0.03) and positively associated with placental relative telomere length in newborn girls. In newborn boys, only higher expression of placental miR-21 was weakly (p = 0.08) associated with shorter placental telomere length. Significant miRNAs explain around 6-8% of the telomere length variance at birth. CONCLUSIONS Placental miR-21, miR-34a, miR-146a, miR-210 and miR-222 exhibit sex-specific associations with telomere length in placenta. Our results indicate miRNA expression in placental tissue could be an important determinant in the process of aging starting from early life onwards.
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Affiliation(s)
- Maria Tsamou
- Center for Environmental Sciences, Hasselt University, 3500, Hasselt, Belgium
| | - Dries S Martens
- Center for Environmental Sciences, Hasselt University, 3500, Hasselt, Belgium
| | - Bianca Cox
- Center for Environmental Sciences, Hasselt University, 3500, Hasselt, Belgium
| | - Narjes Madhloum
- Center for Environmental Sciences, Hasselt University, 3500, Hasselt, Belgium
| | - Karen Vrijens
- Center for Environmental Sciences, Hasselt University, 3500, Hasselt, Belgium.
| | - Tim S Nawrot
- Center for Environmental Sciences, Hasselt University, 3500, Hasselt, Belgium.,Environment & Health Unit, Department of Public Health, Leuven University (KU Leuven), 3000, Louvain, Belgium
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Shiraga K, Soe TH, Matsumoto S, Watanabe K, Ohtsuki T. Red and Near-Infrared Light-Directed Cytosolic Delivery of Two Different RNAs Using Photosensitive RNA Carriers. Bioconjug Chem 2018; 29:3174-3179. [PMID: 30063334 DOI: 10.1021/acs.bioconjchem.8b00487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Many cellular events are thought to be controlled by the temporal upregulation of multiple RNAs; the timing of the upregulation of these RNAs is not always the same. In this study, we first show that our light-directed intracellular RNA delivery method induced high concentrations of RNA in a short period. This effect was beneficial for the temporal control of cellular events by functional RNAs. Next, we stimulated the short-term upregulation of two different RNAs at different time points. Cytosolic delivery of a first RNA was induced by red light; thereafter, cytosolic delivery of a second RNA was induced by near-infrared light. The time difference between the introduction of the first and second RNA can be short (0.5-4 h) or long (>8 h). This strategy shows the potential for future applications of the deliberate control of time-dependent RNA concentration to guide various cellular functions by multiple RNAs.
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Affiliation(s)
- Kaori Shiraga
- Department of Interdisciplinary Science and Engineering in Health Systems , Okayama University , 3-1-1 Tsushimanaka , Okayama 700-8530 , Japan
| | - Tet Htut Soe
- Department of Interdisciplinary Science and Engineering in Health Systems , Okayama University , 3-1-1 Tsushimanaka , Okayama 700-8530 , Japan
| | - Sho Matsumoto
- Department of Interdisciplinary Science and Engineering in Health Systems , Okayama University , 3-1-1 Tsushimanaka , Okayama 700-8530 , Japan
| | - Kazunori Watanabe
- Department of Interdisciplinary Science and Engineering in Health Systems , Okayama University , 3-1-1 Tsushimanaka , Okayama 700-8530 , Japan
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems , Okayama University , 3-1-1 Tsushimanaka , Okayama 700-8530 , Japan
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曾 烨, 刘 洁, 陈 志, 郑 思, 张 汉, 周 珏. [Over-expression of miR-519d alters gene expression profiles of cervical cancer SiHa cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:794-799. [PMID: 33168510 PMCID: PMC6765531 DOI: 10.3969/j.issn.1673-4254.2018.07.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To investigate the alterations in gene expression profiles of cervical cancer cell line SiHa over-expressing miR-519d. METHODS SiHa cells were transfected with a miR-519d mimic or a negative control (NC) and the changes in gene expression profiles were examined using NimbleGen human gene expression microarray. Bioinformatics approaches based on the microarray data were used to identify the targeted genes of miR-519d. Real-time quantitative PCR was employed to confirm the expression of the potential target genes. RESULTS A total of 5172 genes were found to be differentially expressed in SiHa cells over-expressing miR-519d, including 2476 up-regulated and 2796 down-regulated genes. We identified 164 potential target genes of miR-519d, and their functions were predicted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis, and STRING database and pSTIING were used to search the key nodes in the protein-protein interactions and transcriptional regulatory networks in cancer. Real-time quantitative PCR confirmed the differential expressions of several candidate target genes. CONCLUSIONS Over-expression of miR-519d alters gene expression profiles in SiHa cells. The 164 target genes of miR-519d we identified may provide insights into the role of miR-519d in cervical tumorigenesis.
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Affiliation(s)
- 烨 曾
- 南方医科大学 南方医院口腔科,广东 广州 510515Department of Stomatology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - 洁 刘
- 南方医科大学 南方医院妇产科,广东 广州 510515Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - 志超 陈
- 南方医科大学 基础医学院生物化学与分子生物学教研室,广东 广州 510515Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - 思荣 郑
- 南方医科大学 基础医学院生物化学与分子生物学教研室,广东 广州 510515Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - 汉荣 张
- 南方医科大学 基础医学院生物化学与分子生物学教研室,广东 广州 510515Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - 珏宇 周
- 南方医科大学 基础医学院生物化学与分子生物学教研室,广东 广州 510515Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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Del Giudice M, Bo S, Grigolon S, Bosia C. On the role of extrinsic noise in microRNA-mediated bimodal gene expression. PLoS Comput Biol 2018; 14:e1006063. [PMID: 29664903 PMCID: PMC5922620 DOI: 10.1371/journal.pcbi.1006063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 04/27/2018] [Accepted: 02/28/2018] [Indexed: 01/01/2023] Open
Abstract
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Bimodal distributions of gene expression levels provide experimental evidence of phenotypic differentiation, where the modes of the distribution often correspond to different physiological states of the system. We theoretically address the presence of bimodal phenotypes in the context of microRNA (miRNA)-mediated regulation. MiRNAs are small noncoding RNA molecules that downregulate the expression of their target mRNAs. The nature of this interaction is titrative and induces a threshold effect: below a given target transcription rate almost no mRNAs are free and available for translation. We investigate the effect of extrinsic noise on the system by introducing a fluctuating miRNA-transcription rate. We find that the presence of extrinsic noise favours the presence of bimodal target distributions which can be observed for a wider range of parameters compared to the case with intrinsic noise only and for lower miRNA-target interaction strength. Our results suggest that combining threshold-inducing interactions with extrinsic noise provides a simple and robust mechanism for obtaining bimodal populations without requiring fine tuning. Furthermore, we characterise the protein distribution's dependence on protein half-life.
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Affiliation(s)
- Marco Del Giudice
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy
- Italian Institute for Genomic Medicine, Torino, Italy
| | - Stefano Bo
- Nordita, Royal Institute of Technology and Stockholm University, Stockholm, Sweden
| | | | - Carla Bosia
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy
- Italian Institute for Genomic Medicine, Torino, Italy
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Lennox KA, Vakulskas CA, Behlke MA. Non-nucleotide Modification of Anti-miRNA Oligonucleotides. Methods Mol Biol 2018; 1517:51-69. [PMID: 27924473 DOI: 10.1007/978-1-4939-6563-2_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) are important modulators of gene expression. Synthetic anti-microRNA oligonucleotides (AMOs, or anti-miRs) are a form of steric-blocking antisense oligonucleotides (ASOs) that inhibit miRNA function through high-affinity binding and subsequent inactivation and/or degradation of the targeted miRNA. AMOs are a primary tool used to empirically determine the biological targets of a miRNA and can also be used therapeutically when overexpression of a miRNA contributes to a disease state. Chemical modification of synthetic AMOs enhance potency by protecting the oligonucleotide from nuclease degradation and by increasing binding affinity to the target miRNA. A new steric-blocking ASO modification strategy with favorable properties for use in AMOs was recently developed that combines use of high-affinity 2'-O-methyl RNA with terminally positioned non-nucleotide "ZEN" modifiers. This protocol describes use of ZEN AMOs in a dual-luciferase reporter assay as a simplified means to validate AMO performance or to quickly test putative miRNA binding sites in target sequences. This protocol also describes a method using Western blot analysis for quantifying the level of upregulation of proteins made from an mRNA that is thought to be under miRNA regulation, following inhibition of that miRNA by ZEN AMO treatment.
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Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA.
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Amin MA, Varma D. Combining Mitotic Cell Synchronization and High Resolution Confocal Microscopy to Study the Role of Multifunctional Cell Cycle Proteins During Mitosis. J Vis Exp 2017. [PMID: 29286472 DOI: 10.3791/56513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Study of the various regulatory events of the cell cycle in a phase-dependent manner provides a clear understanding about cell growth and division. The synchronization of cell populations at specific stages of the cell cycle has been found to be very useful in such experimental endeavors. Synchronization of cells by treatment with chemicals that are relatively less toxic can be advantageous over the use of pharmacological inhibitory drugs for the study of consequent cell cycle events and to obtain specific enrichment of selected mitotic stages. Here, we describe the protocol for synchronizing human cells at different stages of the cell cycle, including both in S phase and M phase with a double thymidine block and release procedure for studying the functionality of mitotic proteins in chromosome alignment and segregation. This protocol has been extremely useful for studying the mitotic roles of multifunctional proteins which possess established interphase functions. In our case, the mitotic role of Cdt1, a protein critical for replication origin licensing in G1 phase, can be studied effectively only when G2/M-specific Cdt1 can be depleted. We describe the detailed protocol for depletion of G2/M-specific Cdt1 using double thymidine synchronization. We also explain the protocol of cell fixation, and live cell imaging using high resolution confocal microscopy after thymidine release. The method is also useful for analyzing the function of mitotic proteins under both physiological and perturbed conditions such as for Hec1, a component of the Ndc80 complex, as it enables one to obtain large sample sizes of mitotic cells for fixed and live cell analysis as we show here.
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Affiliation(s)
- Mohammed A Amin
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | - Dileep Varma
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University;
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Lee YH, Hsueh YW, Peng YH, Chang KC, Tsai KJ, Sun HS, Su IJ, Chiang PM. Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium. BMC Biol 2017; 15:22. [PMID: 28327113 PMCID: PMC5360049 DOI: 10.1186/s12915-017-0359-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/15/2017] [Indexed: 12/24/2022] Open
Abstract
Background In addition to messenger RNA (mRNA), noncoding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. Besides their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure, and accessibility. To have a comprehensive understanding of the identities and functions of different cell types, a method to comprehensively quantify both mRNA and ncRNA in a sensitive manner is highly desirable. Methods Here we tried to develop a system capable of concurrently profiling both mRNA and ncRNA by polyadenylating RNA in samples before reverse transcription. The sensitivity of the system was maximized by avoiding purification from cell lysis to amplified cDNA and by optimizing the buffer conditions. The single-tube amplification (STA) system was applied to single to 100 cells of 293T cells, human pluripotent stem cells (hPSCs) and their differentiated endothelial progenies to validate its quantitative power and sensitivity by qPCR and high-throughput sequencing. Results Using microRNA (miRNA) as an example, we showed that complementary DNA (cDNA) from ncRNAs could be amplified and specifically detected from a few cells within a single tube. The sensitivity of the system was maximized by avoiding purification from cell lysis to amplified cDNA and by optimizing the buffer conditions. With 100 human embryonic stem cells (hESCs) and their differentiated endothelial cells as input for high-throughput sequencing, the single-tube amplification (STA) system revealed both well-known and other miRNAs selectively enriched in each cell type. The selective enrichment of the miRNAs was further verified by qPCR with 293FT cells and a human induced pluripotent stem cell (hiPSC) line. In addition, the detection of other non-miRNA transcripts indicated that the STA target was not limited to miRNA, but extended to other ncRNAs and mRNAs as well. Finally, the STA system was capable of detecting miRNA and mRNA expression down to single cells, albeit with some loss of sensitivity and power. Conclusions Overall, STA offered a simple and sensitive way to concurrently quantify both mRNA and ncRNA expression in low-cell-number samples for both qPCR and high-throughput sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0359-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi-Hsuan Lee
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ya-Wen Hsueh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan
| | - Yao-Hung Peng
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan
| | - Kung-Chao Chang
- Department of Pathology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan
| | - H Sunny Sun
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ih-Jen Su
- Division of Infectious Diseases, National Health Research Institutes, Tainan, Taiwan
| | - Po-Min Chiang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan.
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Abstract
HeLa is one of the oldest and most commonly used cell lines in biomedical research. Owing to the ease of which they can be effectively synchronized by various methods, HeLa cells have been used extensively for studying the cell cycle. Here, we describe several protocols for synchronizing HeLa cells from different phases of the cell cycle, including G1 phase using the HMG-CoA reductase inhibitor lovastatin, S phase with a double thymidine block procedure, and G2 phase with the CDK1 inhibitor RO-3306. Cells can also be enriched in mitosis using nocodazole and mechanical shake-off. Releasing the cells from these blocks enables researchers to follow gene expression and other events through the cell cycle. We also describe several protocols, including flow cytometry, BrdU labeling, immunoblotting, and time-lapse microscopy, for validating the synchrony of the cells and monitoring the progression of the cell cycle.
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Affiliation(s)
- Hoi Tang Ma
- Division of Life Science, Center for Cancer Research and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Randy Y C Poon
- Division of Life Science, Center for Cancer Research and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
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Lombardi APG, Pisolato R, Vicente CM, Lazari MFM, Lucas TFG, Porto CS. Estrogen receptor beta (ERβ) mediates expression of β-catenin and proliferation in prostate cancer cell line PC-3. Mol Cell Endocrinol 2016; 430:12-24. [PMID: 27107935 DOI: 10.1016/j.mce.2016.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/31/2016] [Accepted: 04/19/2016] [Indexed: 12/11/2022]
Abstract
The aim of the present study was to characterize the mechanism underlying estrogen effects on the androgen-independent prostate cancer cell line PC-3. 17β-estradiol and the ERβ-selective agonist DPN, but not the ERα-selective agonist PPT, increased the incorporation of [methyl-(3)H]thymidine and the expression of Cyclin D2, suggesting that ERβ mediates the proliferative effect of estrogen on PC-3 cells. In addition, upregulation of Cyclin D2 and incorporation of [methyl-(3)H]thymidine induced by 17β-estradiol and DPN were blocked by the ERβ-selective antagonist PHTPP in PC-3 cells. Upregulation of Cyclin D2 and incorporation of [methyl-(3)H]thymidine induced by DPN were also blocked by PKF118-310, a compound that disrupts β-catenin-TCF (T-cell-specific transcription factor) complex, suggesting the involvement of β-catenin in the estradiol effects in PC-3 cells. A diffuse immunostaining for non-phosphorylated β-catenin was detected in the cytoplasm of PC-3 cells. Low levels of non-phosphorylated β-catenin immunostaining were also detected near the plasma membrane and in nuclei. Treatment of PC-3 cells with 17β-estradiol or DPN markedly increased non-phosphorylated β-catenin expression. These effects were blocked by pretreatment with the ERβ-selective antagonist PHTPP, PI3K inhibitor Wortmannin or AKT inhibitor MK-2206, indicating that ERβ-PI3K/AKT mediates non-phosphorylated β-catenin expression. Cycloheximide blocked the DPN-induced upregulation of non-phosphorylated β-catenin, suggesting de novo synthesis of this protein. In conclusion, these results suggest that estrogen may play a role in androgen-independent prostate cancer cell proliferation through a novel pathway, involving ERβ-mediated activation of β-catenin.
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Affiliation(s)
- Ana Paola G Lombardi
- Section of Experimental Endocrinology, Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de maio 100, INFAR, Vila Clementino, São Paulo, SP, 04044-020, Brazil
| | - Raisa Pisolato
- Section of Experimental Endocrinology, Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de maio 100, INFAR, Vila Clementino, São Paulo, SP, 04044-020, Brazil
| | - Carolina M Vicente
- Section of Experimental Endocrinology, Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de maio 100, INFAR, Vila Clementino, São Paulo, SP, 04044-020, Brazil
| | - Maria Fatima M Lazari
- Section of Experimental Endocrinology, Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de maio 100, INFAR, Vila Clementino, São Paulo, SP, 04044-020, Brazil
| | - Thaís F G Lucas
- Section of Experimental Endocrinology, Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de maio 100, INFAR, Vila Clementino, São Paulo, SP, 04044-020, Brazil
| | - Catarina S Porto
- Section of Experimental Endocrinology, Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de maio 100, INFAR, Vila Clementino, São Paulo, SP, 04044-020, Brazil.
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Grolmusz VK, Tóth EA, Baghy K, Likó I, Darvasi O, Kovalszky I, Matkó J, Rácz K, Patócs A. Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression. BMC Genomics 2016; 17:412. [PMID: 27234232 PMCID: PMC4884355 DOI: 10.1186/s12864-016-2747-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Previously, drug-based synchronization procedures were used for characterizing the cell cycle dependent transcriptional program. However, these synchronization methods result in growth imbalance and alteration of the cell cycle machinery. DNA content-based fluorescence activated cell sorting (FACS) is able to sort the different cell cycle phases without perturbing the cell cycle. MiRNAs are key transcriptional regulators of the cell cycle, however, their expression dynamics during cell cycle has not been explored. METHODS Following an optimized FACS, a complex initiative of high throughput platforms (microarray, Taqman Low Density Array, small RNA sequencing) were performed to study gene and miRNA expression profiles of cell cycle sorted human cells originating from different tissues. Validation of high throughput data was performed using quantitative real time PCR. Protein expression was detected by Western blot. Complex statistics and pathway analysis were also applied. RESULTS Beyond confirming the previously described cell cycle transcriptional program, cell cycle dependently expressed genes showed a higher expression independently from the cell cycle phase and a lower amplitude of dynamic changes in cancer cells as compared to untransformed fibroblasts. Contrary to mRNA changes, miRNA expression was stable throughout the cell cycle. CONCLUSIONS Cell cycle sorting is a synchronization-free method for the proper analysis of cell cycle dynamics. Altered dynamic expression of universal cell cycle genes in cancer cells reflects the transformed cell cycle machinery. Stable miRNA expression during cell cycle progression may suggest that dynamical miRNA-dependent regulation may be of less importance in short term regulations during the cell cycle.
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Affiliation(s)
- Vince Kornél Grolmusz
- 2nd Department of Medicine, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary.,"Lendület" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary
| | - Eszter Angéla Tóth
- Department of Immunology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Kornélia Baghy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - István Likó
- "Lendület" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences - Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary
| | - Ottó Darvasi
- "Lendület" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences - Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - János Matkó
- Department of Immunology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - Károly Rácz
- 2nd Department of Medicine, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences - Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary
| | - Attila Patócs
- "Lendület" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences - Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary. .,Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary.
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16
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Zhang W, Xu J, Shi Y, Sun Q, Zhang Q, Guan X. The novel role of miRNAs for tamoxifen resistance in human breast cancer. Cell Mol Life Sci 2015; 72:2575-84. [PMID: 25782411 PMCID: PMC11113898 DOI: 10.1007/s00018-015-1887-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 01/04/2023]
Abstract
The selective estrogen receptor modulator tamoxifen is the most commonly used treatment for patients with ER-positive breast cancer. However, tumor cells often develop resistance to tamoxifen therapy, which is a major obstacle limiting the success of breast cancer treatment. miRNAs, as oncogenic or tumor suppressor genes, regulate the expression and function of their related target genes to affect the biological behaviors of cancer cells, including cancer initiation, progression, metastasis, and therapeutic resistance. In detail, many miRNAs associated with breast cancer tamoxifen resistance have been identified, which offer new targets for breast cancer therapy. Here, we review the miRNAs involved in regulation of tamoxifen resistance in human breast cancer and the mechanism of how the modulation of miRNAs may regulate the sensitivity of breast cancer cells to tamoxifen. We also discuss the future prospects of studies about miRNAs in regulation of tamoxifen resistance and miRNA-based therapeutics for tamoxifen resistance breast cancer patients.
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Affiliation(s)
- Wenwen Zhang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 China
| | - Jing Xu
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 China
| | - Yaqin Shi
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 China
| | - Qian Sun
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 China
| | - Qun Zhang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 China
| | - Xiaoxiang Guan
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 China
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17
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de Araujo CB, Russo LC, Castro LM, Forti FL, do Monte ER, Rioli V, Gozzo FC, Colquhoun A, Ferro ES. A novel intracellular peptide derived from g1/s cyclin d2 induces cell death. J Biol Chem 2014; 289:16711-26. [PMID: 24764300 DOI: 10.1074/jbc.m113.537118] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intracellular peptides are constantly produced by the ubiquitin-proteasome system, and many are probably functional. Here, the peptide WELVVLGKL (pep5) from G1/S-specific cyclin D2 showed a 2-fold increase during the S phase of HeLa cell cycle. pep5 (25-100 μm) induced cell death in several tumor cells only when it was fused to a cell-penetrating peptide (pep5-cpp), suggesting its intracellular function. In vivo, pep5-cpp reduced the volume of the rat C6 glioblastoma by almost 50%. The tryptophan at the N terminus of pep5 is essential for its cell death activity, and N terminus acetylation reduced the potency of pep5-cpp. WELVVL is the minimal active sequence of pep5, whereas Leu-Ala substitutions totally abolished pep5 cell death activity. Findings from the initial characterization of the cell death/signaling mechanism of pep5 include caspase 3/7 and 9 activation, inhibition of Akt2 phosphorylation, activation of p38α and -γ, and inhibition of proteasome activity. Further pharmacological analyses suggest that pep5 can trigger cell death by distinctive pathways, which can be blocked by IM-54 or a combination of necrostatin-1 and q-VD-OPh. These data further support the biological and pharmacological potential of intracellular peptides.
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Affiliation(s)
| | - Lilian C Russo
- the Department of Biochemistry, Support Center for Research in Proteolysis and Cell Signaling (NAPPS), Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil
| | | | - Fábio L Forti
- the Department of Biochemistry, Support Center for Research in Proteolysis and Cell Signaling (NAPPS), Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil
| | | | - Vanessa Rioli
- the Special Laboratory of Applied Toxinology (LETA), Center of Toxins, Immune Response, and Cell Signaling (CETICS), Butantan Institute, 05503-000, São Paulo, SP, Brazil, and
| | - Fabio C Gozzo
- the Institute of Chemistry, State University of Campinas, 13083-862, Campinas, SP, Brazil
| | - Alison Colquhoun
- Cell Biology and Development, Support Center for Research in Proteolysis and Cell Signaling (NAPPS), Biomedical Science Institute, University of São Paulo, São Paulo, 05508-000, SP, Brazil
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Chafin CB, Regna NL, Dai R, Caudell DL, Reilly CM. MicroRNA-let-7a expression is increased in the mesangial cells of NZB/W mice and increases IL-6 production in vitro. Autoimmunity 2014; 46:351-62. [PMID: 24001203 DOI: 10.3109/08916934.2013.773976] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent evidence supports a role for epigenetic alterations in the pathogenesis of systemic lupus erythematosus (SLE). MicroRNAs (miRNAs or miRs) are endogenous epigenetic regulators whose expression is altered in many diseases, including SLE. IL-6 is an inflammatory cytokine produced by mesangial cells during lupus nephritis (LN). IL-6 contains a potential binding site for miRNA-let-7a (let-7a) in its 3' untranslated region (UTR). We found let-7a expression was significantly increased in the mesangial cells of pre-diseased and actively diseased New Zealand Black/White (NZB/W) mice compared to age-matched New Zealand White (NZW) mice. Overexpression of let-7a in vitro increased IL-6 production in stimulated mesangial cells compared to non-transfected controls. Inhibition of let-7a did not significantly affect immune-stimulated IL-6 production. When stimulated mesangial cells overexpressing let-7a were treated with the transcription inhibitor Actinomycin D (ActD), IL-6 was degraded faster, consistent with the direct targeting of the 3' UTR of IL-6 by let-7a. Overexpression of let-7a increased the expression of tristetraprolin (TTP), an RNA-binding protein (RBP) that has 5 potential binding regions in the 3' UTR of IL-6. ActD inhibited the transcription of proteins including TTP that may contribute to the let-7a-mediated increase in immune-stimulated IL-6 production. These data show that NZB/W mice have higher let-7a expression than NZW mice and that increased let-7a expression in vitro increases IL-6 production in stimulated mesangial cells. Further studies examining the role of let-7a expression in inflammation are warranted.
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Affiliation(s)
- Cristen B Chafin
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Ruland R, Florea AM. Are microRNAs key players in epithelial skin cancers? A review focused on basal cell carcinoma and squamous cell carcinoma. ACTA ACUST UNITED AC 2014. [DOI: 10.5339/jlghs.2014.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The cancer of the skin is an increasing problem for public health worldwide. The fair skin populations that are environmentally or occupationally exposed to solar ultraviolet (UV)-radiation are the most affected. Intensive research investigating the molecular mechanisms of skin cancer is ongoing, however the role of noncoding RNAs in the pathology of cutaneous cell carcinoma is not fully understood. Accumulating evidence show that miRNAs play an important role in physiologic, pathologic and carcinogenic processes but their role in epithelial skin cancers (i.e. basal cell carcinoma and squamous cell carcinoma) was to date not sufficiently highlighted. MiRNAs are single-stranded small RNAs which specifically target mRNAs for translational repression and/or mRNA decay. In this review we focus on the latest findings in this area of research reviewing the newest research trends and perspectives.
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Affiliation(s)
- Rebecca Ruland
- Environmental Toxicology, University of Trier, FBVI, Universitätsring 15, 54296, Trier
| | - Ana-Maria Florea
- Environmental Toxicology, University of Trier, FBVI, Universitätsring 15, 54296, Trier
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20
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Thounaojam MC, Kaushik DK, Basu A. MicroRNAs in the brain: it's regulatory role in neuroinflammation. Mol Neurobiol 2013; 47:1034-44. [PMID: 23315269 DOI: 10.1007/s12035-013-8400-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/03/2013] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) are single-stranded noncoding regions of approximately 21 nucleotides that regulate protein synthesis by targeting mRNAs for translational repression or degradation at the post-transcriptional level. These classes of RNAs are highly conserved across species and are known to regulate several protein-coding genes in humans. Therefore, their dysregulation is synonymous with inflammation, autoimmunity, neurodegeneration, viral infections, heart diseases, and cancer, among other conditions. Recent years have witnessed considerable amount of research interest in studies on miRNA-mediated modulation of gene function during neuroinflammation. This review is a meticulous compilation of information on biogenesis of miRNAs and their role in neuroinflammatory diseases. Further, their potential as markers of inflammatory diseases or novel therapeutic agents against neuroinflammation has also been discussed in detail.
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Nam S, Long X, Kwon C, Kim S, Nephew KP. An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells. BMC Genomics 2012; 13:732. [PMID: 23270413 PMCID: PMC3560207 DOI: 10.1186/1471-2164-13-732] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/20/2012] [Indexed: 12/28/2022] Open
Abstract
Background A major goal of the field of systems biology is to translate genome-wide profiling data (e.g., mRNAs, miRNAs) into interpretable functional networks. However, employing a systems biology approach to better understand the complexities underlying drug resistance phenotypes in cancer continues to represent a significant challenge to the field. Previously, we derived two drug-resistant breast cancer sublines (tamoxifen- and fulvestrant-resistant cell lines) from the MCF7 breast cancer cell line and performed genome-wide mRNA and microRNA profiling to identify differential molecular pathways underlying acquired resistance to these important antiestrogens. In the current study, to further define molecular characteristics of acquired antiestrogen resistance we constructed an “integrative network”. We combined joint miRNA-mRNA expression profiles, cancer contexts, miRNA-target mRNA relationships, and miRNA upstream regulators. In particular, to reduce the probability of false positive connections in the network, experimentally validated, rather than prediction-oriented, databases were utilized to obtain connectivity. Also, to improve biological interpretation, cancer contexts were incorporated into the network connectivity. Results Based on the integrative network, we extracted “substructures” (network clusters) representing the drug resistant states (tamoxifen- or fulvestrant-resistance cells) compared to drug sensitive state (parental MCF7 cells). We identified un-described network clusters that contribute to antiestrogen resistance consisting of miR-146a, -27a, -145, -21, -155, -15a, -125b, and let-7s, in addition to the previously described miR-221/222. Conclusions By integrating miRNA-related network, gene/miRNA expression and text-mining, the current study provides a computational-based systems biology approach for further investigating the molecular mechanism underlying antiestrogen resistance in breast cancer cells. In addition, new miRNA clusters that contribute to antiestrogen resistance were identified, and they warrant further investigation.
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Affiliation(s)
- Seungyoon Nam
- Cancer Genomics Branch, National Cancer Center, Goyang-si, Gyeonggi-do, 410-769, Korea.
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Long-lived microRNA-Argonaute complexes in quiescent cells can be activated to regulate mitogenic responses. Proc Natl Acad Sci U S A 2012; 110:157-62. [PMID: 23248281 DOI: 10.1073/pnas.1219958110] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cellular proliferation depends on the integration of mitogenic stimuli with environmental conditions. Increasing evidence suggests that microRNAs play a regulatory role in this integration. Here we show that during periods of cellular quiescence, mature microRNAs are stabilized and stored in Argonaute protein complexes that can be activated by mitogenic stimulation to repress mitogen-stimulated targets, thus influencing subsequent cellular responses. In quiescent cells, the majority of microRNAs exist in low molecular weight, Argonaute protein-containing complexes devoid of essential components of the RNA-induced silencing complex (RISC). For at least 3 wk, this pool of Argonaute-associated microRNAs is stable and can be recruited into RISC complexes subsequent to mitogenic stimulation. Using several model systems, we demonstrate that stable Argonaute protein-associated small RNAs are capable of repressing mitogen-induced transcripts. Therefore, mature microRNAs may represent a previously unappreciated form of cellular memory that allows cells to retain posttranscriptional regulatory information over extended periods of cellular quiescence.
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Clinical correlations of miR-21 expression in colorectal cancer patients and effects of its inhibition on DLD1 colon cancer cells. Int J Colorectal Dis 2012; 27:1401-8. [PMID: 22476768 DOI: 10.1007/s00384-012-1461-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/09/2012] [Indexed: 02/04/2023]
Abstract
PURPOSE MicroRNA-21 (miR-21) is one of the miRNAs that are frequently and highly overexpressed in tumor tissue of colorectal cancer (CRC) patients; however, only a little is known about its functional role in CRC. METHODS We examined the expression level of miR-21 in 44 paired samples of tumoral and non-tumoral colon tissues diagnosed for CRC using TaqMan real-time PCR method. Furthermore, we used miR-21 inhibitor (anti-miR-21) to transient knockdown of miR-21 in DLD-1 colon cancer cells and examined the effects of miR-21 silencing on viability, apoptosis, chemosensitivity, cell cycle, and migration of DLD1 cells. RESULTS The expression levels of miR-21 were significantly increased in CRC tumor tissue (P < 0.0001). Significant differences in miR-21 levels were observed also between CRC tissues of patients with CRC in different clinical stages: I vs. II (P = 0.033) and I vs. IV (P = 0.021). Kaplan-Meier analysis proved that the miR-21 expression levels are correlated to shorter overall survival of CRC patients (P = 0.0341). MiR-21 silencing in DLD1 cell line had no effect on the cell viability; however, when combined with chemotherapeutics (5-FU, L-OHP, and SN38), it contributed to the decrease of cell viability. Suppression of miR-21 decreased cell migration ability of DLD-1 cells by nearly 30 % (P = 0.016). CONCLUSION We have confirmed the overexpression of miR-21 in CRC samples and its correlation with advanced disease and shorter overall survival. These findings could be described in part by the fact that CRC cells with increased expression of miR-21 have higher migration ability.
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MicroRNA turnover: when, how, and why. Trends Biochem Sci 2012; 37:436-46. [PMID: 22921610 DOI: 10.1016/j.tibs.2012.07.002] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are short (∼22 nucleotide) RNAs that are important for the regulation of numerous biological processes. Accordingly, the expression of miRNAs is itself tightly controlled by mechanisms acting at the level of transcription as well as processing of miRNA precursors. Recently, active degradation of mature miRNAs has been identified as another mechanism that is important for miRNA homeostasis. Here we review the molecular factors and cellular conditions that promote miRNA turnover. We also discuss what is known about the physiological relevance of miRNA decay.
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Cooper S. On a heuristic point of view concerning the expression of numerous genes during the cell cycle. IUBMB Life 2011; 64:10-7. [DOI: 10.1002/iub.571] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/08/2011] [Indexed: 12/12/2022]
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Abstract
HeLa is one of the oldest and most commonly used cell lines in biomedical research. Owing to the ease of which they can be effectively synchronized by various methods, HeLa cells have been used extensively for studies of the cell cycle. Here we describe several protocols for synchronization of HeLa cells from different phases of the cell cycle. Synchronization in G(1) phase can be achieved with the HMG-CoA reductase inhibitor lovastatin, S phase with a double thymidine block procedure, and G(2) phase with the CDK inhibitor RO3306. Cells can also be enriched in mitosis by treating with nocodazole and mechanical shake-off. Release of the cells from these blocks enables researchers to follow gene expression and other events through the cell cycle. We also describe several protocols, including flow cytometry, BrdU labeling, immunoblotting, and time-lapse microscopy, for validating the synchrony of the cells and monitoring the progression of the cell cycle after release.
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Affiliation(s)
- Hoi Tang Ma
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.
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MicroRNases and the Regulated Degradation of Mature Animal miRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 700:140-55. [DOI: 10.1007/978-1-4419-7823-3_12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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