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Franke A, Bayer T, Clemmesen C, Wendt F, Lehmann A, Roth O, Schneider RF. Climate challenges for fish larvae: Interactive multi-stressor effects impair acclimation potential of Atlantic herring larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:175659. [PMID: 39181268 DOI: 10.1016/j.scitotenv.2024.175659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 08/15/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Fish early life stages are particularly vulnerable and heavily affected by changing environmental factors. The interactive effects of multiple climate change-related stressors on fish larvae remain, however, largely underexplored. As rising temperatures can increase the abundance and virulence of bacteria, we investigated the combination of a spring heat wave and bacterial exposure on the development of Atlantic herring larvae (Clupea harengus). Eggs and larvae of Western Baltic Spring-spawners were reared at a normal and high temperature ramp and exposed to Vibrio alginolyticus and V. anguillarum, respectively. Subsequently, mRNA and miRNA transcriptomes, microbiota composition, growth and survival were assessed. Both high temperature and V. alginolyticus exposure induced a major downregulation of gene expression likely impeding larval cell proliferation. In contrast, interactive effects of elevated temperature and V. alginolyticus resulted in minimal gene expression changes, indicating an impaired plastic response, which may cause cellular damage reducing survival in later larval stages. The heat wave alone or in combination with V. alginolyticus induced a notable shift in miRNA expression leading to the down- but also upregulation of predicted target genes. Moreover, both increased temperature and the Vibrio exposures significantly altered the larval microbiota composition, with warming reducing microbial richness and diversity. The outcomes of this study highlight the high sensitivity of herring early life stages towards multiple climate change-related stressors. Our results indicate that interactive effects of rapidly changing environmental factors may exceed the larval stress threshold impairing essential acclimation responses, which may contribute to the ongoing recruitment decline of Western Baltic Spring-Spawning herring.
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Affiliation(s)
- Andrea Franke
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Im Technologiepark 5, 26129 Oldenburg, Germany; Alfred-Wegener-Institute, Helmholtz-Centre for Polar and Marine Research (AWI), Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Till Bayer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße 1-3, 24148 Kiel, Germany.
| | - Catriona Clemmesen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße 1-3, 24148 Kiel, Germany.
| | - Fabian Wendt
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße 1-3, 24148 Kiel, Germany.
| | - Andreas Lehmann
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße 1-3, 24148 Kiel, Germany.
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Am Botanischen Garten 1-9, Kiel University, 24118 Kiel, Germany.
| | - Ralf F Schneider
- Marine Evolutionary Biology, Zoological Institute, Am Botanischen Garten 1-9, Kiel University, 24118 Kiel, Germany.
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2
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He B, Xu HM, Li SW, Zhang YF, Tian JW. Emerging regulatory roles of noncoding RNAs induced by bisphenol a (BPA) and its alternatives in human diseases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124447. [PMID: 38942269 DOI: 10.1016/j.envpol.2024.124447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Bisphenols (BPs), including BPA, BPF, BPS, and BPAF, are synthetic phenolic organic compounds and endocrine-disrupting chemicals. These organics have been broadly utilized to produce epoxy resins, polycarbonate plastics, and other products. Mounting evidence has shown that BPs, especially BPA, may enter into the human body and participate in the development of human diseases mediated by nuclear hormone receptors. Moreover, BPA may negatively affect human health at the epigenetic level through processes such as DNA methylation and histone acetylation. Recent studies have demonstrated that, as part of epigenetics, noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and small nucleolar RNAs (snoRNAs), have vital impacts on BP-related diseases, such as reproductive system diseases, nervous system diseases, digestive system diseases, endocrine system diseases, and other diseases. Moreover, based on the bioinformatic analysis, changes in ncRNAs may be relevant to normal activities and functions and BP-induced diseases. Thus, we conducted a meta-analysis to identify more promising ncRNAs as biomarkers and therapeutic targets for BP exposure and relevant human diseases. In this review, we summarize the regulatory functions of ncRNAs induced by BPs in human diseases and latent molecular mechanisms, as well as identify prospective biomarkers and therapeutic targets for BP exposure and upper diseases.
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Affiliation(s)
- Bo He
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Hai-Ming Xu
- Department of Occupational and Environmental Medicine, School of Public Health and Management, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China
| | - Shu-Wei Li
- Department of Neurology, Qingdao Huangdao District Central Hospital, Qingdao 266555, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China.
| | - Jia-Wei Tian
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China.
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Noches V, Campos-Melo D, Droppelmann CA, Strong MJ. Epigenetics in the formation of pathological aggregates in amyotrophic lateral sclerosis. Front Mol Neurosci 2024; 17:1417961. [PMID: 39290830 PMCID: PMC11405384 DOI: 10.3389/fnmol.2024.1417961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/23/2024] [Indexed: 09/19/2024] Open
Abstract
The progressive degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) is accompanied by the formation of a broad array of cytoplasmic and nuclear neuronal inclusions (protein aggregates) largely containing RNA-binding proteins such as TAR DNA-binding protein 43 (TDP-43) or fused in sarcoma/translocated in liposarcoma (FUS/TLS). This process is driven by a liquid-to-solid phase separation generally from proteins in membrane-less organelles giving rise to pathological biomolecular condensates. The formation of these protein aggregates suggests a fundamental alteration in the mRNA expression or the levels of the proteins involved. Considering the role of the epigenome in gene expression, alterations in DNA methylation, histone modifications, chromatin remodeling, non-coding RNAs, and RNA modifications become highly relevant to understanding how this pathological process takes effect. In this review, we explore the evidence that links epigenetic mechanisms with the formation of protein aggregates in ALS. We propose that a greater understanding of the role of the epigenome and how this inter-relates with the formation of pathological LLPS in ALS will provide an attractive therapeutic target.
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Affiliation(s)
- Veronica Noches
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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Sekar V, Mármol-Sánchez E, Kalogeropoulos P, Stanicek L, Sagredo EA, Widmark A, Doukoumopoulos E, Bonath F, Biryukova I, Friedländer MR. Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE. Nat Biotechnol 2024; 42:1296-1302. [PMID: 37735263 PMCID: PMC11324520 DOI: 10.1038/s41587-023-01951-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.
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Affiliation(s)
- Vaishnovi Sekar
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Laura Stanicek
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eduardo A Sagredo
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Albin Widmark
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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Yan Y, Liao L. MicroRNA Expression Profile in Patients Admitted to ICU as Novel and Reliable Approach for Diagnostic and Therapeutic Purposes. Mol Biotechnol 2024; 66:1357-1375. [PMID: 37314613 DOI: 10.1007/s12033-023-00767-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/06/2023] [Indexed: 06/15/2023]
Abstract
The ability to detect early metabolic changes in patients who have an increased mortality risk in the intensive care units (ICUs) could increase the likelihood of predicting recovery patterns and assist in disease management. Markers that can predict the disease progression of patients in the ICU might also be beneficial for improving their medical profile. Although biomarkers have been used in the ICU more frequently in recent years, the clinical use of most of them is limited. A wide range of biological processes are influenced by microRNAs (miRNAs) that modulate the translation and stability of specific mRNAs. Studies suggest that miRNAs may serve as a diagnostic and therapeutic biomarker in ICUs by profiling miRNA dysregulation in patient samples. To improve the predictive value of biomarkers for ICU patients, researchers have proposed both investigating miRNAs as novel biomarkers and combining them with other clinical biomarkers. Herein, we discuss recent approaches to the diagnosis and prognosis of patients admitted to an ICU, highlighting the use of miRNAs as novel and robust biomarkers for this purpose. In addition, we discuss emerging approaches to biomarker development and ways to improve the quality of biomarkers so that patients in ICU get the best outcomes possible.
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Affiliation(s)
- Youqin Yan
- ICU Department, People's Hospital of Changshan, Changshan, China
| | - Linjun Liao
- ICU Department, People's Hospital of Changshan, Changshan, China.
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6
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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Dunlop RA, Banack SA, Cox PA. L1CAM immunocapture generates a unique extracellular vesicle population with a reproducible miRNA fingerprint. RNA Biol 2023; 20:140-148. [PMID: 37042019 PMCID: PMC10101655 DOI: 10.1080/15476286.2023.2198805] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Micro RNAs (miRNAs) are short, non-coding RNAs with significant potential as diagnostic and prognostic biomarkers. However, a lack of reproducibility across studies has hindered their introduction into clinical settings. Inconsistencies between studies include a lack of consensus on the miRNAs associated with a specific disease and the direction of regulation. These differences may reflect the heterogenous nature of pathologies with multiple phenotypes, such as amyotrophic lateral sclerosis (ALS). It is also possible that discrepancies are due to different sampling, processing, and analysis protocols across labs. Using miRNA extracted from L1CAM immunoaffinity purified extracellular vesicles (neural-enriched extracellular vesicles or NEE), we thrice replicated an 8-miRNA fingerprint diagnostic of ALS, which includes the miRNA species and direction of regulation. We aimed to determine if the extra purification steps required to generate NEE created a unique extracellular vesicle (EV) fraction that might contribute to the robustness and replicability of our assay. We compared three fractions from control human plasma: 1) total heterogenous EVs (T), 2) L1CAM/neural enriched EVs (NEE), and 3) the remaining total-minus-NEE fraction (T-N). Each fraction was characterized for size, total protein content, and protein markers, then total RNA was extracted, and qPCR was run on 20 miRNAs. We report that the miRNA expression within NEE was different enough compared to T and T-N to justify the extra steps required to generate this fraction. We conclude that L1CAM immunocapture generates a unique fraction of EVs that consistently and robustly replicates a miRNA fingerprint which differentiates ALS patients from controls.
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8
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Expression of miRNA-Targeted and Not-Targeted Reporter Genes Shows Mutual Influence and Intercellular Specificity. Int J Mol Sci 2022; 23:ijms232315059. [PMID: 36499386 PMCID: PMC9740606 DOI: 10.3390/ijms232315059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
The regulation of translation by RNA-induced silencing complexes (RISCs) composed of Argonaute proteins and micro-RNAs is well established; however, the mechanisms underlying specific cellular responses to miRNAs and how specific complexes arise are not completely clear. To explore these questions, we performed experiments with Renilla and firefly luciferase reporter genes transfected in a psiCHECK-2 plasmid into human HCT116 or Me45 cells, where only the Renilla gene contained sequences targeted by microRNAs (miRNAs) in the 3'UTR. The effects of targeting were miRNA-specific; miRNA-21-5p caused strong inhibition of translation, whereas miRNA-24-3p or Let-7 family caused no change or an increase in reporter Renilla luciferase synthesis. The mRNA-protein complexes formed by transcripts regulated by different miRNAs differed from each other and were different in different cell types, as shown by sucrose gradient centrifugation. Unexpectedly, the presence of miRNA targets on Renilla transcripts also affected the expression of the co-transfected but non-targeted firefly luciferase gene in both cell types. Renilla and firefly transcripts were found in the same sucrose gradient fractions and specific anti-miRNA oligoribonucleotides, which influenced the expression of the Renilla gene, and also influenced that of firefly gene. These results suggest that, in addition to targeted transcripts, miRNAs may also modulate the expression of non-targeted transcripts, and using the latter to normalize the results may cause bias. We discuss some hypothetical mechanisms which could explain the observed miRNA-induced effects.
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Hao R, Lu H, Guo Y, Liu Q, Wang L, Wang Y, Huang A, Tu Z. Bioinformatics analysis of constructing a HCV-related hepatocellular carcinoma miRNA-mRNA regulation network. Medicine (Baltimore) 2021; 100:e26964. [PMID: 34414965 PMCID: PMC8376384 DOI: 10.1097/md.0000000000026964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/01/2021] [Indexed: 01/04/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the tumors with a higher mortality rate globally, which significantly threatens people's health. Hepatitis C virus (HCV) infection is a major driving factor of HCC. This study aims to determine the key microRNA (miRNA), hub genes, and related pathways, construct potential miRNA-mRNA regulatory networks, and clarify the new molecular mechanism of HCV-related HCC. In this study, 16 differentially expressed miRNAs (DE miRNAs) were identified. The prediction of potential transcription factors and target genes not only found that SP1 and ERG1 may potentially regulate most of the screened DE miRNAs, but it also obtained 2923 and 1782 predicted target genes for the up-regulation and down-regulation of DE miRNAs, respectively. Subsequently, the introduction of differentially expressed genes dataset GSE62232 for target gene verification yielded 98 and 147 potential up-regulation and down-regulation target genes. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes pathway enrichment analysis showed that they were mainly enriched in the cell cycle process, that is, subsequently, 20 hub genes were screened out through the protein-protein interaction network, and related genes were further evaluated using the GEPIA database. Based on the above analysis, the miRNA-hub gene regulatory network was constructed. In short, this research's hub genes and miRNAs closely related to HCV-related HCC were screened and identified through bioinformatics analysis and then built their connection. These results are expected to find potential therapeutic targets for HCV-related HCC.
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Affiliation(s)
- Rui Hao
- Department of Microbiology, Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - He Lu
- Department of Microbiology, Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yanan Guo
- Department of Microbiology, Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Qianqian Liu
- Department of Microbiology, Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Lu Wang
- Department of Microbiology, Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yang Wang
- Department of Microbiology, Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zeng Tu
- Department of Microbiology, Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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Ahmad W, Gull B, Baby J, Mustafa F. A Comprehensive Analysis of Northern versus Liquid Hybridization Assays for mRNAs, Small RNAs, and miRNAs Using a Non-Radiolabeled Approach. Curr Issues Mol Biol 2021; 43:457-484. [PMID: 34206608 PMCID: PMC8929067 DOI: 10.3390/cimb43020036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 12/27/2022] Open
Abstract
Northern blotting (NB), a gold standard for RNA detection, has lost its charm due to its hands-on nature, need for good quality RNA, and radioactivity. With the emergence of the field of microRNAs (miRNAs), the necessity for sensitive and quantitative NBs has again emerged. Here, we developed highly sensitive yet non-radiolabeled, fast, economical NB, and liquid hybridization (LH) assays without radioactivity or specialized reagents like locked nucleic acid (LNA)- or digoxigenin-labeled probes for mRNAs/small RNAs, especially miRNAs using biotinylated probes. An improvised means of hybridizing oligo probes along with efficient transfer, cross-linking, and signal enhancement techniques was employed. Important caveats of each assay were elaborated upon, especially issues related to probe biotinylation, use of exonuclease, and bioimagers not reported earlier. We demonstrate that, while the NBs were sensitive for mRNAs and small RNAs, our LH protocol could efficiently detect these and miRNAs using less than 10-100 times the total amount of RNA, a sensitivity comparable to radiolabeled probes. Compared to NBs, LH was a faster, more sensitive, and specific approach for mRNA/small RNA/miRNA detection. A comparison of present work with six seminal studies is presented along with detailed protocols for easy reproducibility. Overall, our study provides effective platforms to study large and small RNAs in a sensitive, efficient, and cost-effective manner.
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Dudeja SS, Suneja-Madan P, Paul M, Maheswari R, Kothe E. Bacterial endophytes: Molecular interactions with their hosts. J Basic Microbiol 2021; 61:475-505. [PMID: 33834549 DOI: 10.1002/jobm.202000657] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 01/19/2023]
Abstract
Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.
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Affiliation(s)
- Surjit S Dudeja
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Pooja Suneja-Madan
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Minakshi Paul
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Rajat Maheswari
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Faculty for Biosciences, Friedrich Schiller University of Jena, Jena, Germany
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12
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Yang D, Hu Z, Zhang Y, Zhang X, Xu J, Fu H, Zhu Z, Feng D, Cai Q. CircHIPK3 Promotes the Tumorigenesis and Development of Gastric Cancer Through miR-637/AKT1 Pathway. Front Oncol 2021; 11:637761. [PMID: 33680975 PMCID: PMC7933501 DOI: 10.3389/fonc.2021.637761] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022] Open
Abstract
Circular RNA is a kind of RNA with a covalently closed loop, which has a complex ability to modulate genes in the process of tumorigenesis and metastasis. Nevertheless, how circular RNA functions in gastric cancer (GC) remains unclear. The effect of circHIPK3 in vitro was studied here. Quantitative real-time PCR (qRT-PCR) was employed to found that circHIPK3 markedly increased in GC tissues and cell lines. And low expression of circHIPK3 suppressed the GC cells growing and metabolizing. Then the bioinformatics tool predicted the downstream target of circHIPK3, and it was proved by the dual-luciferase report experiment. According to the results of bioinformatics analysis and experimental data, it was clarified that circHIPK3 acted as a sponge of miR-637, releasing its direct target AKT1. The dual-luciferase assay revealed that mir-637 could bind circHIPK3 and AKT1. qRT-PCR data indicated that overexpression circHIPK3 led to the low level of miR-637 and overexpressed miR-637 would reduce AKT1 level. Finally, we demonstrated that the low expression of miR-637 or overexpression of AKT1 could attenuate the anti-proliferative effects of si-circHIPK3. These results suggest that the circHIPK3/miR-637/AKT1 regulatory pathway may be associated with the oncogene and growth of gastric cancer. In short, a new circular RNA circHIPK3 and its function are identified, and the regulatory pathway of circHIPK3/miR-637/AKT1 in the tumorigenesis and development of gastric cancer is discovered.
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Affiliation(s)
- Dejun Yang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Zunqi Hu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Yu Zhang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Xin Zhang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Jiapeng Xu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Hongbing Fu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Zhenxin Zhu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Dan Feng
- Department of Oncology, Changhai Hospital, Navy Medical University, Shanghai, China
| | - Qingping Cai
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
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MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis. Biochem Soc Trans 2021; 48:595-612. [PMID: 32267487 PMCID: PMC7200637 DOI: 10.1042/bst20190854] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.
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Domingo S, Solé C, Moliné T, Ferrer B, Cortés-Hernández J. MicroRNAs in Several Cutaneous Autoimmune Diseases: Psoriasis, Cutaneous Lupus Erythematosus and Atopic Dermatitis. Cells 2020; 9:cells9122656. [PMID: 33321931 PMCID: PMC7763020 DOI: 10.3390/cells9122656] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNA molecules that regulate the gene expression at a post-transcriptional level and participate in maintaining the correct cell homeostasis and functioning. Different specific profiles have been identified in lesional skin from autoimmune cutaneous diseases, and their deregulation cause aberrant control of biological pathways, contributing to pathogenic conditions. Detailed knowledge of microRNA-affected pathways is of crucial importance for understating their role in skin autoimmune diseases. They may be promising therapeutic targets with novel clinical implications. They are not only present in skin tissue, but they have also been found in other biological fluids, such as serum, plasma and urine from patients, and therefore, they are potential biomarkers for the diagnosis, prognosis and response to treatment. In this review, we discuss the current understanding of the role of described miRNAs in several cutaneous autoimmune diseases: psoriasis (Ps, 33 miRNAs), cutaneous lupus erythematosus (CLE, 2 miRNAs) and atopic dermatitis (AD, 8 miRNAs). We highlight their role as crucial elements implicated in disease pathogenesis and their applicability as biomarkers and as a novel therapeutic approach in the management of skin inflammatory diseases.
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Affiliation(s)
- Sandra Domingo
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
| | - Cristina Solé
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
- Correspondence: ; Tel.: +34-9-3489-4045
| | - Teresa Moliné
- Department of Pathology, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Berta Ferrer
- Department of Pathology, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Josefina Cortés-Hernández
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
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15
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Kunigenas L, Stankevicius V, Dulskas A, Budginaite E, Alzbutas G, Stratilatovas E, Cordes N, Suziedelis K. 3D Cell Culture-Based Global miRNA Expression Analysis Reveals miR-142-5p as a Theranostic Biomarker of Rectal Cancer Following Neoadjuvant Long-Course Treatment. Biomolecules 2020; 10:E613. [PMID: 32316138 PMCID: PMC7226077 DOI: 10.3390/biom10040613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/05/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023] Open
Abstract
Altered expression of miRNAs in tumor tissue encourages the translation of this specific molecular pattern into clinical practice. However, the establishment of a selective biomarker signature for many tumor types remains an inextricable challenge. For this purpose, a preclinical experimental design, which could maintain a fast and sensitive discovery of potential biomarkers, is in demand. The present study suggests that the approach of 3D cell cultures as a preclinical cancer model that is characterized to mimic a natural tumor environment maintained in solid tumors could successfully be employed for the biomarker discovery and validation. Subsequently, in this study, we investigated an environment-dependent miRNA expression changes in colorectal adenocarcinoma DLD1 and HT29 cell lines using next-generation sequencing (NGS) technology. We detected a subset of 16 miRNAs differentially expressed in both cell lines cultivated in multicellular spheroids compared to expression levels in cells grown in 2D. Furthermore, results of in silico miRNA target analysis showed that miRNAs, which were differentially expressed in both cell lines grown in MCS, are involved in the regulation of molecular mechanisms implicated in cell adhesion, cell-ECM interaction, and gap junction pathways. In addition, integrins and platelet-derived growth factor receptors were determined to be the most significant target genes of deregulated miRNAs, which was concordant with the environment-dependent gene expression changes validated by RT-qPCR. Our results revealed that 3D microenvironment-dependent deregulation of miRNA expression in CRC cells potentially triggers essential molecular mechanisms predominantly including the regulation of cell adhesion, cell-cell, and cell-ECM interactions important in CRC initiation and development. Finally, we demonstrated increased levels of selected miR-142-5p in rectum tumor tissue samples after neoadjuvant long course treatment compared to miR-142-5p expression levels in tumor biopsy samples collected before the therapy. Remarkably, the elevation of miR-142-5p expression remained in tumor samples compared to adjacent normal rectum tissue as well. Therefore, the current study provides valuable insights into the molecular miRNA machinery of CRC and proposes a potential miRNA signature for the assessment of CRC in further clinical research.
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Affiliation(s)
- Linas Kunigenas
- National Cancer Institute, LT-08660 Vilnius, Lithuania; (L.K.); (A.D.); (E.B.); (E.S.)
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-08412 Vilnius, Lithuania
| | - Vaidotas Stankevicius
- National Cancer Institute, LT-08660 Vilnius, Lithuania; (L.K.); (A.D.); (E.B.); (E.S.)
- Life Sciences Center, Institute of Biotechnology, Vilnius University, LT-08412 Vilnius, Lithuania
| | - Audrius Dulskas
- National Cancer Institute, LT-08660 Vilnius, Lithuania; (L.K.); (A.D.); (E.B.); (E.S.)
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, LT-08406 Vilnius, Lithuania
- University of Applied Sciences, Faculty of Health Care, LT-08303 Vilnius, Lithuania
| | - Elzbieta Budginaite
- National Cancer Institute, LT-08660 Vilnius, Lithuania; (L.K.); (A.D.); (E.B.); (E.S.)
| | - Gediminas Alzbutas
- Thermo Fisher Scientific, LT-02241 Vilnius, Lithuania;
- Institute of Informatics, Faculty of Mathematics and Informatics, Vilnius University, LT-08303 Vilnius, Lithuania
| | - Eugenijus Stratilatovas
- National Cancer Institute, LT-08660 Vilnius, Lithuania; (L.K.); (A.D.); (E.B.); (E.S.)
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, LT-08406 Vilnius, Lithuania
| | - Nils Cordes
- Department of Radiation Oncology, University Hospital Carl Gustav Carus, Technische Universität, Dresden, Germany
- OncoRay—National Center for Radiation Research in Oncology, Faculty of Medicine, Technische Universität, D–01307 Dresden, Germany;
- Helmholtz–Zentrum Dresden–Rossendorf, Institute of Radiooncology–OncoRay, D–01328 Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, D–69192 Heidelberg, Germany
- German Cancer Research Center (DKFZ), D–69192 Heidelberg, Germany
| | - Kestutis Suziedelis
- National Cancer Institute, LT-08660 Vilnius, Lithuania; (L.K.); (A.D.); (E.B.); (E.S.)
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-08412 Vilnius, Lithuania
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16
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Tapeh BEG, Alivand MR, Solali S. The role of microRNAs in acute lymphoblastic leukaemia: From biology to applications. Cell Biochem Funct 2019; 38:334-346. [PMID: 31833074 DOI: 10.1002/cbf.3466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) that are characterized by small, noncoding RNA have an essential role in the pathogenesis of human diseases, including cancer. Furthermore, miRNAs, as a new paradigm of epigenetic regulators, play an important role in normal development and cellular function. This literature review summarizes the recurrent mechanism of gene regulation through miRNAs and, consequently, the impact of regulated genes on different cellular processes, including proliferation, metastasis, prognosis, and apoptosis. Additionally, what is important to note is that the expression of miRNAs in various cancer cells is different, and miRNAs have various target genes in various cancers. Accordingly, a proper understanding of gene regulation by miRNAs contributes to new perspectives in miRNA-based therapeutic strategies. SIGNIFICANCE OF THE STUDY: MiRNAs are considered as a crucial regulator of gene expression. The genes also play an important role in the expression of miRNAs; as a result, there is a relationship between them. In recent years, targeted therapy with miRNAs has been a significant challenge. Studying the mechanisms through which miRNAs regulate various cancer cell processes, including apoptosis, proliferation, and metastasis, is very critical in the treatment of cancer through miRNAs. Definitely, a proper understanding of the impacts of aberrant expression of miRNAs on cancer cell processes leads to new therapeutic strategies in the targeted therapy with miRNAs.
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Affiliation(s)
- Behnam Emamgolizadeh Gurt Tapeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Solali
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Division of Hematology and Blood Banking, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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17
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Hawez A, Al-Haidari A, Madhi R, Rahman M, Thorlacius H. MiR-155 Regulates PAD4-Dependent Formation of Neutrophil Extracellular Traps. Front Immunol 2019; 10:2462. [PMID: 31736940 PMCID: PMC6838784 DOI: 10.3389/fimmu.2019.02462] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
Accumulating data suggest that neutrophil extracellular traps (NETs) exert a key function in several diseases. Peptidylarginine deiminase 4 (PAD4) regulates NET formation via citrullination of histones. The aim of this study was to examine the role of miR-155 in controlling PAD4-dependent generation of NETs. Bone marrow neutrophils were stimulated with PMA and MIP-2. Pre-incubation of neutrophils with translational inhibitors (cycloheximide or puromycin) markedly decreased NET formation induced by PMA or MIP-2. Neutrophil transfection with a mimic miR-155 increased PMA-induced PAD4 mRNA expression and NET formation. In contrast, transfection with an antagomiR-155 decreased induction of PAD4 mRNA and NETs in response to PMA challenge. Bioinformatical examination of PAD4 revealed a potential binding site in AU-rich elements at the 3′-UTR region. MiR-155 binding to PAD4 was examined by use of target site blockers and RNA immunoprecipitation, revealing that miR-155 regulation of PAD4 mRNA is mediated via AU-rich elements in the 3′-UTR region. In conclusion, our findings demonstrate that miR-155 positively regulates neutrophil expression of PAD4 and expulsion of extracellular traps. Thus, our novel results indicate that targeting miR-155 might be useful to inhibit exaggerated NET generation in inflammatory diseases.
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Affiliation(s)
- Avin Hawez
- Section for Surgery, Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| | - Amr Al-Haidari
- Section for Surgery, Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| | - Raed Madhi
- Section for Surgery, Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| | - Milladur Rahman
- Section for Surgery, Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| | - Henrik Thorlacius
- Section for Surgery, Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
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18
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MicroRNAs - novel biomarkers for malignant pleural effusions. Contemp Oncol (Pozn) 2019; 23:133-140. [PMID: 31798327 PMCID: PMC6883963 DOI: 10.5114/wo.2019.89241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 08/09/2019] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is one of the most common causes of cancer death. Its poor prognosis can be attributed to the patients’ advanced or metastatic presentation at the time of diagnosis. To improve and accelerate the diagnosis, better therapeutic and diagnostic methods are constantly being sought. MicroRNAs (miRNAs) are short nucleotide sequences of single-stranded, non-coding RNA that function as critical post-transcriptional regulators of gene expression. They are identified not only intracellularly, but also in physiological and pathological body fluids. These molecules are responsible for the regulation of approximately 33% of human genes, either regulating the expression of both oncogenes and suppressor genes or acting directly as an oncogene or suppressor gene itself. MiRNAs can contribute to the formation of cancer. The high specificity and sensitivity of miRNAs have been demonstrated with various malignant diseases, and for this reason, they raise particular interest as new and perspective biomarkers of tumours. Our work summarises the available information from recent years regarding the possibility of using miRNAs as biomarkers in the diagnosis of neoplasms. In this review, we focused on malignant pleural effusions with an emphasis on non-small cell lung cancer (NSCLC).
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19
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Vos PD, Leedman PJ, Filipovska A, Rackham O. Modulation of miRNA function by natural and synthetic RNA-binding proteins in cancer. Cell Mol Life Sci 2019; 76:3745-3752. [PMID: 31165201 PMCID: PMC11105495 DOI: 10.1007/s00018-019-03163-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/02/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
RNA-binding proteins (RBPs) and microRNAs (miRNAs) are the most important regulators of mRNA stability and translation in eukaryotic cells; however, the complex interplay between these systems is only now coming to light. RBPs and miRNAs regulate a unique set of targets in either a positive or negative manner and their regulation is mainly opposed to each other on overlapping targets. In some cases, the levels of RBPs or miRNAs regulate the cellular levels of one another and decreased levels of either results in changes in translation of their targets. There is growing evidence that these regulatory circuits are crucial in the development and progression of cancer; however, the rules underlying synergism and antagonism between miRNAs and RNA-binding proteins remain unclear. Synthetic biology seeks to develop artificial systems to better understand their natural counterparts and to develop new, useful technologies for manipulation of gene expression at the RNA level. The recent development of artificial RNA-binding proteins promises to enable a much greater understanding of the importance of the functional interactions between RNA-binding proteins and miRNAs, as well as enabling their manipulation for therapeutic purposes.
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Affiliation(s)
- Pascal D Vos
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
- School of Molecular and Chemical Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Peter J Leedman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
- Medical School, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
- School of Molecular and Chemical Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA, 6102, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, 6102, Australia.
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20
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Nziza N, Duroux-Richard I, Apparailly F. MicroRNAs in juvenile idiopathic arthritis: Can we learn more about pathophysiological mechanisms? Autoimmun Rev 2019; 18:796-804. [DOI: 10.1016/j.autrev.2019.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/03/2019] [Indexed: 01/05/2023]
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21
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Yuan Y, Weidhaas JB. Functional microRNA binding site variants. Mol Oncol 2019; 13:4-8. [PMID: 30536617 PMCID: PMC6322190 DOI: 10.1002/1878-0261.12421] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/15/2018] [Accepted: 11/26/2018] [Indexed: 12/19/2022] Open
Abstract
Germline single nucleotide polymorphisms are one of the most common genetic variations. Polymorphisms that cause nonsynonymous mutations in gene coding regions are known to cause serious deleterious downstream effects. However, even polymorphisms in noncoding regions can have profound functional consequences by disrupting essential regulatory sites. Specifically, polymorphisms that alter microRNA binding sites can disrupt the regulation of hallmark biological pathways implicated in tumorigenesis and tumor progression. Many of these microRNA-associated polymorphisms (miR-SNPs) have recently been shown to be important biomarkers of cancer risk, prognosis, and treatment outcomes. This review will summarize the functional impact of key miR-SNPs and define a subset of miR-SNPs that may be clinically useful prognostic or predictive biomarkers.
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Affiliation(s)
- Ye Yuan
- Department of Radiation OncologyUCLALos AngelesCAUSA
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22
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Prolonged Waking and Recovery Sleep Affect the Serum MicroRNA Expression Profile in Humans. Clocks Sleep 2018; 1:75-86. [PMID: 33089155 PMCID: PMC7509676 DOI: 10.3390/clockssleep1010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/20/2018] [Indexed: 01/28/2023] Open
Abstract
MicroRNAs (miRNAs) are small, abundant, non-coding RNA fragments that regulate gene expression and silencing at the post-transcriptional level. The miRNAs each control various downstream targets and play established roles in different biological processes. Given that miRNAs were recently proposed to contribute to the molecular control of sleep-wake regulation in animal models and narcoleptic patients, we investigated the impact of acute sleep deprivation on blood miRNA expression in healthy adult men of two different age groups. Twenty-two young (mean age: 24 ± 3 years) and nine older (65 ± 1 years) volunteers completed a controlled in-lab study, consisting of 8 h baseline sleep, followed by 40 h of extended wakefulness, and a 10-h recovery sleep opportunity. At the same circadian time in all three conditions (at 4:23 p.m. ± 23 min), qPCR expression profiling of 86 miRNAs was performed in blood serum. Thirteen different miRNAs could be reliably quantified and were analyzed using mixed-model ANOVAs. It was found that miR-30c and miR-127 were reliably affected by previous sleep and wakefulness, such that expression of these miRNAs was upregulated after extended wakefulness and normalized after recovery sleep. Together with previous findings in narcolepsy patients, our preliminary data indicate that miR-30c and its target proteins may provide a biomarker of elevated sleep debt in humans.
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Fu Y, Chen L, Chen C, Ge Y, Kang M, Song Z, Li J, Feng Y, Huo Z, He G, Hou M, Chen S, Xu A. Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiency. Genome Res 2018; 28:1656-1663. [PMID: 30228199 PMCID: PMC6211650 DOI: 10.1101/gr.231506.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 09/11/2018] [Indexed: 11/24/2022]
Abstract
3' UTRs play important roles in the gene regulation network via their influence on mRNA stability, translational efficiency, and subcellular localization. For a given gene, 3' UTRs of different lengths generated by alternative polyadenylation (APA) may result in functional differences in regulation. The mechanistic details of how length changes of 3' UTRs alter gene function remain unclear. By combining APA sequencing and polysome profiling, we observed that mRNA isoforms with shorter 3' UTRs were bound with more polysomes in six cell lines but not in NIH3T3 cells, suggesting that changing 3' UTRs to shorter isoforms may lead to a higher gene translational efficiency. By interfering with the expression of TNRC6A and analyzing AGO2-PAR-CLIP data, we revealed that the APA effect on translational efficiency was mainly regulated by miRNAs, and this regulation was cell cycle dependent. The discrepancy between NIH3T3 and other cell lines was due to contact inhibition of NIH3T3. Thus, the crosstalk between APA and miRNAs may be needed for the regulation of protein translational efficiency.
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Affiliation(s)
- Yonggui Fu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Liutao Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Chengyong Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Yutong Ge
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Mingjing Kang
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Zili Song
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Jingwen Li
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Yuchao Feng
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Zhanfeng Huo
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Guopei He
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Mengmeng Hou
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Shangwu Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
| | - Anlong Xu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 100029, China
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24
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Role of microRNAs in inner ear development and hearing loss. Gene 2018; 686:49-55. [PMID: 30389561 DOI: 10.1016/j.gene.2018.10.075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/12/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023]
Abstract
The etiology of hearing loss tends to be multi-factorial and affects a significant proportion of the global population. Despite the differences in etiology, a common physical pathological change that leads to hearing loss is damage to the mechanosensory hair cells of the inner ear. MicroRNAs (miRNAs) have been shown to play a role in inner ear development and thus, may play a role in the development or prevention of hearing loss. In this paper, we review the mechanism of action of miRNAs in the auditory system. We present an overview about the role of miRNAs in inner ear development, summarize the current research on the role of miRNAs in gene regulation, and discuss the effects of both miRNA mutations as well as overexpression. We discuss the crucial role of miRNAs in ensuring normal physiological development of the inner ear. Any deviation from the proper function of miRNA in the cochlea seems to contribute to deleterious damage to the structure of the auditory system and subsequently results in hearing loss. As interest for miRNA research increases, this paper serves as a platform to review current understandings and postulate future avenues for research. A better knowledge about the role of miRNA in the auditory system will help in developing novel treatment modalities for restoring hearing function based on regeneration of damaged inner ear hair cells.
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25
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Ro JJ, Lee HJ, Kim BH. PyA-cluster system for the detection and imaging of miRNAs in living cells through double-three-way junction formation. Chem Commun (Camb) 2018; 54:7471-7474. [PMID: 29915829 DOI: 10.1039/c8cc03982h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Herein, we describe an extended version of a fluorescence probe for detecting miRNAs through the novel application of a PyA-cluster system. By testing various (CG)n sequences in the middle of the oligonucleotide strand of the probe, we obtained an optimal sequence that formed a double-three-way-junction structure, with two PyA units positioned close together, in the presence of the target miRNA. This system readily detected the locations of target miRNAs in living cells and allowed visualization of structural changes through variations in the color of the fluorescence.
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Affiliation(s)
- Jong Jin Ro
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
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MiR-155-5p controls colon cancer cell migration via post-transcriptional regulation of Human Antigen R (HuR). Cancer Lett 2018; 421:145-151. [DOI: 10.1016/j.canlet.2018.02.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/29/2018] [Accepted: 02/15/2018] [Indexed: 12/13/2022]
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27
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Al-Haidari AA, Syk I, Thorlacius H. MiR-155-5p positively regulates CCL17-induced colon cancer cell migration by targeting RhoA. Oncotarget 2017; 8:14887-14896. [PMID: 28146427 PMCID: PMC5362452 DOI: 10.18632/oncotarget.14841] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/16/2017] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer is the second most common cause of cancer-related death, which is due to migration of tumor cells to distant sites of metastasis. Accumulating data indicate that mciroRNAs play an important role in several aspects of colon cancer cell biology. Herein, we examined the role of miR-155-5p in colon cancer cell migration induced by the CCL17-CCR4 axis in HT-29 colon cancer cells. We found that miR-155-5p knockdown in serum starved colon cancer cells decreased CCL17-induced cell chemotaxis. Moreover, knocking down miR-155-5p markedly decreased CCL17-provoked activation of RhoA in colon cancer cells. Bioinformatics analysis predicted two putative binding sites in the AU-rich element at the 3'-UTR of RhoA mRNA. MiR-155-5p binding to RhoA mRNA was verified using a target site blocker and functionally validated by RNA immunoprecipitation assays, showing that miR-155-5p-dependent regulation of RhoA mRNA is mediated by AU-rich elements present in the 3'-UTR region. Taken together, these results show that miR-155-5p positively regulates RhoA mRNA levels and translation as well as cell migration in serum starved colon cancer cells and indicate that targeting miR-155-5p might be a useful strategy to antagonize colon cancer metastasis.
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Affiliation(s)
- Amr A Al-Haidari
- Department of Clinical Sciences, Section of Surgery, Lund University, 20502 Malmö, Sweden
| | - Ingvar Syk
- Department of Clinical Sciences, Section of Surgery, Lund University, 20502 Malmö, Sweden
| | - Henrik Thorlacius
- Department of Clinical Sciences, Section of Surgery, Lund University, 20502 Malmö, Sweden
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28
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Mengardi C, Limousin T, Ricci EP, Soto-Rifo R, Decimo D, Ohlmann T. microRNAs stimulate translation initiation mediated by HCV-like IRESes. Nucleic Acids Res 2017; 45:4810-4824. [PMID: 28077561 PMCID: PMC5416841 DOI: 10.1093/nar/gkw1345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/22/2016] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression by recognizing and hybridizing to a specific sequence generally located in the 3΄ untranslated region (UTR) of targeted mRNAs. miRNA-induced inhibition of translation occurs during the initiation step, most probably at the level of ribosome scanning. In this process, the RNA-induced silencing complex interacts both with PABP and the 43S pre-initiation complex to disrupt scanning of the 40S ribosome. However, in some specific cases, miRNAs can stimulate translation. Although the mechanism of miRNA-mediated upregulation is unknown, it appears that the poly(A) tail and the lack of availability of the TNRC6 proteins are amongst major determinants. The genomic RNA of the Hepatitis C Virus is uncapped, non-polyadenylated and harbors a peculiar internal ribosome entry site (IRES) that binds the ribosome directly to the AUG codon. Thus, we have exploited the unique properties of the HCV IRES and other related IRESes (HCV-like) to study how translation initiation can be modulated by miRNAs on these elements. Here, we report that miRNA binding to the 3΄ UTR can stimulate translation of a reporter gene given that its expression is driven by an HCV-like IRES and that it lacks a poly(A) tail at its 3΄ extremity.
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Affiliation(s)
- Chloé Mengardi
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Taran Limousin
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Emiliano P Ricci
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Ricardo Soto-Rifo
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Didier Decimo
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Théophile Ohlmann
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
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Abstract
More than six decades ago Watson and Crick published the chemical structure of DNA. This discovery revolutionized our approach to medical science and opened new perspectives for the diagnosis and treatment of many diseases including cancer. Since then, progress in molecular biology, together with the rapid advance of technologies, allowed to clone hundreds of protein-coding genes that were found mutated in all types of cancer. Normal and aberrant gene functions, interactions, and mechanisms of mutations were studied to identify the intricate network of pathways leading to cancer. With the acknowledgment of the genetic nature of cancer, new diagnostic, prognostic, and therapeutic strategies have been attempted and developed, but very few have found their way in the clinical field. In an effort to identify new translational targets, another great discovery has changed our way to look at genes and their functions. MicroRNAs have been the first noncoding genes involved in cancer. This review is a brief chronological history of microRNAs and cancer. Through the work of few of the greatest scientists of our times, this chapter describes the discovery of microRNAs from C. elegans to their debut in cancer and in the medical field, the concurrent development of technologies, and their future translational applications. The purpose was to share the exciting path that lead to one of the most important discoveries in cancer genetics in the past 20 years.
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Affiliation(s)
- Alessandra Drusco
- Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Carlo M Croce
- Wexner Medical Center, The Ohio State University, Columbus, OH, United States.
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Zhao B, Lucas KJ, Saha TT, Ha J, Ling L, Kokoza VA, Roy S, Raikhel AS. MicroRNA-275 targets sarco/endoplasmic reticulum Ca2+ adenosine triphosphatase (SERCA) to control key functions in the mosquito gut. PLoS Genet 2017; 13:e1006943. [PMID: 28787446 PMCID: PMC5560755 DOI: 10.1371/journal.pgen.1006943] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 08/17/2017] [Accepted: 07/26/2017] [Indexed: 12/17/2022] Open
Abstract
The yellow fever mosquito Aedes aegypti is the major vector of arboviruses, causing numerous devastating human diseases, such as dengue and yellow fevers, Chikungunya and Zika. Female mosquitoes need vertebrate blood for egg development, and repeated cycles of blood feeding are tightly linked to pathogen transmission. The mosquito’s posterior midgut (gut) is involved in blood digestion and also serves as an entry point for pathogens. Thus, the mosquito gut is an important tissue to investigate. The miRNA aae-miR-275 (miR-275) has been shown to be required for normal blood digestion in the female mosquito; however, the mechanism of its action has remained unknown. Here, we demonstrate that miR-275 directly targets and positively regulates sarco/endoplasmic reticulum Ca2+adenosine triphosphatase, which is implicated in active transport of Ca2+ from the cytosol to the sarco/endoplasmic reticulum. We utilized a combination of the gut-specific yeast transcription activator protein Gal4/upstream activating sequence (Gal4/UAS) system and miRNA Tough Decoy technology to deplete the endogenous level of miR-275 in guts of transgenic mosquitoes. This gut-specific reduction of miR-275 post blood meal decreased SERCA mRNA and protein levels of the digestive enzyme late trypsin. It also resulted in a significant reduction of gut microbiota. Moreover, the decrease of miR-275 and SERCA correlated with defects in the Notch signaling pathway and assembly of the gut actin cytoskeleton. The adverse phenotypes caused by miR-275 silencing were rescued by injections of miR-275 mimic. Thus, we have discovered that miR-275 directly targets SERCA, and the maintenance of its level is critical for multiple gut functions in mosquitoes. Female mosquitoes transmit numerous devastating human diseases. The mosquito gut, in addition to its primary function as a site of blood digestion, represents the entry point for pathogen colonization in mosquito vectors. The conserved microRNA, miR-275, was shown to be required for blood digestion and egg development. In this study, we investigated the target of miR-275 contributing to the regulation of mosquito gut functions. We achieved spatiotemporal suppression of miR-275 using a transgenic Tough Decoy RNA approach in the A. aegypti female mosquito gut. Furthermore, we have uncovered that miR-275 targets sarco/endoplasmic reticulum Ca2+- adenosine triphosphatase (SERCA), affecting numerous gut functions including blood digestion, production of digestive proteases, and assembly of the gut actin cytoskeleton. SERCA is essential for maintenance of Ca2+ homeostasis, and its disturbance, in humans, leads to cardiac hypertrophy, heart failure and cancers. Therefore, the finding that the miRNA miR-275 targets SERCA not only contributes to the knowledge of mosquito gut regulation but also significantly adds to the general understanding of mechanisms governing this critical molecule.
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Affiliation(s)
- Bo Zhao
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Keira J Lucas
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Tusar T Saha
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Jisu Ha
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
| | - Lin Ling
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Vladimir A Kokoza
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Sourav Roy
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Alexander S Raikhel
- Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
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31
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Tian Y, Jiang Y, Shang Y, Zhang YP, Geng CF, Wang LQ, Chang YQ. Establishment of lysozyme gene RNA interference systemand its involvement in salinity tolerance in sea cucumber (Apostichopus japonicus). FISH & SHELLFISH IMMUNOLOGY 2017; 65:71-79. [PMID: 28359949 DOI: 10.1016/j.fsi.2017.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/22/2017] [Accepted: 03/26/2017] [Indexed: 06/07/2023]
Abstract
The lysozyme gene was silenced using RNA interference (RNAi) to analyze the function of lysozyme in sea cucumber under salt stress. The interfering efficiency of four lysozyme RNAi oligos ranged from 0.55 to 0.70. From the four oligos, p-miR-L245 was used for further interfering experiments because it had the best silencing efficiency. Peristomial film injection of p-miR-L245 (10 μg) was used for further interfering experiments. The lowest gene expression, determined by RT-PCR assay, in muscle, coelomic fluid, and parapodium occurred 48 h after p-miR-L245 injection, while that of body wall and tube foot was 96 h and 24 h, respectively. Lysozyme activity in muscle and body wall was significantly lower than the controls. The lowest lysozyme activity in muscle, body wall and parapodium, was found at 48, 72, and 48 h, respectively, which was consistent with the transcription expression of lysozyme. The lowest point of lysozyme activity was at 96 h in coelomic fluid and tube foot, which was laid behind lysozyme expression in transcription level. The expression profile of the lysozyme transcription level and lysozyme activity in the body wall and tube foot increased at 12 h after p-miR-L245 injection before the interference effect appeared. NKA gene expression was expressed at a high level in the positive control (PC) and negative control (NC) groups at 12, 24, and 48 h, while NKA was expressed at low levels in the lysozyme RNAi injection group at 12 and 24 h. The level of NKA gene expression recovered to the level of the PC and NC group at 48, 72, and 96 h after the lysozyme RNAi injection. NKCC1 gene expression was high in the PC and NC groups at 96 h, while the NKCC1 was expressed at a low level 96 h after lysozyme RNAi injection. The results suggest that lysozyme decay involves NKA and NKCC1 gene expression under salinity 18 psμ. The K+ and Cl- concentration after lysozyme RNAi injection was lower than in the PC and NC group.
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Affiliation(s)
- Yi Tian
- Key Laboratory of Mariculture, Ministry of Agriculture, Dalian Ocean University, 116023, Dalian, China.
| | - Yanan Jiang
- Key Laboratory of Mariculture, Ministry of Agriculture, Dalian Ocean University, 116023, Dalian, China
| | - Yanpeng Shang
- Key Laboratory of Mariculture, Ministry of Agriculture, Dalian Ocean University, 116023, Dalian, China
| | - Yu-Peng Zhang
- Key Laboratory of Mariculture, Ministry of Agriculture, Dalian Ocean University, 116023, Dalian, China
| | - Chen-Fan Geng
- Key Laboratory of Mariculture, Ministry of Agriculture, Dalian Ocean University, 116023, Dalian, China
| | - Li-Qiang Wang
- Key Laboratory of Mariculture, Ministry of Agriculture, Dalian Ocean University, 116023, Dalian, China
| | - Ya-Qing Chang
- Key Laboratory of Mariculture, Ministry of Agriculture, Dalian Ocean University, 116023, Dalian, China
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Oliveto S, Mancino M, Manfrini N, Biffo S. Role of microRNAs in translation regulation and cancer. World J Biol Chem 2017; 8:45-56. [PMID: 28289518 PMCID: PMC5329714 DOI: 10.4331/wjbc.v8.i1.45] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/20/2016] [Accepted: 01/18/2017] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are pervasively expressed and regulate most biological functions. They function by modulating transcriptional and translational programs and therefore they orchestrate both physiological and pathological processes, such as development, cell differentiation, proliferation, apoptosis and tumor growth. miRNAs work as small guide molecules in RNA silencing, by negatively regulating the expression of several genes both at mRNA and protein level, by degrading their mRNA target and/or by silencing translation. One of the most recent advances in the field is the comprehension of their role in oncogenesis. The number of miRNA genes is increasing and an alteration in the level of miRNAs is involved in the initiation, progression and metastases formation of several tumors. Some tumor types show a distinct miRNA signature that distinguishes them from normal tissues and from other cancer types. Genetic and biochemical evidence supports the essential role of miRNAs in tumor development. Although the abnormal expression of miRNAs in cancer cells is a widely accepted phenomenon, the cause of this dysregulation is still unknown. Here, we discuss the biogenesis of miRNAs, focusing on the mechanisms by which they regulate protein synthesis. In addition we debate on their role in cancer, highlighting their potential to become therapeutic targets.
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33
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Kratassiouk G, Pritchard LL, Cuvellier S, Vislovukh A, Meng Q, Groisman R, Degerny C, Deforzh E, Harel-Bellan A, Groisman I. The WEE1 regulators CPEB1 and miR-15b switch from inhibitor to activators at G2/M. Cell Cycle 2016; 15:667-77. [PMID: 27027998 DOI: 10.1080/15384101.2016.1147631] [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: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs) in the AGO-containing RISC complex control messenger RNA (mRNA) translation by binding to mRNA 3' untranslated region (3'UTR). The relationship between miRNAs and other regulatory factors that also bind to mRNA 3'UTR, such as CPEB1 (cytoplasmic polyadenylation element-binding protein), remains elusive. We found that both CPEB1 and miR-15b control the expression of WEE1, a key mammalian cell cycle regulator. Together, they repress WEE1 protein expression during G1 and S-phase. Interestingly, the 2 factors lose their inhibitory activity at the G2/M transition, at the time of the cell cycle when WEE1 expression is maximal, and, moreover, rather activate WEE1 translation in a synergistic manner. Our data show that translational regulation by RISC and CPEB1 is essential in cell cycle control and, most importantly, is coordinated, and can be switched from inhibition to activation during the cell cycle.
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Affiliation(s)
- Gueorgui Kratassiouk
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France
| | - Linda L Pritchard
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France
| | - Sylvain Cuvellier
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France.,d Inserm U1016, Institut Cochin, Département Génétique et Développement , Paris , France
| | - Andrii Vislovukh
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France.,e Department of Translation Mechanisms , Institute of Molecular Biology and Genetics, National Academy of Sciences , Kiev , Ukraine
| | - Qingwei Meng
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France.,f The Breast Department of the Third Affiliated Hospital of Harbin Medical University , Harbin , China
| | - Regina Groisman
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France
| | - Cindy Degerny
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France
| | - Evgeny Deforzh
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France
| | - Annick Harel-Bellan
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France
| | - Irina Groisman
- a Université Paris Sud, Laboratoire Epigénétique et Cancer, Formation de Recherche en Evolution 3377 , Gif-Sur-Yvette , France.,b Centre National de la Recherche Scientifique (CNRS) , Gif-Sur-Yvette , France.,c Commissariat à l'Energie Atomique (CEA) , Saclay, Gif-sur-Yvette , France
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Geisler A, Fechner H. MicroRNA-regulated viral vectors for gene therapy. World J Exp Med 2016; 6:37-54. [PMID: 27226955 PMCID: PMC4873559 DOI: 10.5493/wjem.v6.i2.37] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 03/02/2016] [Accepted: 03/17/2016] [Indexed: 02/06/2023] Open
Abstract
Safe and effective gene therapy approaches require targeted tissue-specific transfer of a therapeutic transgene. Besides traditional approaches, such as transcriptional and transductional targeting, microRNA-dependent post-transcriptional suppression of transgene expression has been emerging as powerful new technology to increase the specificity of vector-mediated transgene expression. MicroRNAs are small non-coding RNAs and often expressed in a tissue-, lineage-, activation- or differentiation-specific pattern. They typically regulate gene expression by binding to imperfectly complementary sequences in the 3' untranslated region (UTR) of the mRNA. To control exogenous transgene expression, tandem repeats of artificial microRNA target sites are usually incorporated into the 3' UTR of the transgene expression cassette, leading to subsequent degradation of transgene mRNA in cells expressing the corresponding microRNA. This targeting strategy, first shown for lentiviral vectors in antigen presenting cells, has now been used for tissue-specific expression of vector-encoded therapeutic transgenes, to reduce immune response against the transgene, to control virus tropism for oncolytic virotherapy, to increase safety of live attenuated virus vaccines and to identify and select cell subsets for pluripotent stem cell therapies, respectively. This review provides an introduction into the technical mechanism underlying microRNA-regulation, highlights new developments in this field and gives an overview of applications of microRNA-regulated viral vectors for cardiac, suicide gene cancer and hematopoietic stem cell therapy, as well as for treatment of neurological and eye diseases.
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Shao T, Zhao Z, Wu A, Bai J, Li Y, Chen H, Jiang C, Wang Y, Li S, Wang L, Zhang F, Xu J, Li X. Functional dissection of virus-human crosstalk mediated by miRNAs based on the VmiReg database. MOLECULAR BIOSYSTEMS 2016; 11:1319-28. [PMID: 25787233 DOI: 10.1039/c5mb00095e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recently, a number of viruses have been shown to encode microRNAs (miRNAs), and they play important roles in several biological processes, enhancing the intricacies of the virus-host crosstalk. However, systematically deciphering the characteristics of crosstalk mediated by viral and human miRNAs has been hampered by the lack of high-confidence targets. Here, a user-friendly platform is developed to provide experimentally validated and predicted target genes of viral miRNAs as well as their functions, named VmiReg. To explore the virus-human crosstalk meditated by miRNAs, validated human cellular targets of viral and cellular miRNAs are analyzed. As a result, target genes of viral miRNAs are prone to be silenced by human miRNAs. Two kinds of targets have globally significantly high functional similarities and are more often found simultaneously in many important biological functions, even in disease genes, particularly cancer genes, and essential genes. In addition, viral and human miRNA targets are in close proximity within the protein-protein interaction network, indicating frequent communication via physical interactions to participate in the same functions. Finally, multiple dense modules intuitively exhibit crosstalk between viral and cellular miRNAs. Furthermore, most co-regulated genes tend to be in important locations of modules. The lymphoma-related module is one of the typical examples. Our study suggests that the functional importance of cellular genes targeted by viral miRNAs and the intricate virus-host crosstalk mediated by miRNAs may be performed via the sharing of target genes or physical interactions, providing a new direction in further researching the roles of miRNAs in infection.
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Affiliation(s)
- Tingting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Sharma SB, Ruppert JM. MicroRNA-Based Therapeutic Strategies for Targeting Mutant and Wild Type RAS in Cancer. Drug Dev Res 2015; 76:328-42. [PMID: 26284568 DOI: 10.1002/ddr.21270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRs) have been causally implicated in the progression and development of a wide variety of cancers. miRs modulate the activity of key cell signaling networks by regulating the translation of pathway component proteins. Thus, the pharmacological targeting of miRs that regulate cancer cell signaling networks, either by promoting (using miR-supplementation) or by suppressing (using antisense oligonucleotide-based strategies) miR activity is an area of intense research. The RAS-extracellular signal regulated kinase (ERK) pathway represents a major miR-regulated signaling network that endows cells with some of the classical hallmarks of cancer, and is often inappropriately activated in malignancies by somatic genetic alteration through point mutation or alteration of gene copy number. In addition, recent progress indicates that many tumors may be deficient in GTPase activating proteins (GAPs) due to the collaborative action of oncogenic miRs. Recent studies also suggest that in tumors harboring a mutant RAS allele there is a critical role for wild type RAS proteins in determining overall RAS-ERK pathway activity. Together, these two advances comprise a new opportunity for therapeutic intervention. In this review, we evaluate miR-based therapeutic strategies for modulating RAS-ERK signaling in cancers; in particular for more direct modulation of RAS-GTP levels, with the potential to complement current strategies to yield more durable treatment responses. To this end, we discuss the potential for miR-based therapies focused on three prominent miRs including the pan-RAS regulator let-7 and the GAP regulator comprised of miR-206 and miR-21 (miR-206/21).
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Affiliation(s)
- Sriganesh B Sharma
- Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA.,Program in Cancer Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - John Michael Ruppert
- Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA.,The Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV, 26506, USA
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miR-28-5p Involved in LXR-ABCA1 Pathway is Increased in the Plasma of Unstable Angina Patients. Heart Lung Circ 2015; 24:724-30. [DOI: 10.1016/j.hlc.2014.12.160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 11/21/2022]
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Mahdipour M, van Tol HTA, Stout TAE, Roelen BAJ. Validating reference microRNAs for normalizing qRT-PCR data in bovine oocytes and preimplantation embryos. BMC DEVELOPMENTAL BIOLOGY 2015; 15:25. [PMID: 26062615 PMCID: PMC4464232 DOI: 10.1186/s12861-015-0075-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/03/2015] [Indexed: 01/09/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small noncoding RNAs that act as post-transcriptional regulators of gene targets. Accurate quantification of miRNA expression using validated internal controls should aid in the understanding of their role in epigenetic modification of genome function. To date, most studies that have examined miRNA expression levels have used the global mean expression of all expressed genes or the expression of reference mRNAs or nuclear RNAs for normalization. RESULTS We analyzed the suitability of a number of miRNAs as potential expression normalizers in bovine oocytes and early embryos, and porcine oocytes. The stages examined were bovine oocytes at the germinal vesicle (GV) and metaphase II stages, bovine zygotes, 2, 4 and 8 cell embryos, morulae and blastocysts, as well as porcine cumulus oocyte complexes, GV, metaphase I and II oocytes. qRT-PCR was performed to quantify expression of miR-93, miR-103, miR-26a, miR-191, miR-23b, Let-7a and U6 for bovine samples and miR-21, miR-26a, miR-93, miR-103, miR-148a, miR-182 and miR-191 for porcine oocytes. The average starting material for each sample was determined using specific standard curves for each primer set. Subsequently, geNorm and BestKeeper software were used to identify a set of stably expressed miRNAs. Stepwise removal to determine the optimum number of reference miRNAs identified miR-93 and miR-103 as the most stably expressed in bovine samples and miR-26a, miR-191 and miR-93 in porcine samples. CONCLUSIONS The combination of miR-93 and miR-103 is optimal for normalizing miRNA expression for qPCR experiments on bovine oocytes and preimplantation embryos; the preferred combination for porcine oocytes is miR-26a, miR-191 and miR-93.
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Affiliation(s)
- Mahdi Mahdipour
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
| | - Helena T A van Tol
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
| | - Tom A E Stout
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
| | - Bernard A J Roelen
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
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Yu X, Zhang L, Wen G, Zhao H, Luong LA, Chen Q, Huang Y, Zhu J, Ye S, Xu Q, Wang W, Xiao Q. Upregulated sirtuin 1 by miRNA-34a is required for smooth muscle cell differentiation from pluripotent stem cells. Cell Death Differ 2014; 22:1170-80. [PMID: 25526086 DOI: 10.1038/cdd.2014.206] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 12/31/2022] Open
Abstract
microRNA-34a (miR-34a) and sirtuin 1 (SirT1) have been extensively studied in tumour biology and longevity/aging, but little is known about their functional roles in smooth muscle cell (SMC) differentiation from pluripotent stem cells. Using well-established SMC differentiation models, we have demonstrated that miR-34a has an important role in SMC differentiation from murine and human embryonic stem cells. Surprisingly, deacetylase sirtuin 1 (SirT1), one of the top predicted targets, was positively regulated by miR-34a during SMC differentiation. Mechanistically, we demonstrated that miR-34a promoted differentiating stem cells' arrest at G0/G1 phase and observed a significantly decreased incorporation of miR-34a and SirT1 RNA into Ago2-RISC complex upon SMC differentiation. Importantly, we have identified SirT1 as a transcriptional activator in the regulation of SMC gene programme. Finally, our data showed that SirT1 modulated the enrichment of H3K9 tri-methylation around the SMC gene-promoter regions. Taken together, our data reveal a specific regulatory pathway that miR-34a positively regulates its target gene SirT1 in a cellular context-dependent and sequence-specific manner and suggest a functional role for this pathway in SMC differentiation from stem cells in vitro and in vivo.
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Affiliation(s)
- X Yu
- 1] Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK [2] Institute of Bioengineering, Queen Mary University of London, London E1 4NS, UK
| | - L Zhang
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - G Wen
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - H Zhao
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - L A Luong
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Q Chen
- 1] Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK [2] Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - Y Huang
- 1] Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK [2] Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - J Zhu
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - S Ye
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Q Xu
- Cardiovascular Division, King's College London British Heart Foundation Centre, London SE5 9NU, UK
| | - W Wang
- Institute of Bioengineering, Queen Mary University of London, London E1 4NS, UK
| | - Q Xiao
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
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Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation. Int J Genomics 2014; 2014:970607. [PMID: 25180174 PMCID: PMC4142390 DOI: 10.1155/2014/970607] [Citation(s) in RCA: 374] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/09/2014] [Accepted: 07/17/2014] [Indexed: 12/12/2022] Open
Abstract
Discovered in 1993, micoRNAs (miRNAs) are now recognized as one of the major regulatory gene families in eukaryotes. To date, 24521 microRNAs have been discovered and there are certainly more to come. It was primarily acknowledged that miRNAs result in gene expression repression at both the level of mRNA stability by conducting mRNA degradation and the level of translation (at initiation and after initiation) by inhibiting protein translation or degrading the polypeptides through binding complementarily to 3′UTR of the target mRNAs. Nevertheless, some studies revealed that miRNAs have the capability of activating gene expression directly or indirectly in respond to different cell types and conditions and in the presence of distinct cofactors. This reversibility in their posttranslational gene regulatory natures enables the bearing cells to rapidly response to different cell conditions and consequently block unnecessary energy wastage or maintain the cell state. This paper provides an overview of the current understandings of the miRNA characteristics including their genes and biogenesis, as well as their mediated downregulation. We also review up-to-date knowledge of miRNA-mediated gene upregulation through highlighting some notable examples and discuss the emerging concepts of their associations with other posttranscriptional gene regulation processes.
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Aalaei-Andabili SH, Fabbri M, Rezaei N. Reciprocal effects of Toll-like receptors and miRNAs on biological processes in human health and disease: a systematic review. Immunotherapy 2014; 5:1127-42. [PMID: 24088081 DOI: 10.2217/imt.13.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The roles of miRNAs in human diseases are emerging. Manipulation of miRNA expression seems to be an effective approach to control disease severity. It has recently been found that Toll-like receptors and miRNAs work by exerting reciprocal effects. Toll-like receptor stimulation can lead to up-/down-regulation of various miRNA expressions. Lipopolysaccharide induction may result in interactions between different miRNAs. Several miRNAs are involved in cancers, indicating the importance of identifying strategies to properly manipulate their expression level. The control of various miRNA expression levels, taking into consideration the plethora of their target genes and the possibility that this may lead to contracting function, which is an important issue in treatment of any miRNA-based (phenotype) disease.
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Affiliation(s)
- Seyed Hossein Aalaei-Andabili
- Molecular Immunology Research Center & Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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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: 2.4] [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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Zha W, Cao L, Shen Y, Huang M. Roles of Mir-144-ZFX pathway in growth regulation of non-small-cell lung cancer. PLoS One 2013; 8:e74175. [PMID: 24066116 PMCID: PMC3774613 DOI: 10.1371/journal.pone.0074175] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/29/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death worldwide. Non-small cell lung carcinoma (NSCLC) accounts for most of the lung cancer cases and the prognosis of this disease remains poor despite decades of intensive investigation. Thus new insights into underlying mechanisms by which NSCLC develops are avidly needed as the basis for development of new lines of therapeutic strategies. The past decade has witnessed a growing interest on the regulatory roles of micro RNAs on various categories of malignancies. Related data has been well documented in carcinogenesis and pathophysiology of a variety of malignancies. Even so, there is a relative lack of data on roles of mir-144 in tumor biology and there has been no report showing the involvement of mir-144 in NSCLC development. METHODS/PRINCIPAL FINDING From human NSCLC tumor tissue samples and cell culture samples, we found that the expression of mir-144 is associated with malignant phenotype of NSCLC. Further investigations showed that ectopic mir-144 expression dramatically inhibits NSCLC tumor cell growth and induces apoptosis as manifested by elevated apoptotic protein markers and flowcytometry change. Moreover, we also found that ZFX protein expression is also associated with malignant phenotype of NSCLC and knockdown of ZFX protein results in a similar effect as of ectopic mir-144 expression. Finally, we found that ZFX expression is highly adjustable upon presence of mir-144 and ectopic expression of ZFX dramatically dampens mir-144 action of tumor inhibition. CONCLUSIONS Our results for the first time showed mir-144-ZFX pathway is involved in the development of NSCLC, which sheds a light for further investigations on underlying mechanisms toward better understanding and management of NSCLC.
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Affiliation(s)
- Wangjian Zha
- Department of Respiratory Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Liu Cao
- Department of Ophthalmology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ying Shen
- Division of Neurosurgery, Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Mao Huang
- Department of Respiratory Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
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MicroRNAs: Critical Regulators of mRNA Traffic and Translational Control with Promising Biotech and Therapeutic Applications. IRANIAN JOURNAL OF BIOTECHNOLOGY 2013. [DOI: 10.5812/ijb.11081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Aalaei-andabili SH, Rezaei N. Toll like receptor (TLR)-induced differential expression of microRNAs (MiRs) promotes proper immune response against infections: a systematic review. J Infect 2013; 67:251-64. [PMID: 23850616 DOI: 10.1016/j.jinf.2013.07.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/25/2013] [Accepted: 07/06/2013] [Indexed: 12/19/2022]
Abstract
Toll like receptors (TLRs) are one of the major families of pattern recognition receptors (PRRs). MicroRNAs (MiRs) are small noncoding RNAs with regulatory effects on biological process, and it has been recently shown that they can control inflammatory process and the response to an infection by modulating the function of TLRs. In this study, we designed a systematic review to clarify the reciprocal interaction between TLRs and MiRs, in order to identify possible future therapeutic targets and strategies. On the one hand, TLRs stimulation can change expression level of miRs in various ways, which can lead to modulating their effects. On the other hand, MiRs also influence the expression of TLRs and the intensity of the inflammatory reaction. We therefore conclude that the interaction between MiRs and TLRs is a key regulator of innate immune system. Investigations discovering therapeutic approaches by manipulation of miRs expression level may open a new approach for the treatment of inflammatory diseases.
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Bovell LC, Putcha BDK, Samuel T, Manne U. Clinical implications of microRNAs in cancer. Biotech Histochem 2013; 88:388-96. [PMID: 23647010 DOI: 10.3109/10520295.2013.788735] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenously produced non-coding RNAs that serve as micromanagers by negatively regulating gene expression. MiRNAs are implicated in several biological pathways including development of neoplasia. Because altered miRNA expression is implicated in the pathobiology of various cancers, these molecules serve as potential therapeutic targets. Using miRNA mimics to restore levels of aberrantly down-regulated miRNAs or miRNA inhibitors to inactivate over-expressed miRNAs shows promise as the next generation of therapeutic strategies. Manipulation of miRNAs offers an alternative therapeutic approach for chemo- and radiation-resistant tumors. Similarly, miRNA expression patterns can be used for diagnosis and to predict prognosis and efficacy of therapy. We present here an overview of how miRNAs affect cancers, how they may be used as biomarkers, and the clinical implications of miRNAs in cancer.
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Affiliation(s)
- L C Bovell
- Department of Pathology, University of Alabama at Birmingham , Birmingham
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Zhao J, Chen P, Gregersen H. Morpho-mechanical intestinal remodeling in type 2 diabetic GK rats--is it related to advanced glycation end product formation? J Biomech 2013; 46:1128-1134. [PMID: 23403079 DOI: 10.1016/j] [Citation(s) in RCA: 519] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/07/2013] [Accepted: 01/13/2013] [Indexed: 02/06/2023]
Abstract
Little is known about the mechanisms for the biomechanical remodeling in diabetes. The histomorphology, passive biomechanical properties and expression of advanced glycation end product (N epsilon-(carboxymethyl) lysine, AGE) and its receptor (RAGE) were studied in jejunal segments from 8 GK diabetic rats (GK group) and 10 age-matched normal rats (Normal group). The mechanical test was done by using a ramp distension of fluid into the jejunal segments in vitro. Circumferential stress and strain were computed from the length, diameter and pressure data and from the zero-stress state geometry. AGE and RAGE were detected by immunohistochemistry staining. Linear regression analysis was done to study association between the glucose level and AGE/RAGE expression with the histomorphometric and biomechanical parameters. The blood glucose level, the jejunal weight per length, wall thickness, wall area and layer thickness significantly increased in the GK group compared with the Normal group (P<0.05, P<0.01 and P<0.001). The opening angle and absolute values of residual strain decreased whereas the circumferential stiffness of the jejunal wall increased in the GK group (P<0.05 and P<0.01). Furthermore, stronger AGE expression in the villi and crypt and RAGE expression in the villi were found in the GK group (P<0.05 and P<0.01). Most histomorphometric and biomechanical changes were associated with blood glucose level and AGE/RAGE expression. In conclusion, histomorphometric and biomechanical remodeling occurred in type 2 diabetic GK rats. The increasing blood glucose level and the increased AGE/RAGE expression were associated with the remodeling, indicating a causal relationship.
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Affiliation(s)
- Jingbo Zhao
- Mech-Sense, Department of Gastroenterology and Surgery, Aalborg University Hospital, Soendre Skovvej 15, DK 9000 Aalborg, Denmark.
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Ferrer G, Navarro A, Hodgson K, Aymerich M, Pereira A, Baumann T, Monzo M, Moreno C, Montserrat E. MicroRNA expression in chronic lymphocytic leukemia developing autoimmune hemolytic anemia. Leuk Lymphoma 2013; 54:2016-22. [PMID: 23286334 DOI: 10.3109/10428194.2012.763123] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is frequently associated with autoimmune hemolytic anemia (AIHA). However, the mechanisms governing the association between CLL and AIHA are poorly understood. MicroRNAs (miRNAs) have been associated with different clinico-biological forms of CLL and are also known to play a substantial role in autoimmunity. However, there are no studies correlating miRNA expression with the likelihood that patients with CLL will develop AIHA. In this study, we found that malignant B-cells from patients with CLL subsequently developing AIHA present nine down-regulated (i.e. miR-19a, miR-20a, miR-29c, miR-146b-5p, miR-186, miR-223, miR-324-3p, miR-484 and miR-660) miRNAs. Interestingly, two of these miRNAs (i.e. miR-20a and miR-146b-5p) are involved in autoimmune phenomena, and one (i.e. miR-146b-5p) in both autoimmunity and CLL. Furthermore, we demonstrated that miR-146b-5p modulates CD80, a molecule associated with the B-T-cell synapse and in restoration of the antigen presenting cell capacity of CLL cells.
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Affiliation(s)
- Gerardo Ferrer
- Institute of Hematology and Oncology, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
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Yi H, Liang B, Jia J, Liang N, Xu H, Ju G, Ma S, Liu X. Differential roles of miR-199a-5p in radiation-induced autophagy in breast cancer cells. FEBS Lett 2013; 587:436-43. [PMID: 23337876 DOI: 10.1016/j.febslet.2012.12.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/18/2012] [Accepted: 12/26/2012] [Indexed: 12/19/2022]
Abstract
Autophagy is a self-degrading process that is triggered by diverse stimuli including ionizing radiation. In this study we show novel phenomena in which transfection of miR-199a-5p mimic significantly suppresses IR-induced autophagy in MCF7 cells, and up-regulates basal and IR-induced autophagy in MDA-MB-231 breast cancer cells. We also identify DRAM1 and Beclin1 as novel target genes for miR-199a-5p. Overexpression of miR-199a-5p inhibits DRAM1 and Beclin1 expression in MCF7 cells, while it enhances expression of these genes in MDA-MB-231 cells. Furthermore, we show that miR-199a-5p sensitizes MDA-MB-231 cells to irradiation. Therefore, our data identify miR-199a-5p as a novel and unique regulator of autophagy, which plays an important role in cancer biology and cancer therapy.
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Affiliation(s)
- Heqing Yi
- Key Laboratory of Radiobiology (Ministry of Health), School of Public Health, Jilin University, Changchun 130021, China
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Abstract
PURPOSE OF REVIEW The contributions of microRNA (miRNA) to pathogenesis of autoimmune diseases such as Systemic lupus erythematosus (SLE) are beginning to be uncovered. In this review, we discuss the major progress made in understanding of miRNA biology, as well as novel insights into SLE pathogenesis mediated by miRNAs. RECENT FINDINGS MiRNA biogenesis is a deliberately controlled process, which requires multiple layers of regulation involving participation of various protein regulators and posttranscriptional modifications. Its expression regulation is critically modulated by multiple physiopathological factors such as inflammation, stress, Epstein-Barr virus infection and sex hormones. MiRNAs play a crucial role in maintaining immune system development and function, and are implicated in development of numerous immunological disorders. Unique miRNA expression signatures in SLE reveal their clinical relevance. MiRNAs contribute broadly and actively to various aspects of SLE pathogenesis and hold great therapeutic potential. SUMMARY The recent findings underscore the potential importance of miRNAs to pathogenesis, diagnosis and treatment of SLE.
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