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Tiensuu H, Haapalainen AM, Tissarinen P, Pasanen A, Hallman M, Rämet M. MicroRNA expression profile in the basal plate of human placenta associates with spontaneous preterm birth. Placenta 2024; 155:60-69. [PMID: 39137705 DOI: 10.1016/j.placenta.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
INTRODUCTION MicroRNAs regulate post-transcriptional gene expression. Their expression has been linked to many pregnancy complications, including preterm birth. Placental microRNA levels differ between preterm and term pregnancies. Not much is known about the targets that are affected by these differences in microRNA expression. We investigated associations between microRNA expression levels in the basal plate of the placenta and their targets and the onset of preterm birth. METHODS MiRNAomes of spontaneous preterm (n = 6) and term (n = 6) placentas were characterized using RNA sequencing. MicroRNA target and enrichment analyses were performed to explore potential gene targets and pathways. Selected findings were validated using qPCR (n = 41). MicroRNA mimic transfection and luciferase reporter assays were performed to test if certain microRNAs regulate their predicted target, SLIT2, the expression of which has been shown to associate with preterm birth. RESULTS We identified 39 differentially expressed microRNAs from the preterm placentas compared to term. Many downregulated microRNAs were from the placenta-specific C14MC microRNA cluster. Target gene and pathway analyses showed that microRNAs that associate with preterm birth target transcription related factors and genes linked with protein binding and invasive pathways. Eight of the identified microRNAs putatively target SLIT2, including miR-766-3p and miR-489-3p. Luciferase reporter assay suggested that these microRNAs regulate SLIT2 expression. DISCUSSION MicroRNA expression changes are associated with spontaneous preterm birth. A group of microRNAs targeting the same gene or genes belonging to the same pathway can have a significant effect on the critical processes maintaining pregnancy and placental functions.
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Affiliation(s)
- Heli Tiensuu
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland.
| | - Antti M Haapalainen
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Pinja Tissarinen
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Anu Pasanen
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Mikko Hallman
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Mika Rämet
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland; Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520, Tampere, Finland
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2
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Zhao R. Exercise mimetics: a novel strategy to combat neuroinflammation and Alzheimer's disease. J Neuroinflammation 2024; 21:40. [PMID: 38308368 PMCID: PMC10837901 DOI: 10.1186/s12974-024-03031-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
Neuroinflammation is a pathological hallmark of Alzheimer's disease (AD), characterized by the stimulation of resident immune cells of the brain and the penetration of peripheral immune cells. These inflammatory processes facilitate the deposition of amyloid-beta (Aβ) plaques and the abnormal hyperphosphorylation of tau protein. Managing neuroinflammation to restore immune homeostasis and decrease neuronal damage is a therapeutic approach for AD. One way to achieve this is through exercise, which can improve brain function and protect against neuroinflammation, oxidative stress, and synaptic dysfunction in AD models. The neuroprotective impact of exercise is regulated by various molecular factors that can be activated in the same way as exercise by the administration of their mimetics. Recent evidence has proven some exercise mimetics effective in alleviating neuroinflammation and AD, and, additionally, they are a helpful alternative option for patients who are unable to perform regular physical exercise to manage neurodegenerative disorders. This review focuses on the current state of knowledge on exercise mimetics, including their efficacy, regulatory mechanisms, progress, challenges, limitations, and future guidance for their application in AD therapy.
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Affiliation(s)
- Renqing Zhao
- College of Physical Education, Yangzhou University, Yangzhou, China.
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3
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Qu J, Song Z, Cheng X, Jiang Z, Zhou J. Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction. PeerJ 2023; 11:e15889. [PMID: 37641598 PMCID: PMC10460564 DOI: 10.7717/peerj.15889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Background A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. Methods This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA). First, grounded on known SM-miRNAs associations, SM similarity and miRNA similarity, NI was used to predict score of an unknown SM-miRNA pair by reckoning the sum of known associations between neighbors of the SM (miRNA) and the miRNA (SM). Second, utilizing a two-layered generative stochastic artificial neural network, RBM was used to predict SM-miRNA association by learning potential probability distribution from known SM-miRNA associations. At last, an ensemble learning model was conducted to combine NI and RBM for identifying potential SM-miRNA associations. Results Furthermore, we conducted global leave one out cross validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation to assess performance of NIRBMSMMA based on three datasets. Results showed that NIRBMSMMA obtained areas under the curve (AUC) of 0.9912, 0.9875, 0.8376 and 0.9898 ± 0.0009 under global LOOCV, miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation based on dataset 1, respectively. For dataset 2, the AUCs are 0.8645, 0.8720, 0.7066 and 0.8547 ± 0.0046 in turn. For dataset 3, the AUCs are 0.9884, 0.9802, 0.8239 and 0.9870 ± 0.0015 in turn. Also, we conducted case studies to further assess the predictive performance of NIRBMSMMA. These results illustrated the proposed model is a useful tool in predicting potential SM-miRNA associations.
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Affiliation(s)
- Jia Qu
- School of Computer Science and Artificial Intelligence, Changzhou University, Changzhou, Jiangsu, China
| | - Zihao Song
- School of Computer Science and Artificial Intelligence, Changzhou University, Changzhou, Jiangsu, China
| | - Xiaolong Cheng
- School of Computer Science and Artificial Intelligence, Changzhou University, Changzhou, Jiangsu, China
| | - Zhibin Jiang
- Department of Computer Science and Engineering, Shaoxing University, Shaoxing, Zhejiang, China
| | - Jie Zhou
- Department of Computer Science and Engineering, Shaoxing University, Shaoxing, Zhejiang, China
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4
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Balchin C, Tan AL, Wilson OJ, McKenna J, Stavropoulos-Kalinoglou A. The role of microRNAs in regulating inflammation and exercise-induced adaptations in rheumatoid arthritis. Rheumatol Adv Pract 2023; 7:rkac110. [PMID: 36699549 PMCID: PMC9870706 DOI: 10.1093/rap/rkac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/12/2022] [Indexed: 01/25/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenously generated single-stranded RNAs that play crucial roles in numerous biological processes, such as cell development, proliferation, differentiation, metabolism and apoptosis. They negatively regulate target gene expression by repressing translation of messenger RNA into a functional protein. Several miRNAs have been implicated in the development and progression of RA. They are involved in inflammatory and immune processes and are associated with susceptibility to RA and disease activity. They are also considered to be potential markers of disease activity or even therapeutic targets. Likewise, several miRNAs are affected acutely by exercise and regulate exercise-related adaptations in the skeletal muscle and cardiovascular system and aerobic fitness. Interestingly, some miRNAs affected by exercise are also important in the context of RA. Investigating these might increase our understanding of the effects of exercise in RA and improve exercise prescription and, potentially, disease management. In this review, we focus on the miRNAs that are associated with both RA and exercise and discuss their roles in (and potential interactions between) RA and exercise-induced adaptations.
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Affiliation(s)
| | - Ai Lyn Tan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, UK,NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Oliver J Wilson
- Carnegie School of Sport, Leeds Beckett University, Leeds, UK
| | - Jim McKenna
- Carnegie School of Sport, Leeds Beckett University, Leeds, UK
| | - Antonios Stavropoulos-Kalinoglou
- Correspondence to: Antonios Stavropoulos-Kalinoglou, Carnegie School of Sport, Leeds Beckett University, Headingley Campus, 225 Fairfax Hall, Churchwood Avenue, Leeds LS6 3QS, UK. E-mail:
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Rojas-Pirela M, Andrade-Alviárez D, Medina L, Castillo C, Liempi A, Guerrero-Muñoz J, Ortega Y, Maya JD, Rojas V, Quiñones W, Michels PA, Kemmerling U. MicroRNAs: master regulators in host-parasitic protist interactions. Open Biol 2022; 12:210395. [PMID: 35702995 PMCID: PMC9198802 DOI: 10.1098/rsob.210395] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs present in a wide diversity of organisms. MiRNAs regulate gene expression at a post-transcriptional level through their interaction with the 3' untranslated regions of target mRNAs, inducing translational inhibition or mRNA destabilization and degradation. Thus, miRNAs regulate key biological processes, such as cell death, signal transduction, development, cellular proliferation and differentiation. The dysregulation of miRNAs biogenesis and function is related to the pathogenesis of diseases, including parasite infection. Moreover, during host-parasite interactions, parasites and host miRNAs determine the probability of infection and progression of the disease. The present review is focused on the possible role of miRNAs in the pathogenesis of diseases of clinical interest caused by parasitic protists. In addition, the potential role of miRNAs as targets for the design of drugs and diagnostic and prognostic markers of parasitic diseases is also discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Lisvaneth Medina
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Christian Castillo
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Chile
| | - Ana Liempi
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Jesús Guerrero-Muñoz
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Yessica Ortega
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Juan Diego Maya
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Verónica Rojas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Paul A. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
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6
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The Significance of the DUF283 Domain for the Activity of Human Ribonuclease Dicer. Int J Mol Sci 2021; 22:ijms22168690. [PMID: 34445396 PMCID: PMC8395393 DOI: 10.3390/ijms22168690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 01/22/2023] Open
Abstract
Dicers are multidomain proteins, usually comprising an amino-terminal putative helicase domain, a DUF283 domain (domain of unknown function), a PAZ domain, two RNase III domains (RNase IIIa and RNase IIIb) and a dsRNA-binding domain. Dicer homologs play an important role in the biogenesis of small regulatory RNAs by cleaving single-stranded precursors adopting stem-loop structures (pre-miRNAs) and double-strand RNAs into short RNA duplexes containing functional microRNAs or small interfering RNAs, respectively. Growing evidence shows that apart from the canonical role, Dicer proteins can serve a number of other functions. For example, results of our previous studies showed that human Dicer (hDicer), presumably through its DUF283 domain, can facilitate hybridization between two complementary RNAs, thus, acting as a nucleic acid annealer. Here, to test this assumption, we prepared a hDicer deletion variant lacking the amino acid residues 625-752 corresponding to the DUF283 domain. The respective 128-amino acid fragment of hDicer was earlier demonstrated to accelerate base-pairing between two complementary RNAs in vitro. We show that the ΔDUF(625-752) hDicer variant loses the potential to facilitate RNA-RNA base pairing, which strongly proves our hypothesis about the importance of the DUF283 domain for the RNA-RNA annealing activity of hDicer. Interestingly, the in vitro biochemical characterization of the obtained deletion variant reveals that it displays different RNA cleavage properties depending on the pre-miRNA substrate.
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7
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Hernández-Coro A, Sánchez-Hernández BE, Montes S, Martínez-Lazcano JC, González-Guevara E, Pérez-Severiano F. Alterations in gene expression due to chronic lead exposure induce behavioral changes. Neurosci Biobehav Rev 2021; 126:361-367. [PMID: 33819547 DOI: 10.1016/j.neubiorev.2021.03.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/15/2020] [Accepted: 03/27/2021] [Indexed: 02/01/2023]
Abstract
Lead (Pb) is a pollutant commonly found in the environment, despite the implementation of public health policies intended to remove it. Due to its chemical characteristics as a divalent ion, Pb interacts with cells, enzymes, and tissues, causing pathological, physical, and behavioral alterations. Recent biotechnological advances have helped us to understand the mechanisms underlying the damage caused by Pb in human populations and in experimental models, and new evidence on the epigenetic alterations caused by exposition to environmental Pb is available. It is known that Pb exposure impacts on behavior (causing aggressiveness, anxiety, and depression), leading to learning deficit and locomotor activity alterations, and its presence has been linked with the abnormal release of neurotransmitters and other biochemical changes involved in these disorders. Still, further reductionist studies are required to determine the effects of Pb exposure on DNA and protein expression and understand the processes underlying the diseases caused by Pb. This will also indicate possible therapeutic targets to offset the negative effects of the heavy metal. By elucidating the epigenetic changes involved, it would be possible to manipulate them and propose novel therapeutic approaches in this area. This review is aimed to provide an overview of studies that link Pb exposure to behavioral changes, as well as biochemical and epigenetic alterations at a neurotransmitter level, considering the importance of this metal in behavior abnormalities.
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Affiliation(s)
- Abraham Hernández-Coro
- Laboratorio de Neurofarmacología Molecular y Nanotecnología, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Insurgentes Sur #3877, La Fama, 14269, Mexico City, Mexico
| | - Beatriz Eugenia Sánchez-Hernández
- Departamento de Genética, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Vasco de Quiroga #15, Col. Belisario Domínguez Sección 16, Tlalpan, 14080, Mexico City, Mexico
| | - Sergio Montes
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Insurgentes Sur # 3877, La Fama, 14269. Mexico City, Mexico
| | - Juan Carlos Martínez-Lazcano
- Laboratorio de Neurofarmacología Molecular y Nanotecnología, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Insurgentes Sur #3877, La Fama, 14269, Mexico City, Mexico
| | - Edith González-Guevara
- Laboratorio de Neurofarmacología Molecular y Nanotecnología, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Insurgentes Sur #3877, La Fama, 14269, Mexico City, Mexico
| | - Francisca Pérez-Severiano
- Laboratorio de Neurofarmacología Molecular y Nanotecnología, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Insurgentes Sur #3877, La Fama, 14269, Mexico City, Mexico.
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8
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Wuttge DM, Carlsen AL, Teku G, Wildt M, Rådegran G, Vihinen M, Heegaard NHH, Hesselstrand R. Circulating Plasma microRNAs In Systemic Sclerosis-Associated Pulmonary Arterial Hypertension. Rheumatology (Oxford) 2021; 61:309-318. [PMID: 33784391 PMCID: PMC8742821 DOI: 10.1093/rheumatology/keab300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Objectives SSc-associated pulmonary arterial hypertension (SSc-APAH) is a late but devastating complication of SSc. Early identification of SSc-APAH may improve survival. We examined the role of circulating miRNAs in SSc-APAH. Methods Using quantitative RT-PCR the abundance of mature miRNAs in plasma was determined in 85 female patients with ACA-positive lcSSc. Twenty-two of the patients had SSc-APAH. Sixty-three SSc controls without PAH were matched for disease duration. Forty-six selected miRNA plasma levels were correlated with clinical data. Longitudinal samples were analysed from 14 SSc-APAH and 27 SSc patients. Results The disease duration was 12 years for the SSc-APAH patients and 12.7 years for the SSc controls. Plasma expression levels of 11 miRNAs were lower in patients with SSc-APAH. Four miRNAs displayed higher plasma levels in SSc-APAH patients compared with SSc controls. There was significant difference between groups for miR-20a-5p and miR-203a-3p when correcting for multiple comparisons (P = 0.002 for both). Receiver operating characteristics curve showed AUC = 0.69–0.83 for miR-21-5p and miR-20a-5p or their combination. miR-20a-5p and miR-203a-3p correlated inversely with NT-pro-Brain Natriuretic Protein levels (r = −0.42 and −0.47). Mixed effect model analysis could not identify any miRNAs as predictor of PAH development. However, miR-20a-5p plasma levels were lower in the longitudinal samples of SSc-APAH patients than in the SSc controls. Conclusions Our study links expression levels of the circulating plasma miRNAs, especially miR-20a-5p and miR-203a-3p, to the occurrence of SSc-APAH in female patients with ACA-positive lcSSc.
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Affiliation(s)
- Dirk M Wuttge
- Department of Clinical Sciences Lund, Rheumatology, Lund University and Skåne University Hospital, SE-22185, Sweden, Lund
| | - Anting L Carlsen
- Department of Autoimmunology & Biomarkers, Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Gabriel Teku
- Department of Experimental Medical Science, Protein Structure Bioinformatics, Lund University, Lund, SE-22185, Sweden
| | - Marie Wildt
- Department of Clinical Sciences Lund, Rheumatology, Lund University and Skåne University Hospital, SE-22185, Sweden, Lund
| | - Göran Rådegran
- Department of Clinical Sciences Lund, Cardiology, Lund University and the Hemodynamic Lab, the Section for Heart failure and Valvular Disease, VO Heart and Lung Medicine, Skåne University Hospital, Lund, SE-22185, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Protein Structure Bioinformatics, Lund University, Lund, SE-22185, Sweden
| | - Niels H H Heegaard
- Department of Autoimmunology & Biomarkers, Statens Serum Institut, Copenhagen S, DK-2300, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, Odense, DK-5000, Denmark.,Institute of Clinical Research, Clinical Biochemistry, University of Southern Denmark, DK-5000, Odense, Denmark
| | - Roger Hesselstrand
- Department of Clinical Sciences Lund, Rheumatology, Lund University and Skåne University Hospital, SE-22185, Sweden, Lund
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9
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Unknown Areas of Activity of Human Ribonuclease Dicer: A Putative Deoxyribonuclease Activity. Molecules 2020; 25:molecules25061414. [PMID: 32244942 PMCID: PMC7144382 DOI: 10.3390/molecules25061414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/03/2022] Open
Abstract
The Dicer ribonuclease plays a crucial role in the biogenesis of small regulatory RNAs (srRNAs) by processing long double-stranded RNAs and single-stranded hairpin RNA precursors into small interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. Dicer-generated srRNAs can control gene expression by targeting complementary transcripts and repressing their translation or inducing their cleavage. Human Dicer (hDicer) is a multidomain enzyme comprising a putative helicase domain, a DUF283 domain, platform, a PAZ domain, a connector helix, two RNase III domains (RNase IIIa and RNase IIIb) and a dsRNA-binding domain. Specific, ~20-base pair siRNA or miRNA duplexes with 2 nucleotide (nt) 3’-overhangs are generated by Dicer when an RNA substrate is anchored within the platform-PAZ-connector helix (PPC) region. However, increasing number of reports indicate that in the absence of the PAZ domain, binding of RNA substrates can occur by other Dicer domains. Interestingly, truncated variants of Dicer, lacking the PPC region, have been found to display a DNase activity. Inspired by these findings, we investigated how the lack of the PAZ domain, or the entire PPC region, would influence the cleavage activity of hDicer. Using immunopurified 3xFlag-hDicer produced in human cells and its two variants: one lacking the PAZ domain, and the other lacking the entire PPC region, we show that the PAZ domain deletion variants of hDicer are not able to process a pre-miRNA substrate, a dsRNA with 2-nt 3ʹ-overhangs, and a blunt-ended dsRNA. However, the PAZ deletion variants exhibit both RNase and DNase activity on short single-stranded RNA and DNAs, respectively. Collectively, our results indicate that when the PAZ domain is absent, other hDicer domains may contribute to substrate binding and in this case, non-canonical products can be generated.
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10
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Kong D, Guo H, Lu Z, Cui J. MicroRNA-21 Mediates the Inhibiting Effect of Praziquantel on NLRP3 Inflammasome in Schistosoma japonicum Infection. Front Vet Sci 2020; 6:517. [PMID: 32118052 PMCID: PMC7029728 DOI: 10.3389/fvets.2019.00517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/31/2019] [Indexed: 12/21/2022] Open
Abstract
Praziquantel (PZQ), a traditional helminthicide drug, has been shown to exert an anti-inflammatory effect on splenomegaly induced by schistosomiasis via regulating macrophage polarization. Meanwhile, miR-21 has been demonstrated to control macrophage polarization. However, the role of miR-21 in the regulation of macrophage polarization by PZQ in schistosomiasis is still unclear. In the present study, we found that M1-type macrophages were the predominant splenic macrophages in chronic schistosomiasis and that NLRP3 inflammasome–related molecules were upregulated. PZQ inhibited NLRP3 inflammasome in M1 macrophages and reduced the expression of miR-21. Furthermore, using the methods of quantitative real-time PCR and transfection, the downregulation of NLRP3/IL-1β by PZQ in M1 macrophages were reversed by miR-21 overexpression. These results indicated that miR-21 was involved in the inhibiting effect of PZQ on activation of NLRP3 inflammasome. Moreover, miR-21 might target Smad7 to mediate the anti-inflammatory effect of PZQ in polarized macrophages. This study provides an in-depth mechanism of PZQ in the treatment of schistosomiasis.
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Affiliation(s)
- Delong Kong
- Jiangsu Key Laboratory of Immunity and Metabolism, Laboratory of Infection and Immunity, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Hongfei Guo
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Zhongkui Lu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Jie Cui
- Department of Physiology, Xuzhou Medical University, Xuzhou, China
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11
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Zaheer U, Faheem M, Qadri I, Begum N, Yassine HM, Al Thani AA, Mathew S. Expression profile of MicroRNA: An Emerging Hallmark of Cancer. Curr Pharm Des 2020; 25:642-653. [PMID: 30914015 DOI: 10.2174/1386207322666190325122821] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/22/2019] [Indexed: 12/28/2022]
Abstract
MicroRNA (miRNAs), a class of small, endogenous non-coding RNA molecules of about 21-24 nucleotides in length, have unraveled a new modulatory network of RNAs that form an additional level of posttranscriptional gene regulation by targeting messenger RNAs (mRNAs). These miRNAs possess the ability to regulate gene expression by modulating the stability of mRNAs, controlling their translation rates, and consequently regulating protein synthesis. Substantial experimental evidence established the involvement of miRNAs in most biological processes like growth, differentiation, development, and metabolism in mammals including humans. An aberrant expression of miRNAs has been implicated in several pathologies, including cancer. The association of miRNAs with tumor growth, development, and metastasis depicts their potential as effective diagnostic and prognostic biomarkers. Furthermore, exploitation of the role of different miRNAs as oncogenes or tumor suppressors has aided in designing several miRNA-based therapeutic approaches for treating cancer patients whose clinical trials are underway. In this review, we aim to summarize the biogenesis of miRNAs and the dysregulations in these pathways that result in various pathologies and in some cases, resistance to drug treatment. We provide a detailed review of the miRNA expression signatures in different cancers along with their diagnostic and prognostic utility. Furthermore, we elaborate on the potential employment of miRNAs to enhance cancer cell apoptosis, regress tumor progression and even overcome miRNA-induced drug resistance.
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Affiliation(s)
- Uzma Zaheer
- Postgraduate Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Muhammed Faheem
- Department of Biology, King Abdul Aziz University, 80216 Jeddah, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biology, King Abdul Aziz University, 80216 Jeddah, Saudi Arabia
| | - Nargis Begum
- Postgraduate Department of Biotechnology, Jamal Mohamed College, Trichy, India
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, Doha, Qatar.,Department of Biomedical Science, College of Health Science, Qatar University, Doha, Qatar
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, Doha, Qatar
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12
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Quero L, Tiaden AN, Hanser E, Roux J, Laski A, Hall J, Kyburz D. miR-221-3p Drives the Shift of M2-Macrophages to a Pro-Inflammatory Function by Suppressing JAK3/STAT3 Activation. Front Immunol 2020; 10:3087. [PMID: 32047494 PMCID: PMC6996464 DOI: 10.3389/fimmu.2019.03087] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
Objectives: Macrophages are conventionally classified as pro-inflammatory (M1) and anti-inflammatory (M2) functional types. There is evidence for a predominance of macrophages with an inflammatory phenotype (M1) in the rheumatoid arthritis (RA) synovium. MicroRNAs (miRs) play a pivotal role in regulating the inflammatory response in innate immune cells and are found at dysregulated levels in RA patients. Here we explored miRs that tune the inflammatory function of M2-macrophages. Methods: Expression profiles of miR-221-3p and miR-155-5p were analyzed in clinical samples from RA, other inflammatory arthritis (OIA), osteoarthritis (OA), and healthy donors (HD) by qPCR. In vitro generated macrophages were transfected with miR-mimics and inhibitors. Transcriptome profiling through RNA-sequencing was performed on M2-macrophages overexpressing miR-221-3p mimic with or without LPS treatment. Secretion of IL-6, IL-10, IL-12, IL-8, and CXCL13 was measured in M1- and M2-macrophages upon TLR2/TLR3/TLR4-stimulation using ELISA. Inflammatory pathways including NF-κB, IRF3, MAPKs, and JAK3/STAT3 were evaluated by immunoblotting. Direct target interaction of miR-221-3p and predicted target sites in 3'UTR of JAK3 were examined by luciferase reporter gene assay. Results: miR-221-3p in synovial tissue and fluid was increased in RA vs. OA or OIA. Endogenous expression levels of miR-221-3p and miR-155-5p were higher in M1- than M2-macrophages derived from RA patients or HD. TLR4-stimulation of M1- and M2-macrophages resulted in downregulation of miR-221-3p, but upregulation of miR-155-5p. M2-macrophages transfected with miR-221-3p mimics secreted less IL-10 and CXCL13 but more IL-6 and IL-8, exhibited downregulation of JAK3 protein and decreased pSTAT3 activation. JAK3 was identified as new direct target of miR-221-3p in macrophages. Co-transfection of miR-221-3p/miR-155-5p mimics in M2-macrophages increased M1-specific IL-12 secretion. Conclusions: miR-221-3p acts as a regulator of TLR4-induced inflammatory M2-macrophage function by directly targeting JAK3. Dysregulated miR-221-3p expression, as seen in synovium of RA patients, leads to a diminished anti-inflammatory response and drives M2-macrophages to exhibit a M1-cytokine profile.
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Affiliation(s)
- Lilian Quero
- Experimental Rheumatology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - André N Tiaden
- Experimental Rheumatology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Edveena Hanser
- Experimental Rheumatology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Julien Roux
- Bioinformatics Core Facility, Department of Biomedicine, University of Basel, Basel, Switzerland.,Bioinformatic Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Artur Laski
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Diego Kyburz
- Experimental Rheumatology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
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13
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Lu Q, Wu R, Zhao M, Garcia-Gomez A, Ballestar E. miRNAs as Therapeutic Targets in Inflammatory Disease. Trends Pharmacol Sci 2019; 40:853-865. [PMID: 31662207 DOI: 10.1016/j.tips.2019.09.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/30/2022]
Abstract
In the past decade, we have witnessed considerable developments in understanding the roles and functions of miRNAs. In parallel, the identification of alterations in miRNA expression in inflammatory disease indicates their potential as therapeutic targets. Pharmacological treatments targeting abnormally expressed miRNAs for inflammatory diseases are not yet in clinical practice; however, some small compounds and nucleic acids targeting miRNAs have shown promise in preclinical development. Here, we focus on recent advances in understanding miRNA deregulation in inflammatory diseases and provide an overview of the current development of miRNA-based therapeutics in these diseases with an emphasis on newly discovered miRNA therapeutic targets.
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Affiliation(s)
- Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Ruifang Wu
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Antonio Garcia-Gomez
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain.
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14
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Jiang Q, Zhao H, Li R, Zhang Y, Liu Y, Wang J, Wang X, Ju Z, Liu W, Hou M, Huang J. In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins. BMC Genet 2019; 20:46. [PMID: 31096910 PMCID: PMC6524300 DOI: 10.1186/s12863-019-0749-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/02/2019] [Indexed: 02/02/2023] Open
Abstract
Background Single-nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) and their target binding sites affect miRNA function and are involved in biological processes and diseases, including bovine mastitis, a frequent inflammatory disease. Our previous study has shown that bta-miR-2899 is significantly upregulated in the mammary gland tissue of mastitis-infected cow than that of healthy cows. Results In the present study, we used a customized miRNAQTLsnp software and identified 5252 SNPs in 691 bovine pre-miRNAs, which are also located within the quantitative trait loci (QTLs) that are associated with mastitis and udder conformation-related traits. Using luciferase assay in the bovine mammary epithelial cells, we confirmed a candidate SNP (rs109462250, g. 42,198,087 G > A) in the seed region of bta-miR-2899 located in the somatic cell score (SCS)-related QTL (Chr.18: 33.9–43.9 Mbp), which affected the interaction of bta-miR-2899 and its putative target Spi-1 proto-oncogene (SPI1), a pivotal regulator in the innate and adaptive immune systems. Quantitative real-time polymerase chain reaction results showed that the relative expression of SPI1 in the mammary gland of AA genotype cows was significantly higher than that of GG genotype cows. The SNP genotypes were associated with SCS in Holstein cows. Conclusions Altogether, miRNA-related SNPs, which influence the susceptibility to mastitis, are one of the plausible mechanisms underlying mastitis via modulating the interaction of miRNAs and immune-related genes. These miRNA-QTL-SNPs, such as the SNP (rs109462250) of bta-miR-2899 may have implication for the mastitis resistance breeding program in Holstein cattle. Electronic supplementary material The online version of this article (10.1186/s12863-019-0749-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Han Zhao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China.,College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Rongling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Yaran Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Yong Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Jinpeng Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Wenhao Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Minghai Hou
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, 250131, Shandong, People's Republic of China. .,College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, China.
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15
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Mukhopadhyay U, Chanda S, Patra U, Mukherjee A, Rana S, Mukherjee A, Chawla-Sarkar M. Synchronized Orchestration of miR-99b and let-7g Positively Regulates Rotavirus Infection by Modulating Autophagy. Sci Rep 2019; 9:1318. [PMID: 30718795 PMCID: PMC6362297 DOI: 10.1038/s41598-018-38473-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/27/2018] [Indexed: 12/18/2022] Open
Abstract
Rotavirus (RV), the major etiological agent of viral gastroenteritis in young children, kills over 200 thousand infants each year. In spite of available vaccines, rotaviral diarrhoea is still a major problem in developing countries of Asia and Africa. Therefore, the studies on RV infection and host antiviral responses are warranted. The active correlation between virus infection and activation of autophagy machinery and positive influence of autophagy on RV replication have been documented recently. Previous study from our group showed dysregulation of several cellular miRNAs during RV infection, though their significance remained largely unknown. Since cellular microRNAs (miRNAs) have been implicated in the control of several fundamental biological processes including stress response and autophagy, we focused on two miRNAs, miR-99b and let-7g, and analyzed their function to gain insight into the miRNA-autophagy crosstalk during RV infection. This study shows that RV suppresses let-7g expression but enhances miR-99b that in turn augment major autophagy regulators. Ectopic expression of let-7g and knockdown of miR-99b resulted in inhibition of autophagy, hence, reduction of RV replication. Overall, our study highlights new mechanistic insights for understanding the role of miRNAs in modulating RV infection and possibility of using RNA interference as an antiviral therapeutic target.
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Affiliation(s)
- Urbi Mukhopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Shampa Chanda
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Santanu Rana
- Department of Zoology, University of Calcutta, Kolkata, WB, India
| | - Anupam Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
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16
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Liu JL, Li J, Xu JJ, Xiao F, Cui PL, Qiao ZG, Chen XD, Tao WD, Zhang XL. MiR-144 Inhibits Tumor Growth and Metastasis in Osteosarcoma via Dual-suppressing RhoA/ROCK1 Signaling Pathway. Mol Pharmacol 2019; 95:451-461. [PMID: 30674565 DOI: 10.1124/mol.118.114207] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/12/2019] [Indexed: 12/15/2022] Open
Abstract
Several microRNAs (miRNAs) have been found expressed differentially in osteosarcoma (OS), so they may function in the onset and progression of OS. In this study, we found that miR-144 significantly suppresses osteosarcoma cell proliferation, migration, and invasion ability in vitro and inhibited tumor growth and metastasis in vivo. Mechanically, we demonstrated that Ras homolog family member A (RhoA) and its pivotal downstream effector Rho-associated, coiled-coil-containing protein kinase 1 (ROCK1) were direct targets of miR-144. Moreover, the negative correlation between down-regulated miR-144 and up-regulated ROCK1/RhoA was verified in both OS cell lines and clinical patients' specimens. Functionally, RhoA with or without ROCK1 co-overexpression resulted a rescue phenotype on miR-144 inhibited cell growth, migration, and invasion abilities whereas individual overexpression of ROCK1 had no statistical significance compared with controls in miR-144-transfected SAOS2 and U2-OS cells. Taken together, this study demonstrates that miR-144 inhibited tumor growth and metastasis in OS via dual-suppressing of RhoA and ROCK1, which could be a new therapeutic approach for the treatment of OS.
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Affiliation(s)
- Jin Long Liu
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Jing Li
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Jia Jia Xu
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Fei Xiao
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Peng Lei Cui
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Zhi Guang Qiao
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Xiao Dong Chen
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Wei Dong Tao
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
| | - Xiao Ling Zhang
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) (J.L.L., J.J.X., F.X., P.L.C., X.D.C., W.D.T., X.L.Z.); Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine (J.L.); Surgical Department, Kunshan Traditional Medicine Hospital (W.D.T.); and Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (Z.G.Q.), Shanghai, People's Republic of China
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17
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Zhou ZB, Huang GX, Fu Q, Han B, Lu JJ, Chen AM, Zhu L. circRNA.33186 Contributes to the Pathogenesis of Osteoarthritis by Sponging miR-127-5p. Mol Ther 2019; 27:531-541. [PMID: 30692016 DOI: 10.1016/j.ymthe.2019.01.006] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/16/2018] [Accepted: 01/08/2019] [Indexed: 02/06/2023] Open
Abstract
Osteoarthritis (OA), the most prevalent age-related joint disorder, is characterized by chronic inflammation, progressive articular cartilage destruction, and subchondral bone sclerosis. Accumulating evidences indicate that circular RNAs (circRNAs) play a critical role in various diseases, but the function of circRNAs in OA remains largely unknown. Here we showed that circRNA.33186 was significantly upregulated in IL-1β)-treated chondrocytes and in cartilage tissues of a destabilized medial meniscus (DMM)-induced OA mouse model. Knockdown of circRNA.33186 increased anabolic factor (type II collagen) expression and decreased catabolic factor (MMP-13) expression. Knockdown of circRNA.33186 also promoted proliferation and inhibited apoptosis in IL-1β-treated chondrocytes. Silencing of circRNA.33186 in vivo markedly alleviated DMM-induced OA. Mechanistic study showed that circRNA.33186 directly binds to and inhibits miR-127-5p, thereby increasing MMP-13 expression, and contributes to OA pathogenesis. Taken together, our findings demonstrated a fundamental role of circRNA.33186 in OA progression and provide a potential drug target in OA therapy.
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Affiliation(s)
- Zhi-Bin Zhou
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Gao-Xiang Huang
- Department of Pathology, No.924 (No.181) Hospital of People's Liberation Army, Guilin, Guangxi, 541002, China
| | - Qiang Fu
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Bin Han
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Jia-Jia Lu
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Ai-Min Chen
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Lei Zhu
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
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18
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Yu J, Peng J, Luan Z, Zheng F, Su W. MicroRNAs as a Novel Tool in the Diagnosis of Liver Lipid Dysregulation and Fatty Liver Disease. Molecules 2019; 24:molecules24020230. [PMID: 30634538 PMCID: PMC6358728 DOI: 10.3390/molecules24020230] [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: 11/11/2018] [Revised: 12/23/2018] [Accepted: 12/24/2018] [Indexed: 02/07/2023] Open
Abstract
In recent years, metabolic disorder, especially fatty liver disease, has been considered a major challenge to global health. The attention of researchers focused on expanding knowledge of the regulation mechanism behind these diseases and towards the new diagnostics tools and treatments. The pathophysiology of the fatty liver disease is undoubtedly complex. Abnormal hepatic lipid accumulation is a major symptom of most metabolic diseases. Therefore, the identification of novel regulation factors of lipid metabolism is important and meaningful. As a new diagnostic tool, the function of microRNAs during fatty liver disease has recently come into notice in biological research. Accumulating evidence supports the influence of miRNAs in lipid metabolism. In this review, we discuss the potential role of miRNAs in liver lipid metabolism and the pathogenesis of fatty liver disease.
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Affiliation(s)
- Jingwei Yu
- Shenzhen University Medical Center, Shenzhen University Health Science Center, Shenzhen 518060, China.
- Department of Biology, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Jun Peng
- Shenzhen University Medical Center, Shenzhen University Health Science Center, Shenzhen 518060, China.
| | - Zhilin Luan
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, China.
| | - Feng Zheng
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, China.
| | - Wen Su
- Shenzhen University Medical Center, Shenzhen University Health Science Center, Shenzhen 518060, China.
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19
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Ma J, Li Y, Wu M, Zhang C, Che Y, Li W, Li X. Serum immune responses in common carp (Cyprinus carpio L.) to paraquat exposure: The traditional parameters and circulating microRNAs. FISH & SHELLFISH IMMUNOLOGY 2018; 76:133-142. [PMID: 29499338 DOI: 10.1016/j.fsi.2018.02.046] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/23/2018] [Accepted: 02/25/2018] [Indexed: 06/08/2023]
Abstract
Paraquat (PQ) is a herbicide used worldwide, and it was shown to be a high-risk compound to aquatic organisms. This study was conducted to investigate the effects of PQ on traditional serum parameters and circulating microRNAs (miRNAs) in common carp to further elucidate the mechanism of PQ toxicity in fish. In the current study, a subacute toxicity test of common carp exposed to PQ at 1.596 and 3.192 mg/L for 7 d was conducted under laboratory conditions. The results showed that PQ exposure generally reduced the levels of T-AOC, SOD, CAT, and GST, but significantly increased MDA levels in the serum, indicating that PQ exposure induces oxidative stress and lipid peroxidation in the fish. The results of biochemical assays showed that PQ exposure not only significantly altered the activities of LDH, AST, ALT, ACP, AKP, and lysozyme and the contents of IgM and complement 3 but also promoted the expression of pro-inflammatory cytokines, including IFN-γ, IL-1β, IL-6, IL-8, and TNF-α. Additionally, PQ inhibited the levels of the anti-inflammatory cytokines IL-10 and TGF-β, suggesting that PQ exposure may cause fish tissue injury and promote immune inflammatory responses. Furthermore, we found that serum circulating miRNAs, such as ccr-mir-122, ccr-mir-125b, ccr-mir-146a, and ccr-mir-155, were generally promoted in fish following PQ exposure. Based on our results and reports on miRNA-based diagnosis of tissue damage and inflammatory responses in mammals, we suggest that serum ccr-mir-122, ccr-mir-125b, ccr-mir-146a, and ccr-mir-155 could be new biomarkers of PQ toxicity in fish.
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Affiliation(s)
- Junguo Ma
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Yuanyuan Li
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Mengli Wu
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Can Zhang
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Yuqing Che
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Weiguo Li
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xiaoyu Li
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China.
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20
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Su Q, Kumar V, Sud N, Mahato RI. MicroRNAs in the pathogenesis and treatment of progressive liver injury in NAFLD and liver fibrosis. Adv Drug Deliv Rev 2018; 129:54-63. [PMID: 29391222 DOI: 10.1016/j.addr.2018.01.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/05/2018] [Accepted: 01/13/2018] [Indexed: 02/06/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) increases the risk of various liver injuries, ranging from simple steatosis to non-alcoholic steatohepatitis (NASH), fibrosis and cirrhosis, and ultimately hepatocellular carcinoma (HCC). Ample evidence has suggested that aberrant expression of microRNAs (miRNAs) is functionally involved in the activation of cellular stress, inflammation and fibrogenesis in hepatic cells, including hepatocytes, Kupffer and hepatic stellate cells (HSCs), at different pathological stages of NAFLD and liver fibrosis. Here, we overview recent findings on the potential role of miRNAs in the pathogenesis of NAFLD, including lipotoxicity, oxidative stress, metabolic inflammation and fibrogenesis. We critically assess the literatures on both human subjects and animal models of NAFLD and liver fibrosis with miRNA dysregulation and their mechanisms of actions in liver damage. We further highlight the potential use of miRNA mimics or antimiRNAs as therapeutic approaches for the prevention and treatment of NAFLD and liver fibrosis.
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Affiliation(s)
- Qiaozhu Su
- Department of Nutrition and Health Sciences, University of Nebraska, Lincoln, NE 68583, USA.
| | - Virender Kumar
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Neetu Sud
- Department of Nutrition and Health Sciences, University of Nebraska, Lincoln, NE 68583, USA
| | - Ram I Mahato
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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21
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Bai S, Xu B, Guo Y, Qiu J, Yu W, Xie G. High-Discrimination Factor Nanosensor Based on Tetrahedral DNA Nanostructures and Gold Nanoparticles for Detection of MiRNA-21 in Live Cells. Theranostics 2018; 8:2424-2434. [PMID: 29721089 PMCID: PMC5928899 DOI: 10.7150/thno.23852] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/25/2018] [Indexed: 12/28/2022] Open
Abstract
While detection of microRNA with or without signal amplification is highly informative, nanosensors with high specificity for cell-specific RNA detection are rare. Methods: In this study, a tetrahedral DNA nanostructure (TDN) with a specific function was combined with gold nanoparticles (Au-NP) possessing fluorescence quenching effects and a large surface area to fabricate a fluorescence resonance energy transfer based nanosensor (Au-TDNN). The presence of miR-21 (target) can separate the fluorescent dye-labeled detection probe on Au-TDNNs from Au-NPs, which separates the donor and acceptor, thus inducing an intensive fluorescence signal. High specificity for discerning point mutation targets was achieved by rationally designing the nucleic acid strand displacement reaction to occur spontaneously with ΔG0 ≈ 0 based on thermodynamic parameters; under this condition, slight thermodynamic changes caused by base mismatch exert significant effects on hybridization yield. Results: Chemically synthesized DNA of three single-base-changed analogues of target, let-7d, and miR-200b were tested. A discrimination factor (DF) of 15.4 was produced by the expected detection probe on Au-NPs for proximal single-base mismatch. As the control group, the DF produced by an ordinary detection probe on Au-NPs only reached 2.4. The feasibility of the proposed strategy was also confirmed using hepatocyte cancer cells (HepG2). Conclusion: This improved nanosensor opens a new avenue for the specific and easy detection of microRNA in live cells.
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22
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Wallner FK, Hultquist Hopkins M, Woodworth N, Lindvall Bark T, Olofsson P, Tilevik A. Correlation and cluster analysis of immunomodulatory drugs based on cytokine profiles. Pharmacol Res 2017; 128:244-251. [PMID: 29079427 DOI: 10.1016/j.phrs.2017.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 01/14/2023]
Abstract
Drug discovery is a constant struggle to overcome hurdles posed by the complexity of biological systems. One of these hurdles is to find and understand the molecular target and the biological mechanism of action. Although the molecular target has been determined, the true biological effect may be unforeseen also for well-established drugs. Hence, there is a need for novel ways to increase the knowledge of the biological effects of drugs in the developmental process. In this study, we have determined cytokine profiles for 26 non-biological immunomodulatory drugs or drug candidates and used these profiles to cluster the compounds according to their effect in a preclinical ex vivo culture model of arthritis. This allows for prediction of functions and drug target of a novel drug candidate based on profiles obtained in this study. Results from the study showed that the JAK inhibitors tofacitinib and ruxolitinib formed a robust cluster and were found to have a distinct cytokine profile compared to the other drugs. Another robust cluster included the calcineurin inhibitors cyclosporine A and tacrolimus and the protein kinase inhibitors fostamatinib disodium and sotrastaurin acetate, which caused a strong overall inhibition of the cytokine production. The results of this methodology indicate that cytokine profiles can be used to provide a fingerprint-like identification of a drug as a tool to benchmark novel drugs and to improve descriptions of mode of action.
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Affiliation(s)
- Fredrik K Wallner
- Redoxis AB/ProNoxis AB, Medicon Village, 223 81, Lund, Sweden; School of Bioscience, University of Skövde, 541 28, Skövde, Sweden; Wallner Medicinal Chemistry AB, Frimästareg 6, 415 07, Göteborg, Sweden
| | | | - Nina Woodworth
- Redoxis AB/ProNoxis AB, Medicon Village, 223 81, Lund, Sweden
| | | | - Peter Olofsson
- Redoxis AB/ProNoxis AB, Medicon Village, 223 81, Lund, Sweden
| | - Andreas Tilevik
- School of Bioscience, University of Skövde, 541 28, Skövde, Sweden.
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23
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Schmieder S, Weißpflog J, Danz N, Hübner M, Kreth S, Klotzbach U, Sonntag F. Ultrasensitive SPR detection of miRNA-93 using antibody-enhanced and enzymatic signal amplification. Eng Life Sci 2017; 17:1264-1270. [PMID: 32624754 DOI: 10.1002/elsc.201700104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/08/2017] [Accepted: 08/22/2017] [Indexed: 01/01/2023] Open
Abstract
MiRNAs are endogenous noncoding RNA molecules. They play important gene-regulatory roles by binding to the mRNA of target genes thereby leading to either transcript degradation or translational repression. In virtually all diseases, distinct alterations of miRNA expression profiles have been found thus suggesting miRNAs as interesting biomarkers. Here, we present an SPR biosensor that utilizes disposable, injection-molded sensor chip/microfluidic hybrids combined with a lateral imaging optical system for parallel analysis of three one-dimensional spot arrays to detect miRNA-93. To increase the sensitivity of the biosensor we used two different amplification strategies. By adding an RNA-DNA-hybrid antibody for primary signal amplification, a limit of detection of 10 pmol/L was achieved. Based on that method we demonstrate the detection of miRNA-93 in total RNA lysate from HEK-293 cells. Utilizing an enzymatic signal amplification with Poly(A) polymerase, the sensitivity could be increased even further leading to a limit of detection of 1 fmol/L.
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Affiliation(s)
- Stefan Schmieder
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
| | - Janek Weißpflog
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
| | - Norbert Danz
- Microoptical Systems Fraunhofer Institute for Applied Optics and Precision Engineering IOF Jena Germany
| | - Max Hübner
- Walter-Brendel-Centre for Experimental Medicine Ludwig-Maximilians-University Munich Germany.,Department of Anesthesiology Hospital of the Ludwig-Maximilians-University Munich Germany
| | - Simone Kreth
- Walter-Brendel-Centre for Experimental Medicine Ludwig-Maximilians-University Munich Germany.,Department of Anesthesiology Hospital of the Ludwig-Maximilians-University Munich Germany
| | - Udo Klotzbach
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
| | - Frank Sonntag
- Micro- and Biosystems Engineering Fraunhofer Institute for Material and Beam Technology IWS Dresden Germany
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24
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Promiscuous Effects of Some Phenolic Natural Products on Inflammation at Least in Part Arise from Their Ability to Modulate the Expression of Global Regulators, Namely microRNAs. Molecules 2016; 21:molecules21091263. [PMID: 27657035 PMCID: PMC6272860 DOI: 10.3390/molecules21091263] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 12/13/2022] Open
Abstract
Recent years have seen the exploration of a puzzling number of compounds found in human diet that could be of interest for prevention or treatment of various pathologies. Although many of these natural products (NPs) have long been used as remedies, their molecular effects still remain elusive. With the advent of biotechnology revolution, NP studies turned from chemistry and biochemistry toward global analysis of gene expression. Hope is to use genetics to identify groups of patient for whom certain NPs or their derivatives may offer new preventive or therapeutic treatments. Recently, microRNAs have gained the statute of global regulators controlling cell homeostasis by regulating gene expression through genetic and epigenetic regulatory loops. Realization that certain plant polyphenols can modify microRNA expression and thus impact gene expression globally, initiated new, mainly in vitro studies, in particular to determine phytochemicals effects on inflammatory response, whose exacerbation has been linked to several disorders including cancer, auto-immune, metabolic, cardiovascular and neuro-inflammatory diseases. However, very few mechanistic insights have been provided, given the complexity of genetic regulatory networks implicated. In this review, we will concentrate on data showing the potential interest of some plant polyphenols in manipulating the expression of pro- and anti-inflammatory microRNAs in pathological conditions.
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25
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Primary Sjögren’s syndrome: clinical phenotypes, outcome and the development of biomarkers. Immunol Res 2016; 65:331-344. [DOI: 10.1007/s12026-016-8844-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Goules AV, Tzioufas AG. Primary Sjӧgren's syndrome: Clinical phenotypes, outcome and the development of biomarkers. Autoimmun Rev 2016; 15:695-703. [DOI: 10.1016/j.autrev.2016.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 02/29/2016] [Indexed: 11/25/2022]
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27
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Luo Z, Liu M, Zhang H, Xia Y. Association of circulating miR-125b and survival in patients with osteosarcoma-A single center experience. J Bone Oncol 2016; 5:167-172. [PMID: 28008378 PMCID: PMC5154701 DOI: 10.1016/j.jbo.2016.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 06/12/2016] [Accepted: 06/15/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND It is known that miRNAs play various roles in malignant tumors. This study is designed to investigate whether miR-125b levels can be used to predict the clinical response of patients with osteosarcoma (OS) to cisplatin-based chemotherapy. METHODS From January 2010 to July 2015, 82 patients with resectable OS and 56 patients with unresectable OS were enrolled. Blood samples were collected and quantitative real-time PCR was applied to determine miR-125b expression. Clinical data was collected through medical records, and patients were treated according to National Comprehensive Cancer Network guidelines on OS. RESULTS Our study found that patients with low miR-125b expression had shorter disease-free survival (p<0.001) in the OS group, which was verified by Kaplan-Meier analysis and univariate and multivariate Cox analyses (p<0.001). For patients with unresectable OS, low miR-125b expression was found to be associated with advanced tumor stages (p=0.006). No complete remission was observed, and there were 13 patients with partial remission, 21 with stable disease, and 22 with disease progression. Negative correlation was found between miR-125b expression and response to chemotherapy (p<0.001, r=-0.606). Furthermore, ROC analysis indicated that miR-125b at the cut point of 0.61 yielded an area under the ROC curve of 0.793 (p<0.001, 95% CI: 0.664-0.890) in distinguishing chemotherapy-resistant OS from chemotherapy-sensitive OS, with sensitivity and specificity at 76.9% and 79.1%, respectively. Kaplan-Meier analysis and univariate and multivariate Cox analyses showed that patients with low miR-125b expression suffered shorter overall survival (p=0.014, p=0.024, and p=0.049, respectively). CONCLUSION Down-regulation of circulating miR-125b might have the potential to predict cisplatin-based chemotherapy resistance and poor prognosis in OS.
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Affiliation(s)
- Zhiqiang Luo
- Department of Orthopedics, The Second Clinical Hospital of Lanzhou University, Lanzhou, China
| | - Minglu Liu
- The Second Clinical Hospital of the National Defense University of the PLA, Beijing, China
| | - Haihong Zhang
- Department of Orthopedics, The Second Clinical Hospital of Lanzhou University, Lanzhou, China
| | - Yayi Xia
- Department of Orthopedics, The Second Clinical Hospital of Lanzhou University, Lanzhou, China
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28
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Development of a Low-Cost Stem-Loop Real-Time Quantification PCR Technique for EBV miRNA Expression Analysis. Mol Biotechnol 2016; 58:540-50. [DOI: 10.1007/s12033-016-9951-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Abstract
MicroRNAs (miRNAs) are highly conserved, small, 18-25 nucleotide, non-coding RNAs that regulate gene expression at the post-transcriptional level. Each miRNA can regulate hundreds of target genes, and vice versa each target gene can be regulated by numerous miRNAs, suggesting a very complex network and explaining how miRNAs play pivotal roles in fine-tuning essentially all biological processes in all cell types in the liver. Here, we summarize the current knowledge on the role of miRNAs in the pathogenesis and diagnosis of nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) with an outlook to the broader aspects of metabolic syndrome. Furthermore, we discuss the role of miRNAs as potential biomarkers and therapeutic targets in NAFLD/NASH.
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Affiliation(s)
- Gyongyi Szabo
- Department of Medicine, University of Massachusetts Medical School, LRB215, 364 Plantation Street, Worcester, MA, 01605, USA.
| | - Timea Csak
- Department of Medicine, University of Massachusetts Medical School, LRB215, 364 Plantation Street, Worcester, MA, 01605, USA
- Brookdale University Hospital and Medical Center, 1 Brookdale Plaza, Brooklyn, NY, 11212, USA
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30
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Rivera A, Barr T, Rais M, Engelmann F, Messaoudi I. microRNAs Regulate Host Immune Response and Pathogenesis During Influenza Infection in Rhesus Macaques. Viral Immunol 2016; 29:212-27. [PMID: 27008411 DOI: 10.1089/vim.2015.0074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
microRNAs (miRNAs) are small noncoding RNAs that are key regulators of biological processes, including the immune response to viral infections. Differential expression levels of cellular miRNAs and their predicted targets have been described in the lungs of H1N1-infected BALB/c mice, the lungs of H5N1 influenza-infected cynomolgus macaques, and in peripheral blood mononuclear cells (PBMCs) of critically ill patients infected with 2009 pandemic H1N1. However, a longitudinal analysis of changes in the expression of miRNAs and their targets during influenza infection and how they relate to viral replication and host response has yet to be carried out. In the present study, we conducted a comprehensive analysis of innate and adaptive immune responses as well as the expression of several miRNAs and their validated targets in both peripheral blood and bronchoalveolar lavage (BAL) collected from rhesus macaques over the course of infection with the 2009 H1N1 virus A/Mexico/4108/2009 (MEX4108). We describe a distinct set of differentially expressed miRNAs in BAL and PBMCs, which regulate the expression of genes involved in inflammation, immune response, and regulation of cell cycle and apoptosis.
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Affiliation(s)
- Andrea Rivera
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Tasha Barr
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Maham Rais
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Flora Engelmann
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California
| | - Ilhem Messaoudi
- 1 Division of Biomedical Sciences, University of California , Riverside, Riverside, California.,2 Oregon Primate Research Center , Beaverton, Oregon
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31
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Yazdani Y, Farazmandfar T, Azadeh H, Zekavatian Z. The prognostic effect of PTEN expression status in colorectal cancer development and evaluation of factors affecting it: miR-21 and promoter methylation. J Biomed Sci 2016; 23:9. [PMID: 26787105 PMCID: PMC4717643 DOI: 10.1186/s12929-016-0228-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 01/12/2016] [Indexed: 02/07/2023] Open
Abstract
Background PTEN is a tumor suppressor gene which is involved in cellular proliferation, differentiation, and apoptosis. Loss or down-regulation of PTEN plays an important role in human cancers development. In this study, we investigated the effect of miR-21 and promoter methylation on the PTEN expression status in CRC tissues and analyzed association of the PTEN expression status with clinicopathological features in patients with CRC. Results The PTEN expression was positively detected in 67.2 % CRC tissues and all adjacent non-cancerous samples. PTEN mRNA level was negatively correlated with miR-21 level (r = −0.595, P < 0.001). PTEN expression was also correlated directly with the PTEN mRNA level (r = 0.583, P < 0.001) and conversely with miR-21 level (r = −0.632, P < 0.001). PTEN Promoter methylation was significantly associated with PTEN expression status (p = 0.013). PTEN expression was negatively associated with tumor size (p = 0.007) and advanced tumor stage (P = 0.011). Multivariate analysis indicated that tumor stage, tumor differentiation and PTEN expression status were independent prognostic factors for overall carcinoma in CRC patients (P < 0.05). The Kaplan-Meier curve indicated a negative correlation between PTEN expression levels and survival of CRC patients (P = 0.013). Conclusions This study suggests a high frequency of miR-21 overexpression and aberrant promoter methylation in down-regulation of PTEN expression in colorectal carcinoma. Loss of PTEN may be a prognostic factor for patients with CRC.
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Affiliation(s)
- Yaghoub Yazdani
- Infectious Diseases Research Center and Laboratory Science Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Touraj Farazmandfar
- Infectious Diseases Research Center and Laboratory Science Research Center, Golestan University of Medical Sciences, Gorgan, Iran. .,Student Research Committee, Golestan University of Medical Sciences, P.O. Box: 4934174611, Gorgan, Iran.
| | - Hossein Azadeh
- Department of Internal Medicine, Mazandaran University of Medical sciences, Sari, Iran.
| | - Zeinab Zekavatian
- Department of Genetics, Tehran Medical Sciences branch, Islamic Azad University, Tehran, Iran.
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32
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Yu L, Shao C, Ye X, Meng Y, Zhou Y, Chen M. miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining. Sci Rep 2016; 6:18901. [PMID: 26732371 PMCID: PMC4702050 DOI: 10.1038/srep18901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/27/2015] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA-target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.
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Affiliation(s)
- Lan Yu
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Xinghuo Ye
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, P.R. China
| | - Yincong Zhou
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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33
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Samadi AK, Bilsland A, Georgakilas AG, Amedei A, Amin A, Bishayee A, Azmi AS, Lokeshwar BL, Grue B, Panis C, Boosani CS, Poudyal D, Stafforini DM, Bhakta D, Niccolai E, Guha G, Vasantha Rupasinghe HP, Fujii H, Honoki K, Mehta K, Aquilano K, Lowe L, Hofseth LJ, Ricciardiello L, Ciriolo MR, Singh N, Whelan RL, Chaturvedi R, Ashraf SS, Shantha Kumara HMC, Nowsheen S, Mohammed SI, Keith WN, Helferich WG, Yang X. A multi-targeted approach to suppress tumor-promoting inflammation. Semin Cancer Biol 2015; 35 Suppl:S151-S184. [PMID: 25951989 PMCID: PMC4635070 DOI: 10.1016/j.semcancer.2015.03.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/15/2022]
Abstract
Cancers harbor significant genetic heterogeneity and patterns of relapse following many therapies are due to evolved resistance to treatment. While efforts have been made to combine targeted therapies, significant levels of toxicity have stymied efforts to effectively treat cancer with multi-drug combinations using currently approved therapeutics. We discuss the relationship between tumor-promoting inflammation and cancer as part of a larger effort to develop a broad-spectrum therapeutic approach aimed at a wide range of targets to address this heterogeneity. Specifically, macrophage migration inhibitory factor, cyclooxygenase-2, transcription factor nuclear factor-κB, tumor necrosis factor alpha, inducible nitric oxide synthase, protein kinase B, and CXC chemokines are reviewed as important antiinflammatory targets while curcumin, resveratrol, epigallocatechin gallate, genistein, lycopene, and anthocyanins are reviewed as low-cost, low toxicity means by which these targets might all be reached simultaneously. Future translational work will need to assess the resulting synergies of rationally designed antiinflammatory mixtures (employing low-toxicity constituents), and then combine this with similar approaches targeting the most important pathways across the range of cancer hallmark phenotypes.
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Affiliation(s)
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematics and Physical Sciences, National Technical University of Athens, Athens, Greece
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - Anupam Bishayee
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin Health Sciences Institute, Miami, FL, United States
| | - Asfar S Azmi
- Department of Pathology, Wayne State Univeristy, Karmanos Cancer Center, Detroit, MI, USA
| | - Bal L Lokeshwar
- Department of Urology, University of Miami, Miller School of Medicine, Miami, FL, United States; Miami Veterans Administration Medical Center, Miami, FL, United States
| | - Brendan Grue
- Department of Environmental Science, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Carolina Panis
- Laboratory of Inflammatory Mediators, State University of West Paraná, UNIOESTE, Paraná, Brazil
| | - Chandra S Boosani
- Department of BioMedical Sciences, School of Medicine, Creighton University, Omaha, NE, United States
| | - Deepak Poudyal
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, United States
| | - Diana M Stafforini
- Huntsman Cancer Institute and Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States
| | - Dipita Bhakta
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - Gunjan Guha
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - H P Vasantha Rupasinghe
- Department of Environmental Sciences, Faculty of Agriculture and Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hiromasa Fujii
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Kanya Honoki
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Kapil Mehta
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Katia Aquilano
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Leroy Lowe
- Getting to Know Cancer, Truro, Nova Scotia, Canada.
| | - Lorne J Hofseth
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, United States
| | - Luigi Ricciardiello
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | - Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Richard L Whelan
- Department of Surgery, St. Luke's Roosevelt Hospital, New York, NY, United States
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - H M C Shantha Kumara
- Department of Surgery, St. Luke's Roosevelt Hospital, New York, NY, United States
| | - Somaira Nowsheen
- Medical Scientist Training Program, Mayo Graduate School, Mayo Medical School, Mayo Clinic, Rochester, MN, United States
| | - Sulma I Mohammed
- Department of Comparative Pathobiology, Purdue University Center for Cancer Research, West Lafayette, IN, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | | | - Xujuan Yang
- University of Illinois at Urbana Champaign, Champaign, IL, United States
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Abstract
MicroRNAs (miRNAs) are differentially regulated in healthy, activated, inflamed, neoplastic, or otherwise pathological cells and tissues. While their main functions are executed intracellularly, many miRNAs can reproducibly be detected extracellularly in plasma and serum. This circulating, extracellular miRNA is protected against degradation by complexation with carrier proteins and/or by being enclosed in subcellular membrane vesicles. This, together with their tissue- and disease-specific expression, has fuelled the interest in using circulating microRNA profiles as harbingers of disease, i.e., as diagnostic analytes and as clues to dysregulated pathways in disease. Many studies show that inflammation and immune dysregulation, e.g., in autoimmune diseases, are associated with distinct miRNA expression changes in targeted tissues and in innate and adaptive immunity cells such as lymphocytes, natural killer cells, neutrophil granulocytes, and monocyte-macrophages. Exploratory studies (only validated in a few cases) also show that specific profiles of circulating miRNAs are associated with different systemic autoimmune diseases including systemic lupus erythematosus (SLE), systemic sclerosis, and rheumatoid arthritis. Even though the link between cellular alterations and extracellular profiles is still unpredictable, the data suggest that circulating miRNAs in autoimmunity may become diagnostically useful. Here, we review important circulating miRNAs in animal models of inflammation and in systemic autoimmunity and summarize some proposed functions of miRNAs in immune regulation and dysregulation. We conclude that the studies suggest new hypotheses and additional experiments, and that further diagnostic development is highly dependent on analytical method development and on obtaining sufficient numbers of uniformly processed samples from clinically well-characterized patients and controls.
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35
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Liu F, Weng X, Lin P, Zheng C, Xu H, Liu X, Ye H, Li X. Duhuo Jisheng decoction inhibits endoplasmic reticulum stress in chondrocytes induced by tunicamycin through the downregulation of miR-34a. Int J Mol Med 2015; 36:1311-8. [PMID: 26329269 DOI: 10.3892/ijmm.2015.2331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/13/2015] [Indexed: 11/05/2022] Open
Abstract
Our previous study showed that Duhuo Jisheng decoction (DHJSD) inhibited chondrocyte apoptosis by the mitochondria-dependent signaling pathway. Endoplasmic reticulum (ER) stress is upstream of the mitochondria-dependent signaling pathway and has been shown to promote chondrocyte apoptosis that occurs in osteoarthritis (OA). The present study aimed to evaluate whether DHJSD inhibits the chondrocyte apoptosis by regulating ER stress. DHJSD enhanced the viability of tunicamycin (TM)‑exposed chondrocytes, a model of ER stress-induced apoptosis, in a dose‑ and time‑dependent manner, as shown by MTT assay. The present results showed that DHJSD and sodium 4-phenylbutyrate (PBA), an ER stress inhibitor, reduced TM‑induced chondrocyte apoptosis by 4',6-diamidino‑2-phenylindole staining. To gain insight into the mechanisms of DHJSD that are responsible for enhancing the viability and inhibiting TM‑induced chondrocyte apoptosis, the associated mRNA expressions and protein levels were detected by reverse transcription‑polymerase chain reaction (RT‑PCR) and western blot analysis, respectively. The results showed that the expression levels of Xbp1, Xbp1s and Bcl‑2 were increased, and the expression levels of Bip, Atf4, Chop, Bax, caspase‑9 and ‑3 were decreased in the TM‑exposed chondrocytes treated with DHJSD or PBA compared with that in the TM‑exposed chondrocytes. To identify the possible mechanisms, the expression of miR‑34a was examined by the TaqMan microRNA assay, and was downregulated in the TM‑exposed chondrocytes treated with DHJSD or PBA compared with that in the TM-exposed chondrocytes. DHJSD inhibits ER stress in chondrocytes induced by exposure to TM by downregulating miR‑34a, suggesting that DHJSD may be a potential therapeutic agent for OA.
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Affiliation(s)
- Fayuan Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Xiaping Weng
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Pingdong Lin
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Chunsong Zheng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Huifeng Xu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Xianxiang Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Hongzhi Ye
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Xihai Li
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
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36
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Wang J, Song S, Xie C, Han J, Li Y, Shi J, Xin M, Wang J, Luo T, Meng X, Yang B. MicroRNA profiling in the left atrium in patients with non-valvular paroxysmal atrial fibrillation. BMC Cardiovasc Disord 2015; 15:97. [PMID: 26319023 PMCID: PMC4553004 DOI: 10.1186/s12872-015-0085-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023] Open
Abstract
Background We aimed to identify the miRNA expression profiles in left atrial appendage, with the intention of identifying miRNAs that were significantly associated with non-valvular paroxysmal AF. Methods The RNA samples were isolated from healthy controls (n = 5) and patients with atrial fibrillation (n = 8). To confirm the findings obtained by analyzing the miRNA profile, we measured the expression of selected miRNAs in the entire cohort by quantitative PCR. Results Ten specific miRNAs were found to be differentially expressed between atrial fibrillation and healthy controls with more than a 2-fold change (P < 0.05). Consistent with the data obtained for the profile, expression levels of miRNA-155, miRNA-146b-5p and miRNA-19b were significantly increased in patients with atrial fibrillation. Interestingly, levels of miRNA-146b-5p and miRNA-155, which are known to be associated with inflammation, were independently and positively associated with left atrium dimension, atrial fibrillation duration and high sensitivity C-reactive protein levels. By using four Databases (TargetScan, miRanda, Starbase Clip-seq and miRDB) to perform target gene prediction, there were four genes were related to the inflammatory response and fibrosis, and three others encoding cardiac ion channel proteins. As a result of TaqMan qPCR and Western analysis, the relative mRNA and protein expression level of three target genes (DIER-1, TIMP-4 and CACNA1C) were significantly lower in the atrial fibrillation group than that in the healthy control group. Conclusions Expression of inflammation-associated miRNAs is significantly up-regulated in the left atrial appendage of patients with non-valvular paroxysmal atrial fibrillation, which may play a significant role in electrical and structural remodeling. Electronic supplementary material The online version of this article (doi:10.1186/s12872-015-0085-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiangang Wang
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Shiqiu Song
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Changqing Xie
- Department of Internal Medicine, Vidant Medical Center, Broody School of Medicine, East Carolina University, Greenville, North Carolina, 27834, USA.
| | - Jie Han
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Yan Li
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Jiahai Shi
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China.
| | - Meng Xin
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Jun Wang
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Tiange Luo
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Xu Meng
- Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, P.R. China.
| | - Bo Yang
- University of Michigan Cardiovascular Center, University of Michigan, Ann Arbor, Michigan, 48109, USA.
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Hoareau-Aveilla C, Valentin T, Daugrois C, Quelen C, Mitou G, Quentin S, Jia J, Spicuglia S, Ferrier P, Ceccon M, Giuriato S, Gambacorti-Passerini C, Brousset P, Lamant L, Meggetto F. Reversal of microRNA-150 silencing disadvantages crizotinib-resistant NPM-ALK(+) cell growth. J Clin Invest 2015; 125:3505-18. [PMID: 26258416 DOI: 10.1172/jci78488] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 06/23/2015] [Indexed: 01/20/2023] Open
Abstract
The regulatory microRNA miR-150 is involved in the development of hemopathies and is downregulated in T-lymphomas, such as anaplastic large-cell lymphoma (ALCL) tumors. ALCL is defined by the presence or absence of translocations that activate the anaplastic lymphoma kinase (ALK), with nucleophosmin-ALK (NPM-ALK) fusions being the most common. Here, we compared samples of primary NPM-ALK(+) and NPM-ALK(-) ALCL to investigate the role of miR-150 downstream of NPM-ALK. Methylation of the MIR150 gene was substantially elevated in NPM-ALK(+) biopsies and correlated with reduced miR-150 expression. In NPM-ALK(+) cell lines, DNA hypermethylation-mediated miR-150 repression required ALK-dependent pathways, as ALK inhibition restored miR-150 expression. Moreover, epigenetic silencing of miR-150 was due to the activation of STAT3, a major downstream substrate of NPM-ALK, in cooperation with DNA methyltransferase 1 (DNMT1). Accordingly, miR-150 repression was turned off following treatment with the DNMT inhibitor, decitabine. In murine NPM-ALK(+) xenograft models, miR-150 upregulation induced antineoplastic activity. Treatment of crizotinib-resistant NPM-ALK(+) KARPAS-299-CR06 cells with decitabine or ectopic miR-150 expression reduced viability and growth. Altogether, our results suggest that hypomethylating drugs, alone or in combination with other agents, may benefit ALK(+) patients harboring tumors resistant to crizotinib and other anti-ALK tyrosine kinase inhibitors (TKIs). Moreover, these results support further work on miR-150 in these and other ALK(+) malignancies.
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MESH Headings
- Animals
- Cell Line, Tumor
- Crizotinib
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Gene Silencing
- Humans
- Lymphoma, Large-Cell, Anaplastic/drug therapy
- Lymphoma, Large-Cell, Anaplastic/genetics
- Lymphoma, Large-Cell, Anaplastic/metabolism
- Lymphoma, Large-Cell, Anaplastic/pathology
- Male
- Mice
- Mice, Transgenic
- MicroRNAs/biosynthesis
- MicroRNAs/genetics
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Pyrazoles/pharmacology
- Pyridines/pharmacology
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/metabolism
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38
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Latruffe N, Lançon A, Frazzi R, Aires V, Delmas D, Michaille JJ, Djouadi F, Bastin J, Cherkaoui-Malki M. Exploring new ways of regulation by resveratrol involving miRNAs, with emphasis on inflammation. Ann N Y Acad Sci 2015; 1348:97-106. [PMID: 26190093 DOI: 10.1111/nyas.12819] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review presents recent evidence implicating microRNAs (miRNAs) in the beneficial effects of resveratrol (trihydroxystilbene), a nonflavonoid plant polyphenol, with emphasis on its anti-inflammatory effects. Many diseases and pathologies have been linked, directly or indirectly, to inflammation. These include infections, injuries, atherosclerosis, diabetes mellitus, obesity, cancer, osteoarthritis, age-related macular degeneration, demyelination, and neurodegenerative diseases. Resveratrol can both decrease the secretion of proinflammatory cytokines (e.g., IL-6, IL-8, and TNF-α) and increase the production of anti-inflammatory cytokines; it also decreases the expression of adhesion proteins (e.g., ICAM-1) and leukocyte chemoattractants (e.g., MCP-1). Resveratrol's primary targets appear to be the transcription factors AP-1 and NF-κB, as well as the gene COX2. Although no mechanistic link between any particular miRNA and resveratrol has been identified, resveratrol effects depend at least in part upon the modification of the expression of a variety of miRNAs that can be anti-inflammatory (e.g., miR-663), proinflammatory (e.g., miR-155), tumor suppressing (e.g., miR-663), or oncogenic (e.g., miR-21).
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Affiliation(s)
| | - Allan Lançon
- Laboratoire Bio-PeroxIL, Université de Bourgogne, Dijon, France
| | - Raffaele Frazzi
- Department of Research and Statistics, Translational Research Laboratory, IRCCS Arcispedale S.Maria Nuova, Reggio Emilia, Italy
| | - Virginie Aires
- Laboratoire Bio-PeroxIL, Université de Bourgogne, Dijon, France.,INSERM UMR 866, Dijon, France
| | - Dominique Delmas
- Laboratoire Bio-PeroxIL, Université de Bourgogne, Dijon, France.,INSERM UMR 866, Dijon, France
| | | | | | - Jean Bastin
- INSERM U1124, Université Paris Descartes, Paris, France
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39
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Wuttge DM, Carlsen AL, Teku G, Steen SO, Wildt M, Vihinen M, Hesselstrand R, Heegaard NHH. Specific autoantibody profiles and disease subgroups correlate with circulating micro-RNA in systemic sclerosis. Rheumatology (Oxford) 2015; 54:2100-7. [PMID: 26163687 DOI: 10.1093/rheumatology/kev234] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE To evaluate the expression profiles of cell-free plasma miRNAs in SSc and to characterize their correlation with disease subgroups (lcSSc and dcSSc) and with autoantibody profiles. METHODS Using quantitative RT-PCR, the abundance of 45 mature miRNAs in plasma was determined in 95 patients (lcSSc = 63; dcSSc = 32), representing the following autoantibody subgroups: ACA, anti-DNA topoisomerase I, anti-RNA polymerase III and anti-U1-ribonucleoprotein. MiRNA data were correlated with clinical and paraclinical data. Multiple regression was used to model membership of the lcSSc, dcSSc and autoantibody subgroups, based on miRNA expression profiles. RESULTS Thirty-six miRNAs were measurable in all samples. Four (miRNA-223, -181b, -342-3p and -184) were differently expressed in lcSSc and dcSSc (false discovery rate < 0.05). Ten miRNAs exhibited statistically significantly different levels in one or more autoantibody groups, and five (miRNA-409, -184, -92a, -29a and -101) remained significant after correction for multiple comparisons. Multiple regression models accurately predicted ACA and anti-DNA topoisomerase I antibody-positive patients (area under the curve (AUC) = 0.97 and 0.93, respectively) as well as membership of the dcSSc and lcSSc groups (AUC = 0.88). CONCLUSION Circulating miRNA profiles differ between lcSSc and dcSSc patients and between patients with different autoantibodies. This is the first time autoantibody profiles, disease phenotypes and plasma miRNA profiles have been shown to correlate in an autoimmune disease. The data support a pathobiological role of miRNAs because specific miRNAs associate with autoantibody profiles of known diagnostic and prognostic value.
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Affiliation(s)
- Dirk M Wuttge
- Section of Rheumatology, Department of Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden,
| | - Anting Liu Carlsen
- Department of Autoimmunology & Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Gabriel Teku
- Department of Experimental Medical Science, Protein Structure Bioinformatics, Lund University, Lund, Sweden
| | - Samantha O Steen
- Department of Autoimmunology & Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Marie Wildt
- Section of Rheumatology, Department of Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Protein Structure Bioinformatics, Lund University, Lund, Sweden
| | - Roger Hesselstrand
- Section of Rheumatology, Department of Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Niels H H Heegaard
- Department of Autoimmunology & Biomarkers, Statens Serum Institut, Copenhagen S, Denmark, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital and Institute of Clinical Research, Clinical Biochemistry, University of Southern Denmark, Odense, Denmark
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40
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miR-34a and miR-125b Expression in HPV Infection and Cervical Cancer Development. BIOMED RESEARCH INTERNATIONAL 2015; 2015:304584. [PMID: 26180794 PMCID: PMC4477216 DOI: 10.1155/2015/304584] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 12/02/2014] [Indexed: 12/15/2022]
Abstract
We aimed to characterize miR-125b and miR-34a expression in 114 women with different cervical lesions: normal epithelium with (n = 20) and without (n = 29) HPV infection; LSIL (n = 28); HSIL (n = 29); and ICC (n = 8). miRNA expression analysis was performed by comparing the distinct groups with the reference group (women with normal epithelium without HPV). For miR-125b, we observed a twofold (2−ΔΔCt = 2.11; P = 0.038) increased expression among women with normal epithelium with HPV infection and a trend of downregulation in different cervical lesions including an 80% reduction (2−ΔΔCt = 0.21; P = 0.004) in ICC. Similarly, miR-34a expression analysis revealed an increased expression (2−ΔΔCt = 1.69; P = 0.049) among women with normal cervix and HPV infection, and despite no significant correlation with cervical lesions, its expression was increased by twofold (2−ΔΔCt = 2.08; P = 0.042) in ICC. Moreover, miR-125b levels were able to predict invasive cancers with 88% sensitivity and 69% specificity. Results showed that while miR-34a expression seems to be correlated with invasive cervical cancer, miR-125b expression is significantly changed within the different cervical lesions and their levels should be further investigated as possible predictive/prognostic biomarkers using a noninvasive approach.
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41
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Csak T, Bala S, Lippai D, Kodys K, Catalano D, Iracheta-Vellve A, Szabo G. MicroRNA-155 Deficiency Attenuates Liver Steatosis and Fibrosis without Reducing Inflammation in a Mouse Model of Steatohepatitis. PLoS One 2015; 10:e0129251. [PMID: 26042593 PMCID: PMC4456142 DOI: 10.1371/journal.pone.0129251] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/06/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND & AIM MicroRNAs (miRs) regulate hepatic steatosis, inflammation and fibrosis. Fibrosis is the consequence of chronic tissue damage and inflammation. We hypothesized that deficiency of miR-155, a master regulator of inflammation, attenuates steatohepatitis and fibrosis. METHODS Wild type (WT) and miR-155-deficient (KO) mice were fed methionine-choline-deficient (MCD) or -supplemented (MCS) control diet for 5 weeks. Liver injury, inflammation, steatosis and fibrosis were assessed. RESULTS MCD diet resulted in steatohepatitis and increased miR-155 expression in total liver, hepatocytes and Kupffer cells. Steatosis and expression of genes involved in fatty acid metabolism were attenuated in miR-155 KO mice after MCD feeding. In contrast, miR-155 deficiency failed to attenuate inflammatory cell infiltration, nuclear factor κ beta (NF-κB) activation and enhanced the expression of the pro-inflammatory cytokines tumor necrosis factor alpha (TNFα) and monocyte chemoattractant protein-1 (MCP1) in MCD diet-fed mice. We found a significant attenuation of apoptosis (cleaved caspase-3) and reduction in collagen and α smooth muscle actin (αSMA) levels in miR-155 KO mice compared to WTs on MCD diet. In addition, we found attenuation of platelet derived growth factor (PDGF), a pro-fibrotic cytokine; SMAD family member 3 (Smad3), a protein involved in transforming growth factor-β (TGFβ) signal transduction and vimentin, a mesenchymal marker and indirect indicator of epithelial-to-mesenchymal transition (EMT) in miR-155 KO mice. Nuclear binding of CCAAT enhancer binding protein β (C/EBPβ) a miR-155 target involved in EMT was significantly increased in miR-155 KO compared to WT mice. CONCLUSIONS Our novel data demonstrate that miR-155 deficiency can reduce steatosis and fibrosis without decreasing inflammation in steatohepatitis.
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Affiliation(s)
- Timea Csak
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Shashi Bala
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Dora Lippai
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Karen Kodys
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Donna Catalano
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Arvin Iracheta-Vellve
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Gyongyi Szabo
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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42
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Kurzynska-Kokorniak A, Koralewska N, Pokornowska M, Urbanowicz A, Tworak A, Mickiewicz A, Figlerowicz M. The many faces of Dicer: the complexity of the mechanisms regulating Dicer gene expression and enzyme activities. Nucleic Acids Res 2015; 43:4365-80. [PMID: 25883138 PMCID: PMC4482082 DOI: 10.1093/nar/gkv328] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/31/2015] [Indexed: 12/14/2022] Open
Abstract
There is increasing evidence indicating that the production of small regulatory RNAs is not the only process in which ribonuclease Dicer can participate. For example, it has been demonstrated that this enzyme is also involved in chromatin structure remodelling, inflammation and apoptotic DNA degradation. Moreover, it has become increasingly clear that cellular transcript and protein levels of Dicer must be strictly controlled because even small changes in their accumulation can initiate various pathological processes, including carcinogenesis. Accordingly, in recent years, a number of studies have been performed to identify the factors regulating Dicer gene expression and protein activity. As a result, a large amount of complex and often contradictory data has been generated. None of these data have been subjected to an exhaustive review or critical discussion. This review attempts to fill this gap by summarizing the current knowledge of factors that regulate Dicer gene transcription, primary transcript processing, mRNA translation and enzyme activity. Because of the high complexity of this topic, this review mainly concentrates on human Dicer. This review also focuses on an additional regulatory layer of Dicer activity involving the interactions of protein and RNA factors with Dicer substrates.
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Affiliation(s)
| | - Natalia Koralewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Maria Pokornowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Aleksander Tworak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Agnieszka Mickiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
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43
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Goulart LF, Bettella F, Sønderby IE, Schork AJ, Thompson WK, Mattingsdal M, Steen VM, Zuber V, Wang Y, Dale AM, Andreassen OA, Djurovic S. MicroRNAs enrichment in GWAS of complex human phenotypes. BMC Genomics 2015; 16:304. [PMID: 25884492 PMCID: PMC4437677 DOI: 10.1186/s12864-015-1513-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/08/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The genotype information carried by Genome-wide association studies (GWAS) seems to have the potential to explain more of the 'missing heritability' of complex human phenotypes, given improved statistical approaches. Several lines of evidence support the involvement of microRNA (miRNA) and other non-coding RNA in complex human traits and diseases. We employed a novel, genetic annotation-informed enrichment method for GWAS that captures more polygenic effects than standard GWAS analysis, to investigate if miRNA-tagging Single Nucleotide Polymorphisms (SNPs) are enriched of associations with 15 complex human phenotypes. We then leveraged the enrichment using a conditional False Discovery Rate (condFDR) approach to assess any improvement in the detection of individual miRNA SNPs associated with the disorders. RESULTS We found SNPs tagging miRNA transcription regions to be significantly enriched of associations with 10 of 15 phenotypes. The enrichment remained significant after controlling for affiliation to other genomic categories, and was confirmed by replication. Albeit only nominally significant, enrichment was found also in miRNA binding sites for 10 phenotypes out of 15. Leveraging the enrichment in the condFDR framework, we observed a 2-4-fold increase in discovery of SNPs tagging miRNA regions. CONCLUSIONS Our results suggest that miRNAs play an important role in the polygenic architecture of complex human disorders and traits, and therefore that miRNAs are a genomic category that can and should be used to improve gene discovery.
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Affiliation(s)
- Luiz F Goulart
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| | - Francesco Bettella
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
| | - Ida E Sønderby
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| | - Andrew J Schork
- Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA, 92037, USA.
- Cognitive Sciences Graduate Program, University of California at San Diego, La Jolla, CA, 92037, USA.
- Center for Human Development, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Wesley K Thompson
- Department of Psychiatry, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Morten Mattingsdal
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
| | - Vidar M Steen
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.
| | - Verena Zuber
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Yunpeng Wang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
| | - Anders M Dale
- Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA, 92037, USA.
- Department of Psychiatry, University of California at San Diego, La Jolla, CA, 92037, USA.
- Department of Neuroscience, University of California at San Diego, La Jolla, CA, 92037, USA.
- Department of Radiology, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
- Department of Psychiatry, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
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44
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Bergallo M, Gambarino S, Martino S, Montin D, Montanari P, Galliano I, Tovo PA. Comparison of Two Available RNA Extraction Protocols for microRNA Amplification in Serum Samples. J Clin Lab Anal 2015; 30:277-83. [PMID: 25853736 DOI: 10.1002/jcla.21848] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 02/23/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND microRNAs play a critical role in many biological processes such as cell proliferation and maturation, apoptosis, regulation of chronic inflammation and development of cancer. METHODS In this study is described a protocol for the isolation of RNA from serum and subsequent determination of miRNA expression levels using TaqMan-based MGB Real-Time PCR detection. RNA was extracted using two different isolation methods including available kits RNAzol and a modified RNAzol protocol. In all cases, RNA was eluted in RNase free H2 O, kept frozen until analysis and the presence of contaminants assessed by NanoDrop spectrophotometry. RESULTS Higher RNA quantity was observed in RNAzol (378.8 ng/μl) vs RNAzol modified protocol (226.5 ng/μl) and a better performance in terms of RNA extraction yield and purity. Subsequently, measurements of endogenous miRNAs (RNU43), cellular miRNAs (mir155 and mir146a) and EBV miRNAs (mirBART2-5p, mirBART15 and mirBART22) were performed by RT-qPCR. CONCLUSION In contrast to the findings in terms of purity and quantity, the amplifiable RNA was more abundant using RNAzol modified protocol compared to not modified protocol.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Stefano Gambarino
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Silvana Martino
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Davide Montin
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Pier-Angelo Tovo
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
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Zhang BC, Zhang J, Sun L. In-depth profiling and analysis of host and viral microRNAs in Japanese flounder (Paralichthys olivaceus) infected with megalocytivirus reveal involvement of microRNAs in host-virus interaction in teleost fish. BMC Genomics 2014; 15:878. [PMID: 25297525 PMCID: PMC4200114 DOI: 10.1186/1471-2164-15-878] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 09/24/2014] [Indexed: 01/21/2023] Open
Abstract
Background MicroRNAs (miRNAs) regulate gene expression by binding to mRNA transcripts in various biological processes. In mammals and birds, miRNAs are known to play vital parts in both host immune defense and viral infection. However, in lower vertebrates such as teleost, systematic investigations on host and viral miRNAs are lacking. Results In this study, we applied high-throughput sequencing technology to identify and analyze both host and viral miRNAs in Japanese flounder (Paralichthys olivaceus), an economically important teleost fish farmed widely in the world, infected with megalocytivirus at a timescale of 14 days divided into five different time points. The results showed that a total of 381 host miRNAs and 9 viral miRNAs were identified, the latter being all novel miRNAs that have no homologues in the currently available databases. Of the host miRNAs, 251 have been reported previously in flounder and other species, and 130 were discovered for the first time. The expression levels of 121 host miRNAs were significantly altered at 2 d to 14 d post-viral infection (pi), and these miRNAs were therefore classified as differentially expressed host miRNAs. The expression levels of all 9 viral miRNAs increased from 0 d pi to 10 d pi and then dropped from 10 d pi to 14 d pi. For the 121 differentially expressed host miRNAs and the 9 viral miRNAs, 243 and 48 putative target genes, respectively, were predicted in flounder. GO and KEGG enrichment analysis revealed that the putative target genes of both host and viral miRNAs were grouped mainly into the categories of immune response, signal transduction, and apoptotic process. Conclusions The results of our study provide the first evidences that indicate existence in teleost fish (i) infection-responsive host and viral miRNAs that exhibit dynamic changes in expression profiles during the course of viral infection, and (ii) potential involvement of miRNAs in host-viral interaction. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-878) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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Ribeiro J, Sousa H. MicroRNAs as biomarkers of cervical cancer development: a literature review on miR-125b and miR-34a. Mol Biol Rep 2014; 41:1525-31. [PMID: 24402874 DOI: 10.1007/s11033-013-2998-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 12/28/2013] [Indexed: 12/21/2022]
Abstract
MicroRNAs are non-coding RNAs with important functions in several biological processes, such as, regulation of cell cycle, immune response, inflammation, and apoptosis. In fact, deregulation and abnormal expression of these molecules is associated with human pathologies including cancer and several have already emerged as potential prognostic biomarkers in different neoplasias. miR-34a is directly regulated by p53 and acts as tumor suppressor while miR-125b plays a significant role in immune response and apoptosis. In cervical carcinogenesis, HPV proteins seem to interact with both miR-34a and miR-125b changing its expression and promoting persistent infection and cervical cancer development. In this review we describe the potential role of miR-125b and miR-34a in cervical carcinogenesis, including interaction with HPV and mechanism of deregulation. Additionally, their clinical applications in cervical cancer as prognostic/predictive biomarkers are also briefly discussed.
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Affiliation(s)
- Joana Ribeiro
- Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal
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Zhao H, Anand AR, Ganju RK. Slit2-Robo4 pathway modulates lipopolysaccharide-induced endothelial inflammation and its expression is dysregulated during endotoxemia. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 192:385-93. [PMID: 24272999 PMCID: PMC3908786 DOI: 10.4049/jimmunol.1302021] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The secretory protein Slit2 and its receptors Robo1 and Robo4 are considered to regulate mobility and permeability of endothelial cells and other cell types. However, the roles of Slit2 and its two receptors in endothelial inflammatory responses remain to be clarified. In this study, we show that, in primary HUVECs, Slit2 represses LPS-induced secretion of certain inflammatory cytokines/chemokines, cell adhesion molecule ICAM-1 upregulation, and monocyte adhesion. Slit2's anti-inflammatory effect is mediated by its dominant endothelial-specific receptor Robo4. However, the minor receptor Robo1 has proinflammatory properties and is downregulated by Slit2 via targeting of miR-218. Elucidation of molecular mechanism reveals that Slit2 represses inflammatory responses by inhibiting the Pyk2-NF-κB pathway downstream of LPS-TLR4. Further studies reveal that LPS enhances endothelial inflammation by downregulating the anti-inflammatory Slit2 and Robo4 in HUVECs in vitro, as well as in arterial endothelial cells and liver in vivo during endotoxemia. These results suggest that Slit2-Robo4 signaling is important in regulating LPS-induced endothelial inflammation, and LPS, in turn, enhances inflammation by interfering with the expression of the anti-inflammatory Slit2-Robo4 during the disease state. This implies that Slit2-Robo4 is a key regulator of endothelial inflammation, and its dysregulation during endotoxemia is a novel mechanism for LPS-induced vascular pathogenesis.
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Affiliation(s)
- Helong Zhao
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210
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Abstract
Profiling microRNA (miRNA) expression is of widespread interest due to their critical roles in diverse biological processes, including development, cell proliferation, differentiation, and apoptosis. Profiling can be achieved via three major methods: amplification-based (real-time quantitative PCR, qRT-PCR), hybridization-based (microarrays), and sequencing-based (next-generation sequencing (NGS)) technologies. The gold standard is qRT-PCR and serves as a platform for single reverse PCR amplification experiments and for a large number of miRNAs in parallel, both by multiplexing and plate based arrays. Currently, qRT-PCR is used for the validation of miRNA profiling results from other platforms. Hybridization based miRNA profiling by microarrays has become a widely used method especially for biomarker and therapeutic target identification. The data obtained from microarrays also enables functional prediction of miRNAs by correlating miRNA expression patterns to corresponding mRNA and protein profiles. Additionally, miRNA profiling strategies based on deep sequencing allow both the identification of novel miRNAs and relative quantification of miRNAs. Each miRNA profiling strategy has specific strengths and challenges that have to be considered depending on the nature of the research context.In this chapter the high-throughput approaches that can be applied to microRNA profiling are discussed starting from small-scale qRT-PCR technology to a wider one, NGS.
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Gyongyosi A, Docs O, Czimmerer Z, Orosz L, Horvath A, Török O, Mehes G, Nagy L, Balint BL. Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples. Methods Mol Biol 2014; 1182:105-19. [PMID: 25055905 DOI: 10.1007/978-1-4939-1062-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
MicroRNAs are involved in the regulation of various pathophysiological processes such as immune regulation and cancer. Next-generation sequencing methods enable us to monitor their presence in various types of samples but we need flexible methods for validating datasets generated by high-throughput methods. Here we describe the detailed protocols to be used with our MiRNA Primer Design Tool assay design system. The presented methods allow the flexible design of the oligonucleotides needed for the RT-qPCR detection of any variant of small regulatory RNA molecules from virtually any species. This method can be used to measure miRNA levels from formalin-fixed, paraffin-embedded (FFPE) samples and various body fluids. As an example, we show the results of the hsa-miR-515-3p, hsa-miR-325, and hsa-miR-155 quantification using a specific UPL probe (Universal Probe Library) and a stem-loop RT-qPCR assay. The small nucleolar RNA RNU43 is used as endogenous control for normalization of the results. Urine from healthy pregnant women and FFPE samples from patients diagnosed with colorectal cancer and treated with antibody-based anti-EGFR monotherapy were used as samples.
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Affiliation(s)
- Adrienn Gyongyosi
- Department of Biochemistry and Molecular Biology, Center for Clinical Genomics and Personalized Medicine, University of Debrecen Medical and Health Science Center (UD MHSC), Nagyerdei krt. 98, Debrecen, Hungary
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