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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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Zhang X, Yang C, Meng Z, Zhong H, Hou X, Wang F, Lu Y, Guo J, Zeng Y. miR-124 and VAMP3 Act Antagonistically in Human Neuroblastoma. Int J Mol Sci 2023; 24:14877. [PMID: 37834325 PMCID: PMC10573497 DOI: 10.3390/ijms241914877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor that affects developing nerve cells in the fetus, infants, and children. miR-124 is a microRNA (miRNA) enriched in neuronal tissues, and VAMP3 (vesicle-associated membrane protein 3) has been reported to be an miR-124 target, although the relationship between NB and miR-124 or VAMP3 is unknown. Our current work identified that miR-124 levels are high in NB cases and that elevated miR-124 correlates with worse NB outcomes. Conversely, depressed VAMP3 correlates with worse NB outcomes. To investigate the mechanisms by which miR-124 and VAMP3 regulate NB, we altered miR-124 or VAMP3 expression in human NB cells and observed that increased miR-124 and reduced VAMP3 stimulated cell proliferation and suppressed apoptosis, while increased VAMP3 had the opposite effects. Genome-wide mRNA expression analyses identified gene and pathway changes which might explain the NB cell phenotypes. Together, our studies suggest that miR-124 and VAMP3 could be potential new markers of NB and targets of NB treatments.
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Affiliation(s)
- Xiaoxiao Zhang
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengyong Yang
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Meng
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Huanhuan Zhong
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xutian Hou
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fenfen Wang
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiping Lu
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Yan Zeng
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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3
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Studies on the application of single-stranded DNA and PNA probes for electrochemical detection of miRNA 141. Bioelectrochemistry 2023; 150:108363. [PMID: 36608369 DOI: 10.1016/j.bioelechem.2022.108363] [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: 04/06/2022] [Revised: 12/09/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The abnormal concentration of microRNAs (miRNAs) can be associated with occurrence of various diseases including cancer, cardiovascular and neurodegenerative, hence they can be considered as potential biomarkers. An attractive approach could be the application of electrochemical methods, particularly where hybridization event between single-stranded deoxyribonucleic acid (ssDNA) or peptide-nucleic acid (PNA) with miRNA strand happens. Recently, the use of various nanomaterials such as gold nanoparticles, graphene oxide, quantum dots as well as catalyzed hairpin assembly or hybridization chain reaction were proposed to further enhance the performance of elaborated sensors. Herein, we present the studies on selection of receptor layer composition for detection of miRNA 141. The possibility of formation of receptor layer and further duplex monolayer between ssDNA or PNA with miRNA was analyzed by atomic force microscopy (AFM) technique. The interaction of ssDNA and PNA probes with miRNA was further verified using surface plasmon resonance (SPR) and quartz - crystal microbalance (QCM) techniques. On the basis of impedance spectroscopy it was shown that the use of unlabelled ssDNA as receptor layer provided 0.1 pM detection limit. This shows that proposed biosensor that is simple in preparation and use is an attractive alternative to other recently presented approaches.
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Welby E, Rehborg RJ, Harmelink M, Ebert AD. Assessment of cerebral spinal fluid biomarkers and microRNA-mediated disease mechanisms in spinal muscular atrophy patient samples. Hum Mol Genet 2021; 31:1830-1843. [PMID: 34919695 DOI: 10.1093/hmg/ddab365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 11/14/2022] Open
Abstract
Cerebral spinal fluid (CSF) is a promising biospecimen for the detection of central nervous system biomarkers to monitor therapeutic efficacy at the cellular level in neurological diseases. Spinal muscular atrophy (SMA) patients receiving intrathecal antisense oligonucleotide (nusinersen) therapy tend to show improved motor function, but the treatment effect on cellular health remains unknown. The objective of this study was to assess the potential of extracellular RNAs and microRNAs in SMA patient CSF as indicators of neuron and glial health following nusinersen treatment. Extracellular RNA analysis of CSF samples revealed ongoing cellular stress related to inflammation and glial differentiation, even after treatment administration. Downregulated microRNA expression associated with SMA-specific or general motor neuron dysfunction in animal and cellular models, tended to increase in nusinersen treated patient CSF samples and correlated with SMA Type 1 and 2 motor functioning improvements. However, miR-146a, known to be upregulated in SMA induced pluripotent stem cell (iPSC)-derived astrocytes, showed increased expression in nusinersen treated CSF samples. We then used mRNA sequencing and multi-electrode arrays to assess the transcriptional and functional effects of miR-146a on healthy and SMA iPSC-derived motor neurons. miR-146a treatment on iPSC-derived motor neurons led to a downregulation of extracellular matrix genes associated with synaptic perineuronal net and alterations in spontaneous electrophysiological activity. Together, this study suggests that extracellular RNAs and microRNAs may serve as useful biomarkers to monitor cellular health during nusinersen treatment. Moreover, these data highlight the importance of addressing astrocyte health and response to nusinersen in SMA pathogenesis and treatment strategies.
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Affiliation(s)
- Emily Welby
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Rebecca J Rehborg
- Department of Neurology (Child Neurology), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew Harmelink
- Department of Neurology (Child Neurology), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Allison D Ebert
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
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Al-Rawaf HA, Gabr SA, Alghadir AH. The Potential Role of Circulating MicroRNAs in Male Rat Infertility Treated with Kaempferia parviflora. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:9622494. [PMID: 34956389 PMCID: PMC8709766 DOI: 10.1155/2021/9622494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Therapeutic strategies based on herbal plants and diets containing sufficient amounts of antioxidants and essential vitamins are very important factors in treating reproduction and male infertility worldwide. Thus, the aim of this study was to investigate the potential effects of Kaempferia parviflora (KP) on the role of some microRNAs in treated and nontreated infertile rats. In addition, the correlation of expressed microRNAs with sperm count, sperm motility, and sperm viability was identified. The probable use of these microRNAs as a diagnostic marker for predicting the clinical response of infertility to the treatment with KP was also achieved. METHODS In the present study, the potential effects of Kaempferia parviflora (KP) at different doses (140, 280, and 420 mg/kg) for six weeks on male rats with subinfertility were explored. In addition, the effect of KP on the expression of circulating microRNAs and its correlation with the parameters of sexual infertility was identified by performing both in vitro and in vivo assays. In vitro antioxidant activity, sperm functional analysis, serum testosterone, and expression of circulating microRNAs were conducted using colorimetric, ELISA, and real-time RT-PCR analysis, respectively. RESULTS Kaempferia parviflora (KP) at nontoxic doses of 140-420 mg/kg/day for six weeks significantly improved serum testosterone and epididymal sperm parameters (sperm count, motility, and sperm viability), increased testicular weight, and provided a reduction in the percentage of abnormal spermatozoon in infertile male rats. The expression of miR-328 and miR-19b significantly decreased, and miR-34 significantly increased in infertile rats treated with KP compared to infertile nontreated rats. After six weeks of KP therapy, the change in the expression levels of miRNAs was correlated positively with higher levels of serum testosterone and the measures of epididymal sperm parameters. The respective area under the receiver operating characteristic curve (AUC-ROC) was applied to predict the potential use of miR-328, miR-19b, and miR-34 in the diagnosis of male infertility in treated and nontreated infertile male rats. The data showed that AUC cutoff values of 0.91 for miR-328, 0.89 for miR-19b, and 0.86 for miR34 were the best estimated values for the clinical diagnosis of male rats with infertility. In rats treated with KP for six weeks, AUC cutoff values of 0.76 for miR-328, 0.79 for miR-19b, and 0.81 for miR-34 were the best cutoff values reported for the clinical response of infertility to KP therapy after six weeks. CONCLUSIONS In this study, the improvement of male infertility might proceed via antioxidant and antiapoptotic pathways, which significantly improve spermatogenesis and aphrodisiac properties of males. In addition, the expression of miRNAs, miR-328, miR-34, and miR-19b, in KP-treated and nontreated infertile rats significantly correlated with increased serum testosterone levels and epididymal sperm parameters as well. MicroRNAs, miR-328, miR-34, and miR-19b, might be related to oxidative and apoptotic pathways that proceeded in spermatogenesis. Thus, the use of miRNAs could have a role as diagnostic, therapeutic, and predictive markers for assessing the clinical response of Kaempferia parviflora treatment for six weeks. This may have potential applications in the therapeutic strategies based on herbal plants for male infertility. However, in subsequent studies, the genetic regulatory mechanisms of the expressed miRNAs should be fully characterized.
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Affiliation(s)
- Hadeel A. Al-Rawaf
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Sami A. Gabr
- Department of Rehabilitation Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahmad H. Alghadir
- Department of Rehabilitation Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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Xu YW, Ou NJ, Song YX, Wang XH, Kang JQ, Yang YJ, Chen YG, Liu XQ. Seminal plasma miR-210-3p induces spermatogenic cell apoptosis by activating caspase-3 in patients with varicocele. Asian J Androl 2021; 22:513-518. [PMID: 31670279 PMCID: PMC7523610 DOI: 10.4103/aja.aja_114_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The aim of this study was to investigate the role of seminal plasma miR-210-3p in the impairment of semen quality caused by varicocele. This study included 102 patients whose semen quality was normal when they were diagnosed with varicocele. A 2-year follow-up for included patients was performed, and they were divided into Group A (semen quality became abnormal) and Group B (semen quality remained normal) according to the results of semen analysis during the follow-up. Semen parameters and seminal plasma miR-210-3p expression were investigated by semen analysis and quantitative real-time polymerase chain reaction, respectively. In vitro experiments with GC-2 cells were performed to explore the role of miR-210-3p in spermatogenic cells. The results of quantitative real-time polymerase chain reaction showed that the level of seminal plasma miR-210-3p in Group A was higher than that in Group B both after 2-year follow-up and when they were diagnosed with varicocele (both P < 0.01). Apoptosis and proliferation assays showed that miR-210-3p induces apoptosis of spermatogenic cells by promoting caspase-3 activation. In conclusion, our study indicated that seminal plasma miR-210-3p induces spermatogenic cell apoptosis by activating caspase-3 in patients with varicocele. Seminal plasma miR-210-3p may be a potential biomarker for predicting impaired semen quality caused by varicocele.
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Affiliation(s)
- Ya-Wei Xu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ning-Jing Ou
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yu-Xuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Xian-Hao Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jia-Qi Kang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yong-Jiao Yang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Ye-Gang Chen
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Xiao-Qiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
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Pelullo M, Savi D, Quattrucci S, Cimino G, Pizzuti A, Screpanti I, Talora C, Cialfi S. miR-125b/NRF2/HO-1 axis is involved in protection against oxidative stress of cystic fibrosis: A pilot study. Exp Ther Med 2021; 21:585. [PMID: 33850557 DOI: 10.3892/etm.2021.10017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
In the physiopathology of cystic fibrosis (CF), oxidative stress implications are recognized and widely accepted. The cystic fibrosis transmembrane conductance regulator (CFTR) defects disrupt the intracellular redox balance causing CF pathological hallmarks. Therefore, oxidative stress together with aberrant expression levels of detoxification genes and microRNAs (miRNAs/miRs) may be associated with clinical outcome. Using total RNA extracted from epithelial nasal cells, the present study analyzed the expression levels of oxidative stress genes and one miRNA using quantitative PCR in a representative number of patients with CF compared with in healthy individuals. The present pilot study revealed the existence of an association among CFTR, genes involved in the oxidative stress response and miR-125b. The observed downregulation of CFTR gene expression was accompanied by increased expression levels of Nuclear factor erythroid derived-2 like2 and its targets NAD(P)H:Quinone Oxidoreductase and glutathione S-transferase 1. Moreover, the expression levels of heme oxygenase-1 (HO-1) and miR-125b were positively correlated with a forced expiratory volume in 1 sec (FEV1) >60% in patients with CF with chronic Pseudomonas aeruginosa lung infection (r=0.74; P<0.001 and r=0.57; P<0.001, respectively). The present study revealed the activation of an inducible, but not fully functional, oxidative stress response to protect airway cells against reactive oxygen species-dependent injury in CF disease. Additionally, the correlations of HO-1 and miR-125b expression with an improved FEV1 value suggested that these factors may synergistically protect the airway cells from oxidative stress damage, inflammation and apoptosis. Furthermore, HO-1 and miR-125b may be used as prognostic markers explaining the wide CF phenotypic variability as an additional control level over the CFTR gene mutations.
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Affiliation(s)
- Maria Pelullo
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, I-00161 Rome, Italy
| | - Daniela Savi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, I-00161 Rome, Italy
| | - Serena Quattrucci
- Department of Pediatrics, Sapienza University of Rome, I-00161 Rome, Italy
| | - Giuseppe Cimino
- Department of Pediatrics, Sapienza University of Rome, I-00161 Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, I-00161 Rome, Italy
| | - Isabella Screpanti
- Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy
| | - Claudio Talora
- Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy
| | - Samantha Cialfi
- Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy
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Liu J, Yang T, Zhang Y, Wang S. Promotion of BZW2 by LINC00174 through miR-4500 inhibition enhances proliferation and apoptosis evasion in laryngeal papilloma. Cancer Cell Int 2020; 20:471. [PMID: 33005104 PMCID: PMC7525952 DOI: 10.1186/s12935-020-01559-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background We aimed to explore the roles of basic leucine zipper and W2 domains (BZW) 2 in the human papillomavirus-infected laryngeal papillomatosis. Methods In the present study, BZW 2 knockdown and overexpressed cell lines were constructed. CCK-8 and colony formation assays were used to determine cell proliferation. Caspase-3 activity and nucleosomes fragmentation assays were used to determine cell apoptosis. qRT-PCR and Western blot were employed to evaluate the mRNA and protein levels of target genes, respectively. Luciferase and biotin-coupled miRNA pulldown assays were used to examine the interactions between mRNA and mRNA. Results We observed the levels of BZW2 were up-regulated in the laryngeal papilloma (LP) tissues as compared with adjacent tissues. The knockdown of BZW2 significantly inhibited cell proliferation and promoted cell apoptosis in the LP cells. Additionally, we identified the expressions of BZW2 negatively regulated by miR-4500. Luciferase and biotin-coupled miRNA pulldown assays demonstrated that LINC00174 competed with the BZW2 for binding with miR-4500. Moreover, the results showed that LINC00174/miR-4500/BZW2 axis regulated cell proliferation and apoptosis. Conclusion Our results demonstrated that the regulation of LINC00174/miR-4500/BZW2 axis might be used as an effective strategy for treatment of human papillomavirus-infected laryngeal papillomatosis.
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Affiliation(s)
- Jiajia Liu
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Tao Yang
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Ying Zhang
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Shuhui Wang
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
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Xie W, Shui C, Fang X, Peng Y, Qin L. miR-197-3p reduces epithelial-mesenchymal transition by targeting ABCA7 in ovarian cancer cells. 3 Biotech 2020; 10:375. [PMID: 32832335 DOI: 10.1007/s13205-020-02362-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/25/2020] [Indexed: 12/18/2022] Open
Abstract
The present study was designed to explore the role of microRNA-197-3p in regulating the epithelial-mesenchymal cellular transition in ovarian cancer. The results showed that miR-197 to be significantly (P < 0.05) downregulated in human ovarian cancer tissues and cell lines. Overexpression of miR-197 significantly (P < 0.05) reduced the proliferation of OVACAR-3 cancer cells. Additionally, the colony formation of the OVACAR-3 cells was inhibited by 59% relative to control. The migration and invasion of the OVACAR-3 cells was inhibited by 64% and 72%, respectively, upon miR-197 overexpression. Western blot analysis showed miR-197 was found to upregulate the expression of E-cadherin, while the expression of N-cadherin, vimentin, and snail proteins was found to decrease significantly (P < 0.05). TargetScan analysis together with dual luciferase assay revealed that miR-197 exerts its effects by targeting ABCA7 in ovarian cancer. ABCA7 was significantly (P < 0.05) overexpressed in ovarian cancer tissues and cell lines. However, silencing of ABCA7 resulted in significant inhibition of cell proliferation, migration, and invasion. Nonetheless, overexpression of ABCA7 could abolish the tumor-suppressive effects of miR-197 on the OVACAR-3 cells. Taken together, miR-197 acts a tumor-suppressive in ovarian cancer and points towards its therapeutic implications in the treatment of ovarian cancer.
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Affiliation(s)
- Weiquan Xie
- Department of Obstetrics and Gynaecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, 445000 Hubei China
| | - Chengyu Shui
- Department of Obstetrics and Gynaecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, 445000 Hubei China
| | - Xiping Fang
- Department of Oncology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, No. 158 Wuyang Avenue, Enshi, 445000 Hubei China
| | - Yuqiu Peng
- Department of Science and Education, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, 445000 Hubei China
| | - Li Qin
- Department of Obstetrics and Gynaecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, 445000 Hubei China
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Valadão de Souza DR, Pessôa R, Nascimento A, Nukui Y, Pereira J, Casseb J, Penalva de Oliveira AC, da Silva Duarte AJ, Clissa PB, Sanabani SS. Small RNA profiles of HTLV-1 asymptomatic carriers with monoclonal and polyclonal rearrangement of the T-cell antigen receptor γ-chain using massively parallel sequencing: A pilot study. Oncol Lett 2020; 20:2311-2321. [PMID: 32782548 PMCID: PMC7400997 DOI: 10.3892/ol.2020.11803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/21/2020] [Indexed: 12/19/2022] Open
Abstract
In the present pilot study, massively parallel sequencing (MPS) technology was used to investigate cellular small RNA (sRNA) levels in the peripheral blood mononuclear cells (PBMCs) of human T-lymphotropic virus type I (HTLV–I) infected asymptomatic carriers with monoclonal (ASM) and polyclonal (ASP) T cell receptor (TCR) γ gene. Blood samples from 15 HTLV–I asymptomatic carriers (seven ASM and eight ASP) were tested for the clonal TCR-γ gene and submitted for sRNA library construction together with blood samples of five healthy controls (HCs) using Illumina sequencing platform. The sRNA-sequencing reads were aligned, annotated and profiled using various bioinformatics tools. Based on these results, possible markers were validated in the study samples by performing reverse transcription-quantitative (RT-q)PCR analysis. A total of 76 known sRNAs and 52 putative novel sRNAs were identified. Among them, 44 known and 34 potential novel sRNAs were differentially expressed in the ASM and ASP libraries compared with HCs. In addition, 10 known sRNAs were exclusively dysregulated in the ASM group and one (transfer RNA 65) was significantly upregulated in the ASP group. Homo sapiens (hsa) microRNA (miRNA/mir)-23a-3p, −28-5p, hsa-let-7e-5p and hsa-mir-28-3p and −361-5p were the most abundantly upregulated mature miRNAs and hsa-mir-363-3p, −532-5p, −106a-5p, −25-3p and −30e-5p were significantly downregulated miRNAs (P<0.05) with a >2-fold difference between the ASM and ASP groups compared with HCs. Based on these results, hsa-mir-23a-3p and −363-3p were selected for additional validation. However, the quantification of these two miRNAs using RT-qPCR did not provide any significant differences. While the present study failed to identify predictive sRNA markers to distinguish between ASM and ASP, the MPS results revealed differential sRNA expression profiles in the PBMCs of HTLV-1 asymptomatic carriers (ASM and ASP) compared with HCs.
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Affiliation(s)
- Daniela Raguer Valadão de Souza
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | - Rodrigo Pessôa
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | - Andrezza Nascimento
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | - Youko Nukui
- Department of Hematology, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | - Juliana Pereira
- Department of Hematology, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | - Jorge Casseb
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | | | - Alberto José da Silva Duarte
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | | | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation Unit 03,Clinics Hospital, Faculty of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
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Emamgholipour S, Ebrahimi R, Bahiraee A, Niazpour F, Meshkani R. Acetylation and insulin resistance: a focus on metabolic and mitogenic cascades of insulin signaling. Crit Rev Clin Lab Sci 2020:1-19. [DOI: 10.1080/10408363.2019.1699498] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Solaleh Emamgholipour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reyhane Ebrahimi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Students’ Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Bahiraee
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Farshad Niazpour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Meshkani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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12
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Ebrahimi R, Bahiraee A, Niazpour F, Emamgholipour S, Meshkani R. The role of microRNAs in the regulation of insulin signaling pathway with respect to metabolic and mitogenic cascades: A review. J Cell Biochem 2019; 120:19290-19309. [PMID: 31364207 DOI: 10.1002/jcb.29299] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/27/2019] [Indexed: 12/18/2022]
Abstract
Insulin resistance (IR) is a shared pathological condition among type 2 diabetes, obesity, cardiovascular disease, and other metabolic disorders. It is growing significantly all over the world and consequently, a substantial effort is needed for developing the potential novel diagnostics and therapeutics. An insulin signaling pathway is tightly modulated by different mechanisms including the epigenetic modifications. Today, a deal of great attention has been shifted towards the regulatory role of noncoding RNAs on target proteins of the insulin signaling pathway. Noncoding RNAs are a major area of the epigenetics which control gene expression at the posttranscriptional levels and include a large class of microRNAs (miRNAs). With this in view, many studies have implicated the mediatory effects of miRNAs on the downstream metabolic and mitogenic proteins of the insulin signaling pathway. Since providing new biomarkers for the early diagnosis of IR and related metabolic traits are very significant, we intended to review the possible role of miRNAs in the regulation of the insulin signaling pathway, with a primary focus on the downstream target proteins of the metabolic and mitogenic cascades.
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Affiliation(s)
- Reyhane Ebrahimi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Bahiraee
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Farshad Niazpour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Solaleh Emamgholipour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Meshkani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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13
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Wright C, Rajpurohit A, Burke EE, Williams C, Collado-Torres L, Kimos M, Brandon NJ, Cross AJ, Jaffe AE, Weinberger DR, Shin JH. Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. BMC Genomics 2019; 20:513. [PMID: 31226924 PMCID: PMC6588940 DOI: 10.1186/s12864-019-5870-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias. Furthermore, evaluations of the quantification of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited. No study had yet evaluated the quantification of isomiRs of altered length or compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases. RESULTS All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency. CONCLUSIONS Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
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Affiliation(s)
- Carrie Wright
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,AstraZeneca Postdoc Program, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Anandita Rajpurohit
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Emily E Burke
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Courtney Williams
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Martha Kimos
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Nicholas J Brandon
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Alan J Cross
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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14
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Xu Y, Zhang Y, Yang Y, Liu X, Chen Y. Seminal plasma miR‐210‐3p is a biomarker for screening dyszoospermia caused by varicocele. Andrologia 2019; 51:e13244. [PMID: 30714182 DOI: 10.1111/and.13244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/05/2019] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
- Yawei Xu
- Department of Urology, Tianjin Institute of Urology The Second Hospital of Tianjin Medical University Tianjin China
| | - Yuanyuan Zhang
- Department of Thyroid Surgery The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Yongjiao Yang
- Department of Urology, Tianjin Institute of Urology The Second Hospital of Tianjin Medical University Tianjin China
| | - Xiaoqiang Liu
- Department of Urology Tianjin Medical University General Hospital Tianjin China
| | - Yegang Chen
- Department of Urology, Tianjin Institute of Urology The Second Hospital of Tianjin Medical University Tianjin China
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15
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Mohamed ZI, Tee SF, Chow TJ, Loh SY, Yong HS, Bakar AKA, Tang PY. Functional characterization of two variants in the 3'-untranslated region (UTR) of transcription factor 4 gene and their association with schizophrenia in sib-pairs from multiplex families. Asian J Psychiatr 2019; 40:76-81. [PMID: 30771755 DOI: 10.1016/j.ajp.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 01/30/2019] [Accepted: 02/07/2019] [Indexed: 12/12/2022]
Abstract
Transcription factor 4 (TCF4) gene plays an important role in nervous system development and it always associated with the risk of schizophrenia. Since miRNAs regulate targetgenes by binding to 3'UTRs of target mRNAs, the functional variants located in 3'UTR of TCF4 are highly suggested to affect the gene expressions in schizophrenia. To test the hypothesis regarding the effects of the variants located in 3'UTR of TCF4, we conducted an in silico analysis to identify the functional variants and their predicted functions. In this study, we sequenced the 3'UTR of TCF4 in 13 multiplex schizophrenia families and 14 control families. We found two functional variants carried by three unrelated patients. We determined that the C allele of rs1272363 and the TC insert of rs373174214 might suppress post- transcriptional expression. Secondly, we cloned the region that flanked these two variants into a dual luciferase reporter system and compared the luciferase activities between the pmirGLO-TCF4 (control), pmirGLO-TCF4-rs373174214 and pmirGLO-TCF4-rs1273263. Both pmirGLO-TCF4-rs373174214 and pmirGLO-TCF4-rs1273263 caused lower reporter gene activities, as compared to the control. However, only the C allele of rs1272363 reduced the luciferase activity significantly (p = 0.0231). Our results suggested that rs1273263 is a potential regulator of TCF4 expression, and might be associated with schizophrenia.
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Affiliation(s)
- Zahra Isnaini Mohamed
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Cheras 43000 Kajang, Malaysia
| | - Shiau Foon Tee
- Department of Chemical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Cheras 43000 Kajang, Malaysia
| | - Tze Jen Chow
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Cheras 43000 Kajang, Malaysia
| | - Siew Yim Loh
- Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hoi Sen Yong
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Pek Yee Tang
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Cheras 43000 Kajang, Malaysia.
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16
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Signaling network between the dysregulated expression of microRNAs and mRNAs in propofol-induced developmental neurotoxicity in mice. Sci Rep 2018; 8:14172. [PMID: 30242182 PMCID: PMC6155049 DOI: 10.1038/s41598-018-32474-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 08/29/2018] [Indexed: 12/18/2022] Open
Abstract
Mounting evidence has demonstrated that general anesthetics could induce acute neuroapoptosis in developing animals followed by long-term cognitive dysfunction, with the mechanisms remaining largely unknown. The aim of this study was to investigate the effect of the intravenous anesthetic propofol on the profiles of microRNAs (miRNAs) and messenger RNAs (mRNAs), and their interactive signaling networks in the developing mouse hippocampus. Postnatal day 7 (P7) mice were exposed to propofol for 3 hours. Hippocampi were harvested from both P7 (3 hours after exposure) and P60 mice for the analysis of the expression of 726 miRNAs and 24,881 mRNAs, and apoptosis. Long-term memory ability of P60 mice was analyzed using the Morris Water Maze. Propofol induced acute apoptosis in the hippocampus, and impaired memory function of mice. There were 100 altered mRNAs and 18 dysregulated miRNAs in the propofol-treated hippocampi compared with the intralipid-treated control tissues on P7. Bioinformatics analysis of these abnormally expressed genes on P7 indicated that 34 dysregulated miRNA-mRNA target pairs were related to pathological neurological and developmental disorder processes such as cell viability, cell morphology and migration, neural stem cell proliferation and neurogenesis, oligodendrocyte myelination, reactive oxygen species, and calcium signaling. Neonatal propofol exposure also resulted in the abnormal expression of 49 mRNAs and 4 miRNAs in P60 mouse hippocampi. Specifically, bioinformatics analysis indicates that among these dysregulated mRNAs and miRNAs, there were 2 dysregulated miRNA-mRNA targets pairs (Fam46a/miR-363-3p and Rgs3/miR-363-3p) that might be related to the effect of propofol on long-term cognitive function. Collectively, our novel investigation indicates that acute and long-term dysregulated miRNA-mRNA signaling networks potentially participate in propofol-induced developmental neurotoxicity.
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17
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Frankel D, Delecourt V, Harhouri K, De Sandre-Giovannoli A, Lévy N, Kaspi E, Roll P. MicroRNAs in hereditary and sporadic premature aging syndromes and other laminopathies. Aging Cell 2018; 17:e12766. [PMID: 29696758 PMCID: PMC6052405 DOI: 10.1111/acel.12766] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
Hereditary and sporadic laminopathies are caused by mutations in genes encoding lamins, their partners, or the metalloprotease ZMPSTE24/FACE1. Depending on the clinical phenotype, they are classified as tissue‐specific or systemic diseases. The latter mostly manifest with several accelerated aging features, as in Hutchinson–Gilford progeria syndrome (HGPS) and other progeroid syndromes. MicroRNAs are small noncoding RNAs described as powerful regulators of gene expression, mainly by degrading target mRNAs or by inhibiting their translation. In recent years, the role of these small RNAs has become an object of study in laminopathies using in vitro or in vivo murine models as well as cells/tissues of patients. To date, few miRNAs have been reported to exert protective effects in laminopathies, including miR‐9, which prevents progerin accumulation in HGPS neurons. The recent literature has described the potential implication of several other miRNAs in the pathophysiology of laminopathies, mostly by exerting deleterious effects. This review provides an overview of the current knowledge of the functional relevance and molecular insights of miRNAs in laminopathies. Furthermore, we discuss how these discoveries could help to better understand these diseases at the molecular level and could pave the way toward identifying new potential therapeutic targets and strategies based on miRNA modulation.
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Affiliation(s)
- Diane Frankel
- Aix Marseille Univ; INSERM; MMG; Marseille France
- APHM, Hôpital la Timone; Service de Biologie Cellulaire; Marseille France
| | | | | | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ; INSERM; MMG; Marseille France
- APHM, Hôpital la Timone; Département de Génétique Médicale; Marseille France
| | - Nicolas Lévy
- Aix Marseille Univ; INSERM; MMG; Marseille France
- APHM, Hôpital la Timone; Département de Génétique Médicale; Marseille France
| | - Elise Kaspi
- Aix Marseille Univ; INSERM; MMG; Marseille France
- APHM, Hôpital la Timone; Service de Biologie Cellulaire; Marseille France
| | - Patrice Roll
- Aix Marseille Univ; INSERM; MMG; Marseille France
- APHM, Hôpital la Timone; Service de Biologie Cellulaire; Marseille France
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18
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Abstract
Since more than 70% of clinically used drugs are excreted from the body through metabolic processes, drug metabolism is a key determinant of pharmacokinetics, drug response and drug toxicity. Much progress has been made in understanding drug-drug interactions via the inhibition or induction of cytochrome P450s (P450, CYP), as well as the effects of genetic polymorphisms of P450s on pharmacokinetics, and this has facilitated the progress of optimized pharmacotherapy in the clinic. Now, similar information is needed for non-CYP enzymes, especially concerning Phase I enzymes, based on advanced basic and clinical studies. Recently, it was revealed that post-transcriptional regulation by microRNAs or RNA editing plays a significant role in regulating the expression of drug-metabolizing enzymes, thus conferring variability in the detoxification and metabolic activation of drugs or chemicals. Changes in the expression profile of microRNAs in tissues or body fluids can be a biomarker of drug response and toxicity; therefore, such studies could also be useful for drug repositioning. In addition, microRNAs are involved in pharmacogenetics, because single nucleotide polymorphisms in microRNA binding sites of mRNAs, or microRNAs themselves, may cause changes in gene expression. Some microRNA-related polymorphisms could be biomarkers of the clinical outcome of pharmacotherapy. In this review article, recent progress and future directions for drug metabolism studies are discussed.
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Affiliation(s)
- Miki Nakajima
- Faculty of Pharmaceutical Sciences, Kanazawa University
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19
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Kiessling S, Ucar A, Chowdhury K, Oster H, Eichele G. Genetic background-dependent effects of murine micro RNAs on circadian clock function. PLoS One 2017; 12:e0176547. [PMID: 28448626 PMCID: PMC5407787 DOI: 10.1371/journal.pone.0176547] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/12/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRs) are important regulators of a wide range of biological processes. Antagomir studies suggest an implication of miR-132 in the functionality of the mammalian circadian clock. miR-212 and miR-132 are tandemly processed from the same transcript and share the same seed region. We found the clock modulator miR-132 and miR-212 to be expressed rhythmically in the central circadian clock. Consequently, mRNAs implicated in circadian functions may likely be targeted by both miRs. To further characterize the circadian role we generated mice with stable deletion of the miR-132/212 locus and compared the circadian behavior of mutant and wild-type control animals on two genetic backgrounds frequently used in chronobiological research, C57BL/6N and 129/Sv. Surprisingly, the wheel-running activity phenotype of miR mutant mice was highly background specific. A prolonged circadian free-running period in constant darkness was found in 129/Sv, but not in C57BL/6N miR-132/212 knockout mice. In contrast, in C57BL/6N, but not in 129/Sv miRNA-132/212 knockout mice a lengthened free-running period was observed in constant light conditions. Furthermore, miR-132/212 knockout mice on 129/Sv background exhibited enhanced photic phase shifts of locomotor activity accompanied by reduced light induction of Period gene transcription in the SCN. This phenotype was absent in miRNA-132/212 knockout mice on a C57BL/6N background. Together, our results reveal a strain and light regimen-specific function of miR-132/212 in the circadian clock machinery suggesting that miR-132 and miR-212 act as background-dependent circadian rhythm modulators.
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Affiliation(s)
- Silke Kiessling
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Nutrition and Immunology, Technical University of Munich, Freising, Germany
- * E-mail:
| | - Ahmet Ucar
- Department of Molecular Cell Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- University of Manchester, Faculty of Biology, Medicine and Health, Division of Clinical and Molecular Cancer Sciences, Manchester, United Kingdom
| | - Kamal Chowdhury
- Department of Molecular Cell Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henrik Oster
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Chronophysiology Group, Medical Department I, University of Lübeck, Lübeck, Germany
| | - Gregor Eichele
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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20
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Salehi S, Emadi-Baygi M, Rezaei M, Kelishadi R, Nikpour P. Identification of a New Single-nucleotide Polymorphism within the Apolipoprotein A5 Gene, Which is Associated with Metabolic Syndrome. Adv Biomed Res 2017; 6:24. [PMID: 28401071 PMCID: PMC5360002 DOI: 10.4103/2277-9175.201688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background: Metabolic syndrome (MetS) is a common disorder which is a constellation of clinical features including abdominal obesity, increased level of serum triglycerides (TGs) and decrease of serum high-density lipoprotein-cholesterol (HDL-C), elevated blood pressure, and glucose intolerance. The apolipoprotein A5 (APOA5) is involved in lipid metabolism, influencing the level of plasma TG and HDL-C. In the present study, we aimed to investigate the associations between four INDEL variants of APOA5 gene and the MetS risk. Materials and Methods: In this case–control study, we genotyped 116 Iranian children and adolescents with/without MetS by using Sanger sequencing method for these INDELs. Then, we explored the association of INDELs with MetS risk and their clinical components by logistic regression and one-way analysis of variance analyses. Results: We identified a novel insertion polymorphism, c. *282–283 insAG/c. *282–283 insG variant, which appears among case and control groups. rs72525532 showed a significant difference for TG levels between various genotype groups. In addition, there were significant associations between newly identified single-nucleotide polymorphism (SNP) and rs72525532 with MetS risk. Conclusions: These results show that rs72525532 and the newly identified SNP may influence the susceptibility of the individuals to MetS.
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Affiliation(s)
- Samaneh Salehi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran; Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Majdaddin Rezaei
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Roya Kelishadi
- Department of Paediatrics, Child Growth and Development Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan, Iran
| | - Parvaneh Nikpour
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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21
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Nardelli C, Granata I, Iaffaldano L, D'Argenio V, Del Monaco V, Maruotti GM, Omodei D, Del Vecchio L, Martinelli P, Salvatore F, Guarracino MR, Sacchetti L, Pastore L. miR-138/miR-222 Overexpression Characterizes the miRNome of Amniotic Mesenchymal Stem Cells in Obesity. Stem Cells Dev 2017; 26:4-14. [DOI: 10.1089/scd.2016.0127] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Carmela Nardelli
- CEINGE-Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Ilaria Granata
- LabGTP (Laboratory of Genomics, Transcriptomics and Proteomics), Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Naples, Italy
| | - Laura Iaffaldano
- CEINGE-Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | | | - Giuseppe Maria Maruotti
- Dipartimento di Neuroscienze e Scienze Riproduttive ed Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Daniela Omodei
- Institute of Genetics and Biophysics “Adriano-Buzzati Traverso,” CNR, Naples, Italy
| | - Luigi Del Vecchio
- CEINGE-Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Pasquale Martinelli
- Dipartimento di Neuroscienze e Scienze Riproduttive ed Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Mario Rosario Guarracino
- LabGTP (Laboratory of Genomics, Transcriptomics and Proteomics), Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Naples, Italy
| | | | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate S.C.a R.L., Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
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22
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Deng S, Wang H, Jia C, Zhu S, Chu X, Ma Q, Wei J, Chen E, Zhu W, Macon CJ, Jayaweera DT, Dykxhoorn DM, Dong C. MicroRNA-146a Induces Lineage-Negative Bone Marrow Cell Apoptosis and Senescence by Targeting Polo-Like Kinase 2 Expression. Arterioscler Thromb Vasc Biol 2016; 37:280-290. [PMID: 27908889 DOI: 10.1161/atvbaha.116.308378] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Lineage-negative bone marrow cells (lin- BMCs) are enriched in endothelial progenitor cells and mediate vascular repair. Aging-associated senescence and apoptosis result in reduced number and functionality of lin- BMCs, impairing their prorepair capacity. The molecular mechanisms underlying lin- BMC senescence and apoptosis are poorly understood. MicroRNAs (miRNAs) regulate many important biological processes. The identification of miRNA-mRNA networks that modulate the health and functionality of lin- BMCs is a critical step in understanding the process of vascular repair. The aim of this study was to characterize the role of the miR-146a-Polo-like kinase 2 (Plk2) network in regulating lin- BMC senescence, apoptosis, and their angiogenic capability. APPROACH AND RESULTS Transcriptome analysis in lin- BMCs isolated from young and aged wild-type and ApoE-/- (apolipoprotein E) mice showed a significant age-associated increase in miR-146a expression. In silico analysis, expression study and Luciferase reporter assay established Plk2 as a direct target of miR-146a. miR-146a overexpression in young lin- BMCs inhibited Plk2 expression, resulting in increased senescence and apoptosis, via p16Ink4a/p19Arf and p53, respectively, as well as impaired angiogenic capacity in vitro and in vivo. Conversely, suppression of miR-146a in aged lin- BMCs increased Plk2 expression and rejuvenated lin- BMCs, resulting in decreased senescence and apoptosis, leading to improved angiogenesis. CONCLUSIONS (1) miR-146a regulates lin- BMC senescence and apoptosis by suppressing Plk2 expression that, in turn, activates p16Ink4a/p19Arf and p53 and (2) modulation of miR-146a or its target Plk2 may represent a potential therapeutic intervention to improve lin- BMC-mediated angiogenesis and vascular repair.
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Affiliation(s)
- Shanming Deng
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Huilan Wang
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Chunling Jia
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Shoukang Zhu
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Xianming Chu
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Qi Ma
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Jianqin Wei
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Emily Chen
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Wei Zhu
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Conrad J Macon
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Dushyantha T Jayaweera
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Derek M Dykxhoorn
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.)
| | - Chunming Dong
- From the Department of Medicine (S.D., H.W., C.J., S.Z., X.C., Q.M., J.W., E.C., W.Z., C.J.M., D.T.J, C.D.) and John T. Macdonald Foundation Department of Human Genetics (D.M.D.), Miller School of Medicine, University of Miami, FL; and Department of Cardiology, The Affiliated Hospital of Qingdao University, China (X.C.).
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Xu W, Wang F, Yu Z, Xin F. Epigenetics and Cellular Metabolism. GENETICS & EPIGENETICS 2016; 8:43-51. [PMID: 27695375 PMCID: PMC5038610 DOI: 10.4137/geg.s32160] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/25/2016] [Accepted: 08/01/2016] [Indexed: 01/03/2023]
Abstract
Living eukaryotic systems evolve delicate cellular mechanisms for responding to various environmental signals. Among them, epigenetic machinery (DNA methylation, histone modifications, microRNAs, etc.) is the hub in transducing external stimuli into transcriptional response. Emerging evidence reveals the concept that epigenetic signatures are essential for the proper maintenance of cellular metabolism. On the other hand, the metabolite, a main environmental input, can also influence the processing of epigenetic memory. Here, we summarize the recent research progress in the epigenetic regulation of cellular metabolism and discuss how the dysfunction of epigenetic machineries influences the development of metabolic disorders such as diabetes and obesity; then, we focus on discussing the notion that manipulating metabolites, the fuel of cell metabolism, can function as a strategy for interfering epigenetic machinery and its related disease progression as well.
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Affiliation(s)
- Wenyi Xu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fengzhong Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhongsheng Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Fengjiao Xin
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Common miR-590 Variant rs6971711 Present Only in African Americans Reduces miR-590 Biogenesis. PLoS One 2016; 11:e0156065. [PMID: 27196440 PMCID: PMC4873136 DOI: 10.1371/journal.pone.0156065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/09/2016] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are recognized as important regulators of cardiac development, hypertrophy and fibrosis. Recent studies have demonstrated that genetic variations which cause alterations in miRNA:target interactions can lead to disease. We hypothesized that genetic variations in miRNAs that regulate cardiac hypertrophy/fibrosis might be involved in generation of the cardiac phenotype in patients diagnosed with hypertrophic cardiomyopathy (HCM). To investigate this question, we Sanger sequenced 18 miRNA genes previously implicated in myocyte hypertrophy/fibrosis and apoptosis, using genomic DNA isolated from the leukocytes of 199 HCM patients. We identified a single nucleotide polymorphism (rs6971711, C57T SNP) at the 17th position of mature miR-590-3p (= 57th position of pre-miR-590) that is common in individuals of African ancestry. SNP frequency was higher in African American HCM patients (n = 55) than ethnically-matched controls (n = 100), but the difference was not statistically significant (8.2% vs. 6.5%; p = 0.5). Using a cell culture system, we discovered that presence of this SNP resulted in markedly lower levels of mature miR-590-5p (39 ± 16%, p<0.003) and miR-590-3p (20 ± 2%, p<0.003), when compared with wild-type (WT) miR-590, without affecting levels of pri-miR-590 and pre-miR-590. Consistent with this finding, the SNP resulted in reduced target suppression when compared to WT miR-590 (71% suppression by WT vs 60% suppression by SNP, p<0.03). Since miR-590 can regulate TGF-β, Activin A and Akt signaling, SNP-induced reduction in miR-590 biogenesis could influence cardiac phenotype by de-repression of these signaling pathways. Since the SNP is only present in African Americans, population studies in this patient population would be valuable to investigate effects of this SNP on myocyte function and cardiac physiology.
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You WD, Tang QL, Wang L, Lei J, Feng JF, Mao Q, Gao GY, Jiang JY. Alteration of microRNA expression in cerebrospinal fluid of unconscious patients after traumatic brain injury and a bioinformatic analysis of related single nucleotide polymorphisms. Chin J Traumatol 2016; 19:11-5. [PMID: 27033266 PMCID: PMC4897835 DOI: 10.1016/j.cjtee.2016.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
PURPOSE It is becoming increasingly clear that genetic factors play a role in traumatic brain injury (TBI), whether in modifying clinical outcome after TBI or determining susceptibility to it. MicroRNAs are small RNA molecules involved in various pathophysiological processes by repressing target genes at the post- transcriptional level, and TBI alters microRNA expression levels in the hippocampus and cortex. This study was designed to detect differentially expressed microRNAs in the cerebrospinal fluid (CSF) of TBI patients remaining unconscious two weeks after initial injury and to explore related single nucleotide polymorphisms (SNPs). METHODS We used a microarray platform to detect differential microRNA expression levels in CSF samples from patients with post-traumatic coma compared with samples from controls. A bioinformatic scan was performed covering microRNA gene promoter regions to identify potential functional SNPs. RESULTS Totally 26 coma patients and 21 controls were included in this study, with similar distribution of age and gender between the two groups. Microarray showed that fourteen microRNAs were differentially expressed, ten at higher and four at lower expression levels in CSF of traumatic coma patients compared with controls (p<0.05). One SNP (rs11851174 allele: C/T) was identified in the motif area of the microRNA hsa-miR-431-3P gene promoter region. CONCLUSION The altered microRNA expression levels in CSF after brain injury together with SNP identified within the microRNA gene promoter area provide a new perspective on the mechanism of impaired consciousness after TBI. Further studies are needed to explore the association between the specific microRNAs and their related SNPs with post-traumatic unconsciousness.
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26
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Lu J, Gu H, Tang Q, Wu W, Yuan B, Guo D, Wei Y, Sun H, Xia Y, Ding H, Hu L, Chen D, Sha J, Wang X. Common SNP in hsa-miR-196a-2 increases hsa-miR-196a-5p expression and predisposes to idiopathic male infertility in Chinese Han population. Sci Rep 2016; 6:19825. [PMID: 26805933 PMCID: PMC4726409 DOI: 10.1038/srep19825] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/07/2015] [Indexed: 01/05/2023] Open
Abstract
MicroRNA plays an important role in spermatogenesis. Whether pre-miRNAs polymorphisms are associated with idiopathic male infertility remains obscure. In this study, 1378 idiopathic infertile males and 486 fertile controls were included between 2006 and 2014. Genotype of three polymorphisms (hsa-mir-146a rs2910164, hsa-mir-196a-2 rs11614913, and hsa-mir-499 rs3746444) and expression of miRNA in seminal plasma were examined by TaqMan method. The role of hsa-miR-196a-5p in cell proliferation, apoptosis and cell cycle were also examined in GC-2 cells. Our results demonstrated that rs11614913 of hsa-miR-196a-2 was significantly associated with idiopathic infertility (TT vs. CT: P = 0.014; TT vs. CC: P = 0.005; TT vs. CT + CC: P = 0.003). In following stratified analysis, we found that rs11614913 exhibited a significantly higher risk of asthenospermia, oligozoospermia and azoospermia. However, no significant association was observed between the other two polymorphisms and idiopathic male infertility risk. In a genotype-expression correlation analysis, rs11614913 CC was significantly associated with elevated expression of hsa-miR-196a-5p (P < 0.05). Additionally, apoptosis levels were significantly increased in hsa-miR-196a-5p mimic treated GC-2 cells, while decreased in hsa-miR-196a-5p inhibitor treated GC-2 cells. Our data revealed a significant relationship between hsa-miR-196a-2 polymorphism and idiopathic male infertility.
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Affiliation(s)
- Jing Lu
- State Key Laboratory of Reproductive Medicine, Department of Reproduction, Nanjing Maternal and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Hao Gu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Qiuqin Tang
- State Key Laboratory of Reproductive Medicine, Department of Obstetrics, Nanjing Maternal and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Wei Wu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China.,Wuxi Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Wuxi 214002, China
| | - Beilei Yuan
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Dan Guo
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Yongyue Wei
- Department of Epidemiology and Biostatistics, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 210029, China
| | - Hong Sun
- Department of Microbial and Molecular Systems, KULeuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Hongjuan Ding
- State Key Laboratory of Reproductive Medicine, Department of Obstetrics, Nanjing Maternal and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Lingqing Hu
- Wuxi Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Wuxi 214002, China
| | - Daozhen Chen
- Wuxi Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Wuxi 214002, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
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Goda N, Murase H, Kasezawa N, Goda T, Yamakawa-Kobayashi K. Polymorphism in microRNA-binding site in HNF1B influences the susceptibility of type 2 diabetes mellitus: a population based case-control study. BMC MEDICAL GENETICS 2015; 16:75. [PMID: 26329304 PMCID: PMC4557749 DOI: 10.1186/s12881-015-0219-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/18/2015] [Indexed: 02/05/2023]
Abstract
Background Recent genome-wide association studies (GWAS) have identified many SNPs associated with type 2 diabetes mellitus (T2DM). However, the functional roles for most of the SNPs have not been elucidated. MicroRNAs (miRNAs) are key regulators of gene expression involved in the development and progression of various diseases including T2DM. In this study, we investigated whether commonly occurring SNPs modulate miRNA-directed regulation of gene expression, and whether such SNPs in miRNA-binding sites are associated with the susceptibility for T2DM. Methods Genotypes of eleven 3′ untranslated region (UTR) SNPs of seven susceptibility genes for T2DM were determined in 353 T2DM patients and 448 control subjects. In addition, the interactions of miRNAs with the 3′UTR in the hepatocyte nuclear factor 1β (HNF1B) gene were investigated using luciferase reporter assays. Results One 3′UTR SNP (rs2229295) in the HNF1B gene was significantly associated with T2DM, and the frequency of an A allele (rs2229295) in T2DM patients was decreased compared with that in controls. Luciferase reporter assays showed that the SNP (rs2229295) altered the binding of two miRNAs (hsa-miR-214-5p and hsa-miR-550a-5p). Conclusions We have detected the interactions of hsa-miR-214-5p/hsa-miR-550a-5p and the 3′UTR SNP of the HNF1B gene by in vitro luciferase reporter assays, and propose that the binding of such miRNAs regulates the expression of the HNF1B gene and the susceptibility of T2DM. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0219-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naoki Goda
- Laboratory of Human Genetics, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
| | - Haruna Murase
- Laboratory of Human Genetics, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
| | - Nobuhiko Kasezawa
- Department of Data Managements for Health Evaluation & Promotion, Shizuoka Medical Center, Shizuoka, 422-8033, Japan. .,Present address: Fuji iki-iki Hospital, Health Promotion Center, Temma, Fuji-shi, Shizuoka, 419-0205, Japan.
| | - Toshinao Goda
- Laboratory of Nutritional Physiology, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
| | - Kimiko Yamakawa-Kobayashi
- Laboratory of Human Genetics, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
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Quantitative Assessment of the Association between Genetic Variants in MicroRNAs and Colorectal Cancer Risk. BIOMED RESEARCH INTERNATIONAL 2015; 2015:276410. [PMID: 26078942 PMCID: PMC4452836 DOI: 10.1155/2015/276410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 04/22/2015] [Accepted: 05/05/2015] [Indexed: 12/24/2022]
Abstract
Background. The associations between polymorphisms in microRNAs and the susceptibility of colorectal cancer (CRC) were inconsistent in previous studies. This study aims to quantify the strength of the correlation between the four common polymorphisms among microRNAs (hsa-mir-146a rs2910164, hsa-mir-149 rs2292832, hsa-mir-196a2 rs11614913, and hsa-mir-499 rs3746444) and CRC risk. Methods. We searched PubMed, Web of Knowledge, and CNKI to find relevant studies. The combined odds ratio (OR) with 95% confidence interval (95% CI) was used to estimate the strength of the association in a fixed or random effect model. Results. 15 studies involving 5,486 CRC patients and 7,184 controls were included. Meta-analyses showed that rs3746444 had association with CRC risk in Caucasians (OR = 0.57, 95% CI = 0.34–0.95). In the subgroup analysis, we found significant associations between rs2910164 and CRC in hospital based studies (OR = 1.24, 95% CI = 1.03–1.49). rs2292832 may be a high risk factor of CRC in population based studied (OR = 1.18, 95% CI = 1.08–1.38). Conclusion. This meta-analysis showed that rs2910164 and rs2292832 may increase the risk of CRC. However, rs11614913 polymorphism may reduce the risk of CRC. rs3746444 may have a decreased risk to CRC in Caucasians.
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Zhang W, Yan L, Li Y, Chen W, Hu N, Wang H, Ou H. Roles of miRNA-24 in regulating endothelial nitric oxide synthase expression and vascular endothelial cell proliferation. Mol Cell Biochem 2015; 405:281-9. [DOI: 10.1007/s11010-015-2418-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 04/18/2015] [Indexed: 11/30/2022]
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Bandiera S, Pfeffer S, Baumert TF, Zeisel MB. miR-122--a key factor and therapeutic target in liver disease. J Hepatol 2015; 62:448-57. [PMID: 25308172 DOI: 10.1016/j.jhep.2014.10.004] [Citation(s) in RCA: 427] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/26/2014] [Accepted: 10/02/2014] [Indexed: 02/06/2023]
Abstract
Being the largest internal organ of the human body with the unique ability of self-regeneration, the liver is involved in a wide variety of vital functions that require highly orchestrated and controlled biochemical processes. Increasing evidence suggests that microRNAs (miRNAs) are essential for the regulation of liver development, regeneration and metabolic functions. Hence, alterations in intrahepatic miRNA networks have been associated with liver disease including hepatitis, steatosis, cirrhosis and hepatocellular carcinoma (HCC). miR-122 is the most frequent miRNA in the adult liver, and a central player in liver biology and disease. Furthermore, miR-122 has been shown to be an essential host factor for hepatitis C virus (HCV) infection and an antiviral target, complementary to the standard of care using direct-acting antivirals or interferon-based treatment. This review summarizes our current understanding of the key role of miR-122 in liver physiology and disease, highlighting its role in HCC and viral hepatitis. We also discuss the perspectives of miRNA-based therapeutic approaches for viral hepatitis and liver disease.
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Affiliation(s)
- Simonetta Bandiera
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Sébastien Pfeffer
- Université de Strasbourg, Strasbourg, France; Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, France; Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
| | - Mirjam B Zeisel
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, France.
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Tarquini F, Picchiassi E, Centra M, Pennacchi L, Bini V, Cappuccini B, Torlone E, Coata G, Di Renzo G, Brancorsini S. Body mass index associated to rs2021966 ENPP1 polymorphism increases the risk for gestational diabetes mellitus. Gynecol Endocrinol 2015; 31:83-6. [PMID: 25222839 DOI: 10.3109/09513590.2014.958994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Gestational diabetes mellitus (GDM) is a condition of impaired glucose tolerance occurring in 1-14% of all pregnancies. This wide range reflects pathological involvement of single nucleotide polymorphisms (SNPs) and maternal weight as risk factors. This study evaluated the association of genetic component and maternal factors to identify women with higher risk of developing GDM. About 240 pregnant women characterized by negative Oral Glucose Tolerance Test (-OGTT) and 38 with positive OGGT (+OGTT) were enrolled. SNPs for ENPP1, NRF1, VEGFA, CEBPA, and PIK3R1 were analyzed by SNP genotyping. An association study was performed and differences in genotype and allele frequencies between cases and controls were analyzed by χ(2) test. +OGTT was associated to high values of pre-gestational body mass index (BMI) and age. SNP for ENPP1 gene was associated to +OGTT, while genetic variants for other genes did not correlate to GDM. ENPP1 homozygous for A allele and heterozygous showed altered frequencies in +OGTT when compared with -OGTT. Association of both pre-gestational BMI and age with AA homozygous genotype increased significantly the risk to +OGTT. Our results demonstrate that correlation of age and pre-gestational BMI with homozygous for A allele increased significantly the risk of impaired glucose tolerance and GDM.
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Affiliation(s)
- Federica Tarquini
- Department of Surgical and Biomedical Sciences, Section of Obstetrics and Gynecology , University of Perugia, Perugia , Italy
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A novel locus for a hereditary recurrent neuropathy on chromosome 21q21. Neuromuscul Disord 2014; 24:660-5. [PMID: 24878226 DOI: 10.1016/j.nmd.2014.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/31/2014] [Accepted: 04/11/2014] [Indexed: 01/13/2023]
Abstract
Hereditary recurrent neuropathies are uncommon. Disorders with a known molecular basis falling within this group include hereditary neuropathy with liability to pressure palsies (HNPP) due to the deletion of the PMP22 gene or to mutations in this same gene, and hereditary neuralgic amyotrophy (HNA) caused by mutations in the SEPT9 gene. We report a three-generation family presenting a hereditary recurrent neuropathy without pathological changes in either PMP22 or SEPT9 genes. We performed a genome-wide mapping, which yielded a locus of 12.4 Mb on chromosome 21q21. The constructed haplotype fully segregated with the disease and we found significant evidence of linkage. After mutational screening of genes located within this locus, encoding for proteins and microRNAs, as well as analysis of large deletions/insertions, we identified 71 benign polymorphisms. Our findings suggest a novel genetic locus for a recurrent hereditary neuropathy of which the molecular defect remains elusive. Our results further underscore the clinical and genetic heterogeneity of this group of neuropathies.
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Mining the 3'UTR of autism-implicated genes for SNPs perturbing microRNA regulation. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:92-104. [PMID: 24747189 PMCID: PMC4411356 DOI: 10.1016/j.gpb.2014.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/09/2013] [Accepted: 01/11/2014] [Indexed: 11/24/2022]
Abstract
Autism spectrum disorder (ASD) refers to a group of childhood neurodevelopmental disorders with polygenic etiology. The expression of many genes implicated in ASD is tightly regulated by various factors including microRNAs (miRNAs), a class of noncoding RNAs ~22 nucleotides in length that function to suppress translation by pairing with 'miRNA recognition elements' (MREs) present in the 3'untranslated region (3'UTR) of target mRNAs. This emphasizes the role played by miRNAs in regulating neurogenesis, brain development and differentiation and hence any perturbations in this regulatory mechanism might affect these processes as well. Recently, single nucleotide polymorphisms (SNPs) present within 3'UTRs of mRNAs have been shown to modulate existing MREs or even create new MREs. Therefore, we hypothesized that SNPs perturbing miRNA-mediated gene regulation might lead to aberrant expression of autism-implicated genes, thus resulting in disease predisposition or pathogenesis in at least a subpopulation of ASD individuals. We developed a systematic computational pipeline that integrates data from well-established databases. By following a stringent selection criterion, we identified 9 MRE-modulating SNPs and another 12 MRE-creating SNPs in the 3'UTR of autism-implicated genes. These high-confidence candidate SNPs may play roles in ASD and hence would be valuable for further functional validation.
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Li Y, Konicki WS, Wright JT, Suggs C, Xue H, Kuehl MA, Kulkarni AB, Gibson CW. Mouse genetic background influences the dental phenotype. Cells Tissues Organs 2014; 198:448-56. [PMID: 24732779 DOI: 10.1159/000360157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2014] [Indexed: 11/19/2022] Open
Abstract
Dental enamel covers the crown of the vertebrate tooth and is considered to be the hardest tissue in the body. Enamel develops during secretion of an extracellular matrix by ameloblast cells in the tooth germ, prior to eruption of the tooth into the oral cavity. Secreted enamel proteins direct mineralization patterns during the maturation stage of amelogenesis as the tooth prepares to erupt. The amelogenins are the most abundant enamel proteins and are required for normal enamel development. Phenotypic differences were observed between incisors from individual Amelx (amelogenin) null mice that had a mixed 129xC57BL/6J genetic background and between inbred wild-type (WT) mice with different genetic backgrounds (C57BL/6J, C3H/HeJ, FVB/NJ). We hypothesized that this could be due to modifier genes, as human patients with a mutation in an enamel protein gene causing the enamel defect amelogenesis imperfecta (AI) can also have varied appearance of dentitions within a kindred. Enamel density measurements varied for all WT inbred strains midway during incisor development. Enamel thickness varied between some WT strains, and, unexpectedly, dentin density varied extensively between incisors and molars of all WT and Amelx null strains studied. WTFVB/NJ incisors were more similar to those of Amelx null mice than to those of the other WT strains in terms of incisor height/width ratio and pattern of enamel mineralization. Strain-specific differences led to the conclusion that modifier genes may be implicated in determining both normal development and severity of enamel appearance in AI mouse models and may in future studies be related to phenotypic heterogeneity within human AI kindreds reported in the literature.
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Affiliation(s)
- Yong Li
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pa., USA
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Xu Y, Li W, Liu X, Chen H, Tan K, Chen Y, Tu Z, Dai Y. Identification of dysregulated microRNAs in lymphocytes from children with Down syndrome. Gene 2013; 530:278-86. [DOI: 10.1016/j.gene.2013.07.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 01/05/2023]
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Associations of miR-499 and miR-34b/c Polymorphisms with Susceptibility to Hepatocellular Carcinoma: An Evidence-Based Evaluation. Gastroenterol Res Pract 2013; 2013:719202. [PMID: 24194751 PMCID: PMC3804138 DOI: 10.1155/2013/719202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 08/27/2013] [Indexed: 12/18/2022] Open
Abstract
Background. Hepatocellular carcinoma (HCC) represents the sixth common cancer in the world. Single nucleotide polymorphisms (SNPs) in microRNA genes may be associated with susceptibility to HCC. Recently, several studies have reported possible associations of SNPs miR-499 T>C rs3746444 and miR-34b/c T>C rs4938723 with the risk of HCC. However the results are inconsistent and inconclusive. In this present study, we conducted a meta-analysis to comprehensively evaluate potential associations between the two SNPs and HCC susceptibility. Methods. Through a systematic literature search, 8-case-control studies involving 5464 subjects were identified and included in this meta-analysis. The association between the two common SNPs and HCC risk was estimated by pooled odds ratios (ORs) and 95% confidence intervals (95% CIs). Our results showed no significant association between rs3746444 and susceptibility to HCC, whereas variant genotypes of rs4938723 were associated with increased HCC risk in allele frequency model and heterozygous model (C versus T, OR = 1.11, 95% CI: 1.01-1.23, P = 0.04; TC versus TT, OR = 1.19, 95% CI: 1.03-1.37, P = 0.02). Conclusions. The current evidence did not support association between rs3746444 and HCC risk. SNP rs4938723 may be associated with susceptibility to HCC. Further well-designed studies are required to clarify the relationships between the two SNPs and HCC risk.
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Xu Y, Li W, Liu X, Ma H, Tu Z, Dai Y. Analysis of microRNA expression profile by small RNA sequencing in Down syndrome fetuses. Int J Mol Med 2013; 32:1115-25. [PMID: 24071828 DOI: 10.3892/ijmm.2013.1499] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/22/2013] [Indexed: 11/06/2022] Open
Abstract
Down syndrome (DS) is caused by trisomy of human chromosome 21 (Hsa21) and is associated with numerous deleterious phenotypes, including cognitive impairment, childhood leukemia and immune defects. Five Hsa21‑derived microRNAs (i.e., hsa-miR-99a, let-7c, miR-125b-2, miR-155 and miR-802) are involved in variable phenotypes of DS. However, the changes involved in the genome-wide microRNA expression of DS fetuses under the influence of trisomy 21 have yet to be determined. To investigate the expression characteristic of microRNAs during the development of DS fetuses and identify whether another microRNA gene resides in the Hsa21, Illumina high-throughput sequencing technology was employed to comprehensively characterize the microRNA expression profiles of the DS and normal fetal cord blood mononuclear cells (CBMCs). In total, 149 of 395 identified microRNAs were significantly differentially expressed (fold change >2.0 and P<0.001) and 2 of 181 candidate novel microRNAs were identified as residing within the ̔DS critical region̓ of human chromosome 21 (chr21q22.2‑22.3). Additionally, 7 of 14 Hsa21-derived microRNAs were detected, although not all seven were overexpressed in DS CBMCs compared with the control. Gene ontology enrichment analyses revealed that a set of abnormally expressed microRNAs were involved in the regulation of transcription, gene expression, cellular biosynthetic process and nucleic acid metabolic process. Significantly, most of the mRNA targets in these categories were associated with immune modulation (i.e., SOD1, MXD4, PBX1, BCLAF1 and FOXO1). Findings of the present study provided a considerable insight into understanding the expression characteristic of microRNAs in the DS fetal CBMCs. To the best of our knowledge, this is the first study to examine genome-wide microRNA expression profiles in the DS fetus. Differentially expressed microRNAs may be involved in hemopoietic abnormalities and the immune defects of DS fetuses and newborns.
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Affiliation(s)
- Yong Xu
- Clinical Medical Research Center, Pingshan People's Hospital, Shenzhen, Guangdong 518118, P.R. China
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Qiao Y, Badduke C, Mercier E, Lewis SME, Pavlidis P, Rajcan-Separovic E. miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability. BMC Genomics 2013; 14:544. [PMID: 23937676 PMCID: PMC3750877 DOI: 10.1186/1471-2164-14-544] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 08/06/2013] [Indexed: 12/20/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a family of short, non-coding RNAs modulating expression of human protein coding genes (miRNA target genes). Their dysfunction is associated with many human diseases, including neurodevelopmental disorders. It has been recently shown that genomic copy number variations (CNVs) can cause aberrant expression of integral miRNAs and their target genes, and contribute to intellectual disability (ID). Results To better understand the CNV-miRNA relationship in ID, we investigated the prevalence and function of miRNAs and miRNA target genes in five groups of CNVs. Three groups of CNVs were from 213 probands with ID (24 de novo CNVs, 46 familial and 216 common CNVs), one group of CNVs was from a cohort of 32 cognitively normal subjects (67 CNVs) and one group of CNVs represented 40 ID related syndromic regions listed in DECIPHER (30 CNVs) which served as positive controls for CNVs causing or predisposing to ID. Our results show that 1). The number of miRNAs is significantly higher in de novo or DECIPHER CNVs than in familial or common CNV subgroups (P < 0.01). 2). miRNAs with brain related functions are more prevalent in de novo CNV groups compared to common CNV groups. 3). More miRNA target genes are found in de novo, familial and DECIPHER CNVs than in the common CNV subgroup (P < 0.05). 4). The MAPK signaling cascade is found to be enriched among the miRNA target genes from de novo and DECIPHER CNV subgroups. Conclusions Our findings reveal an increase in miRNA and miRNA target gene content in de novo versus common CNVs in subjects with ID. Their expression profile and participation in pathways support a possible role of miRNA copy number change in cognition and/or CNV-mediated developmental delay. Systematic analysis of expression/function of miRNAs in addition to coding genes integral to CNVs could uncover new causes of ID.
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Affiliation(s)
- Ying Qiao
- Department of Pathology and Lab Medicine, BC Child and Family Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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DONG SHAOHONG, XIONG WEI, YUAN JIANHUI, LI JIANGHUA, LIU JIANJUN, XU XINYUN. MiRNA-146a regulates the maturation and differentiation of vascular smooth muscle cells by targeting NF-κB expression. Mol Med Rep 2013; 8:407-12. [DOI: 10.3892/mmr.2013.1538] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 06/06/2013] [Indexed: 11/05/2022] Open
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Association between genetic variants in pre-miRNA and colorectal cancer risk in a Chinese population. J Cancer Res Clin Oncol 2013; 139:1405-10. [PMID: 23728616 DOI: 10.1007/s00432-013-1456-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/25/2013] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Single-nucleotide polymorphisms (SNPs) in pre-miRNAs may alter microRNA expression levels or processing and then contribute to the susceptibility of cancer development. We hypothesized that SNPs in pre-miRNAs may be associated with the risk of colorectal cancer (CRC). MATERIALS AND METHODS We genotyped four common polymorphisms (i.e., rs11614913, rs3746444, rs2910164, and rs2292832) in pre-miRNAs of 353 CRC patients and 540 healthy controls to investigate the association between the SNPs and the risk of CRC using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. RESULTS The rs11614913 CT, TT genotypes, and T allele were associated with an increased risk of CRC compared with the CC genotype and C allele (CT vs. CC: OR = 7.34, 95% CI 3.76-14.34; TT vs. CC: OR = 13.66, 95% CI 6.76-27.6; T vs. C: OR = 1.99, 95% CI 1.63-2.42, respectively). Interestingly, using the rs2910164 GG genotype as a reference, the rs2910164 GC genotype was associated with an increased risk of CRC (OR = 1.49, 95% CI 1.02-2.18), whereas the rs2910164 CC genotype was associated with a decreased risk of CRC (OR = 0.58, 95% CI 0.37-0.93). When compared with the rs2910164G allele, rs2910164 C allele was associated with a reduced risk of CRC (OR = 0.80, 95% CI 0.66-0.97, p = 0.02). CONCLUSION These findings suggest that rs11614913 and rs2910164 polymorphisms may be associated with the etiology of CRC.
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Edelstein LC, McKenzie SE, Shaw C, Holinstat MA, Kunapuli SP, Bray PF. MicroRNAs in platelet production and activation. J Thromb Haemost 2013; 11 Suppl 1:340-50. [PMID: 23809137 DOI: 10.1111/jth.12214] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent work by the Encyclopedia of DNA Elements project showed that non-protein-coding RNAs account for an unexpectedly large proportion of the human genome. Among these non-coding RNAs are microRNAs (miRNAs), which are small RNA molecules that modulate protein expression by degrading mRNA or repressing mRNA translation. MiRNAs have been shown to play important roles in hematopoiesis including embryonic stem cell differentiation, erythropoiesis, granulocytopoiesis/monocytopoiesis, lymphopoiesis, and megakaryocytopoiesis. Additionally, disordered miRNA biogenesis and quantitative or qualitative alterations in miRNAs and their targets are associated with hematological pathologies. Platelets contain machinery to process pre-miRNAs into mature miRNAs, and specific platelet miRNA levels have been found to correlate with platelet reactivity. This review summarizes the current state of knowledge of miRNAs in megakaryocytes and platelets, and the exciting possibilities for future megakaryocyte-platelet transcriptome research.
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Affiliation(s)
- L C Edelstein
- The Cardeza Foundation for Hematologic Research and Department of Medicine, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Elevated levels of miR-145 correlate with SMAD3 down-regulation in cystic fibrosis patients. J Cyst Fibros 2013; 12:797-802. [PMID: 23632450 DOI: 10.1016/j.jcf.2013.03.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/11/2013] [Accepted: 03/26/2013] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) have recently emerged as important gene regulators in Cystic Fibrosis (CF), a common monogenic disease characterized by severe infection and inflammation, especially in the airway compartments. In the current study, we show that both miR-145 and miR-494 are significantly up-regulated in nasal epithelial tissues from CF patients compared with healthy controls (p<0.001 and p<0.01, respectively) by Quantitative Real-Time PCR. Only miR-494 levels showed a trend of correlation with reduced CFTR mRNA expression and positive sweat test values, supporting the negative regulatory role of this miRNA on CFTR synthesis. Using computational prediction algorithms and luciferase reporter assays, SMAD family member 3 (SMAD3), a key element of the TGF-β1 inflammatory pathway, was identified as a target of miR-145. Indeed, miR-145 synthetic mimics suppressed by approximately 40% the expression of a reporter construct containing the SMAD3 3'-UTR. Moreover, we observed an inverse correlation between SMAD3 mRNA expression and miR-145 in CF nasal tissues (r=-0.68, p=0.0018, Pearson's correlation). Taken together, these results confirm the pivotal role of miRNAs in the CF physio-pathogenesis and suggest that miRNA deregulation play a role in the airway disease severity by modulating CFTR levels as well as the expression of important molecules involved in the inflammatory response. miR-494 and miR-145 may, therefore, be potential biomarker and therapeutic target to specific CF clinical manifestations.
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Bandiera S, Cartault F, Jannot AS, Hatem E, Girard M, Rifai L, Loiseau C, Munnich A, Lyonnet S, Henrion-Caude A. Genetic variations creating microRNA target sites in the FXN 3'-UTR affect frataxin expression in Friedreich ataxia. PLoS One 2013; 8:e54791. [PMID: 23382970 PMCID: PMC3559822 DOI: 10.1371/journal.pone.0054791] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/14/2012] [Indexed: 11/18/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a severe neurodegenerative disease caused by GAA repeat expansion within the first intron of the frataxin gene. It has been suggested that the repeat is responsible for the disease severity due to impaired transcription thereby reducing expression of the protein. However, genotype-phenotype correlation is imperfect, and the influence of other gene regions of the frataxin gene is unknown. We hypothesized that FRDA patients may harbor specific regulatory variants in the 3'-UTR. We sequenced the 3'-UTR region of the frataxin gene in a cohort of 57 FRDA individuals and 58 controls. Seven single nucleotide polymorphisms (SNPs) out of 19 were polymorphic in our case-control sample. These SNPs defined several haplotypes with one reaching 89% of homozygosity in patients versus 24% in controls. In another cohort of 47 FRDA Reunionese patients, 94% patients were found to be homozygous for this haplotype. We found that this FRDA 3'-UTR conferred a 1.2-fold decrease in the expression of a reporter gene versus the alternative haplotype configuration. We established that differential targeting by miRNA could account for this functional variability. We specifically demonstrated the involvement of miR-124 (i.e hsa-mir-124-3p) in the down-regulation of FRDA-3'-UTR. Our results suggest for the first time that post-transcriptional regulation of frataxin occurs through the 3'-UTR and involves miRNA targeting. We propose that the involvement of miRNAs in a FRDA-specific regulation of frataxin may provide a rationale to increase residual levels of frataxin through miRNA-inhibitory molecules.
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Affiliation(s)
- Simonetta Bandiera
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - François Cartault
- INSERM U781 Hôpital Necker–Enfants Malades, Paris, France
- Département de Génétique, Centre Hospitalier Régional de La Réunion, Saint-Denis, La Réunion, France
| | - Anne-Sophie Jannot
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Elie Hatem
- INSERM U781 Hôpital Necker–Enfants Malades, Paris, France
| | - Muriel Girard
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Laila Rifai
- Department of Medical Genetics, National Institute of Health, Rabat, Morocco
| | | | - Arnold Munnich
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Stanislas Lyonnet
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
| | - Alexandra Henrion-Caude
- INSERM U781 Hôpital Necker–Enfants Malades, Université Paris Descartes-Sorbonne Cité, Institut Imagine, Paris, France
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Yan HZ, Xu MD, Li BB, Yu HY. Advances in understanding relationship between miRNA single nucleotide polymorphisms and colorectal cancer. Shijie Huaren Xiaohua Zazhi 2012; 20:2920-2925. [DOI: 10.11569/wcjd.v20.i30.2920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The occurrence and development of colorectal cancer (CRC) are a multifactorial, multi-step evolutionary process. Gene polymorphisms are often involved in tumor development and prognosis. Recent studies have found that certain microRNA (miRNA) single nucleotide polymorphisms were associated with genetic susceptibility to and prognosis of CRC. Understanding the relationship between miRNA single nucleotide polymorphisms and CRC can provide new clues to the detection, prevention, and prognostic evaluation of CRC.
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Kilic T, Topkaya SN, Ozkan Ariksoysal D, Ozsoz M, Ballar P, Erac Y, Gozen O. Electrochemical based detection of microRNA, mir21 in breast cancer cells. Biosens Bioelectron 2012; 38:195-201. [DOI: 10.1016/j.bios.2012.05.031] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/16/2012] [Accepted: 05/24/2012] [Indexed: 12/30/2022]
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Niu N, Schaid DJ, Abo RP, Kalari K, Fridley BL, Feng Q, Jenkins G, Batzler A, Brisbin AG, Cunningham JM, Li L, Sun Z, Yang P, Wang L. Genetic association with overall survival of taxane-treated lung cancer patients - a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study. BMC Cancer 2012; 12:422. [PMID: 23006423 PMCID: PMC3573965 DOI: 10.1186/1471-2407-12-422] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/30/2012] [Indexed: 12/12/2022] Open
Abstract
Background Taxane is one of the first line treatments of lung cancer. In order to identify novel single nucleotide polymorphisms (SNPs) that might contribute to taxane response, we performed a genome-wide association study (GWAS) for two taxanes, paclitaxel and docetaxel, using 276 lymphoblastoid cell lines (LCLs), followed by genotyping of top candidate SNPs in 874 lung cancer patient samples treated with paclitaxel. Methods GWAS was performed using 1.3 million SNPs and taxane cytotoxicity IC50 values for 276 LCLs. The association of selected SNPs with overall survival in 76 small or 798 non-small cell lung cancer (SCLC, NSCLC) patients were analyzed by Cox regression model, followed by integrated SNP-microRNA-expression association analysis in LCLs and siRNA screening of candidate genes in SCLC (H196) and NSCLC (A549) cell lines. Results 147 and 180 SNPs were associated with paclitaxel or docetaxel IC50s with p-values <10-4 in the LCLs, respectively. Genotyping of 153 candidate SNPs in 874 lung cancer patient samples identified 8 SNPs (p-value < 0.05) associated with either SCLC or NSCLC patient overall survival. Knockdown of PIP4K2A, CCT5, CMBL, EXO1, KMO and OPN3, genes within 200 kb up-/downstream of the 3 SNPs that were associated with SCLC overall survival (rs1778335, rs2662411 and rs7519667), significantly desensitized H196 to paclitaxel. SNPs rs2662411 and rs1778335 were associated with mRNA expression of CMBL or PIP4K2A through microRNA (miRNA) hsa-miR-584 or hsa-miR-1468. Conclusions GWAS in an LCL model system, joined with clinical translational and functional studies, might help us identify genetic variations associated with overall survival of lung cancer patients treated paclitaxel.
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Affiliation(s)
- Nifang Niu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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Wu W, Hu Z, Qin Y, Dong J, Dai J, Lu C, Zhang W, Shen H, Xia Y, Wang X. Seminal plasma microRNAs: potential biomarkers for spermatogenesis status. Mol Hum Reprod 2012; 18:489-97. [PMID: 22675043 DOI: 10.1093/molehr/gas022] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (18-25 nt), playing important regulatory roles via interaction with cellular messenger RNAs. The altered expression of miRNAs in specific tissues has been associated with diseases such as cancer and diabetes. We examined the presence of two selected miRNAs (miR-19b and let-7a) in human seminal plasma from fertile men and idiopathic infertile patients with oligozoospermia and non-obstructive azoospermia (NOA) using quantitative real-time PCR. We detected miRNAs in the seminal plasma of humans. The levels of miRNAs in the seminal plasma were reproducible in repeat samples from the same individuals. In addition, we examined the expression patterns of two selected miRNAs in 96 idiopathic infertile males (48 oligozoospermia and 48 NOA) and 48 fertile controls. Another 48 individuals of each group were used for verification. Our data showed that the expression levels of these two miRNAs in the seminal plasma significantly increased in idiopathic infertile males with NOA compared with fertile controls, whereas the expression levels were similar between idiopathic infertile males with oligozoospermia and fertile controls. In conclusion our results indicate that the expression of miR-19b and let-7a in the seminal plasma are reproducible and stable. Aberrant over-expression levels of miR-19b and let-7a may be an indicator of spermatogenic failure.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, 140 Hanzhong Road, Nanjing 210029, China
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Bafunno V, Santacroce R, Chetta M, Peyvandi F, Sessa F, Chinni E, Longo V, Margaglione M. Polymorphic miRNA-mediated gene contribution to inhibitor development in haemophilia A. Haemophilia 2012; 18:1003-7. [DOI: 10.1111/j.1365-2516.2012.02882.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2012] [Indexed: 12/18/2022]
Affiliation(s)
- V. Bafunno
- Department of Biomedical Sciences; Medical Genetics; University of Foggia; Foggia
| | - R. Santacroce
- Department of Biomedical Sciences; Medical Genetics; University of Foggia; Foggia
| | - M. Chetta
- Department of Biomedical Sciences; Medical Genetics; University of Foggia; Foggia
| | - F. Peyvandi
- U.O.S. Dipartimentale per la Diagnosi e la Terapia delle Coagulopatie; A. Bianchi Bonomi Haemophilia and Thrombosis Center; Fondazione IRCCS Ca' Grande Ospedale Maggiore Policlinico; Università degli Studi di Milano and Luigi Villa Foundation; Milan
| | - F. Sessa
- Department of Biomedical Sciences; Medical Genetics; University of Foggia; Foggia
| | - E. Chinni
- Atherosclerosis and Thrombosis Unit; Research Department; Istituto di Ricovero e Cura a Carattere Scientifico; Casa Sollievo della Sofferenza; S. Giovanni Rotondo; Foggia; Italy
| | - V. Longo
- Department of Biomedical Sciences; Medical Genetics; University of Foggia; Foggia
| | - M. Margaglione
- Department of Biomedical Sciences; Medical Genetics; University of Foggia; Foggia
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Haas U, Sczakiel G, Laufer SD. MicroRNA-mediated regulation of gene expression is affected by disease-associated SNPs within the 3'-UTR via altered RNA structure. RNA Biol 2012; 9:924-37. [PMID: 22664914 PMCID: PMC3495750 DOI: 10.4161/rna.20497] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) or their target sites (miR-SNPs) within the 3′-UTR of mRNAs are increasingly thought to play a major role in pathological dysregulation of gene expression. Here, we studied the functional role of miR-SNPs on miRNA-mediated post-transcriptional regulation of gene expression. First, analyses were performed on a SNP located in the miR-155 target site within the 3′-UTR of the Angiotensin II type 1 receptor (AGTR1; rs5186, A > C) mRNA. Second, a SNP in the 3′-UTR of the muscle RAS oncogene homolog (MRAS; rs9818870, C > T) mRNA was studied which is located outside of binding sites of miR-195 and miR-135. Using these SNPs we investigated their effects on local RNA structure, on local structural accessibility and on functional miRNA binding, respectively. Systematic computational RNA folding analyses of the allelic mRNAs in either case predicted significant changes of local RNA structure in the vicinity of the cognate miRNA binding sites. Consistently, experimental in vitro probing of RNA showing differential cleavage patterns and reporter gene-based assays indicated functional differences of miRNA-mediated regulation of the two AGTR1 and MRAS alleles. In conclusion, we describe a novel model explaining the functional influence of 3′-UTR-located SNPs on miRNA-mediated control of gene expression via SNP-related changes of local RNA structure in non-coding regions of mRNA. This concept substantially extends the meaning of disease-related SNPs identified in non protein-coding transcribed sequences within or close to miRNA binding sites.
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Affiliation(s)
- Ulrike Haas
- Institut für Molekulare Medizin, Universität zu Lübeck, Lübeck, Germany
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Zhao B, Jin L, Wei J, Ma Z, Jiang W, Ma L, Jin Y. A simple and fast method for profiling microRNA expression from low-input total RNA by microarray. IUBMB Life 2012; 64:612-6. [DOI: 10.1002/iub.1026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 02/16/2012] [Indexed: 11/10/2022]
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