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Tian Z, Zhou H, Xu Y, Bai J. MicroRNA-495 Inhibits New Bone Regeneration via Targeting High Mobility Group AT-Hook 2 (HMGA2). Med Sci Monit 2017; 23:4689-4698. [PMID: 28963864 PMCID: PMC5633066 DOI: 10.12659/msm.904404] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs play critical roles in post-translational gene expression. In this study, we explored the role of miR-495 in new bone regeneration. Material/Methods Murine calvarial osteoblasts were isolated and cultured. Microarray was performed to identify differential miRNAs in medicarpin-induced osteoblasts differentiation. Luciferase reporter assay was performed to identify the target gene of miRNA. Murine osteoblast cells were transfected with miC, miR-495, or anti-miR-495. CCK-8 and flow cytometry were performed to detect osteoblasts proliferation and apoptosis. Western blot was used to analyze apoptosis-related proteins. qRT-PCR analysis was performed to detect gene expression. ALP activity and mineralized nodule formation test were used to evaluate bone formation. Dill-hole injury model was constructed and micro CT was utilized to measuring bone healing. Results Microarray analysis identified miR-495 as our miRNA of interest and luciferase reporter assay identified HMGA2 as its target gene. Over-expression of miR-495 significantly inhibited ALP activity and mineralized nodule formation as well as the expression of RUNX-2, BMP-2, and Osterix. Also, miR-495 over-expression inhibited osteoblasts proliferation and promoted apoptosis obviously. In this in vivo study, the downregulation of miR-495 promoted murine femur healing. Conclusions MiR-495 inhibits new bone regeneration via targeting high mobility group AT-Hook 2 (HMGA2). We propose that targeting miR-495 may be a promising therapeutic approach for bone regeneration.
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Affiliation(s)
- Zhao Tian
- Department of Hand Surgery, Honghui Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China (mainland)
| | - Haizhen Zhou
- Department of Hand Surgery, Honghui Hospital, Xi'an Jiaotong University College of Medcine, Xi'an, Shaanxi, China (mainland)
| | - Yuben Xu
- Department of Hand Surgery, Honghui Hospital, Xi'an Jiaotong University College of Medcine, Xi'an, Shaanxi, China (mainland)
| | - Jie Bai
- Department of Hand Surgery, Honghui Hospital, Xi'an Jiaotong University College of Medcine, Xi'an, Shaanxi, China (mainland)
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152
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Du J, Zhang X, Cao H, Jiang D, Wang X, Zhou W, Chen K, Zhou J, Jiang H, Ba L. MiR-194 is involved in morphogenesis of spiral ganglion neurons in inner ear by rearranging actin cytoskeleton via targeting RhoB. Int J Dev Neurosci 2017; 63:16-26. [PMID: 28941704 DOI: 10.1016/j.ijdevneu.2017.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 02/05/2023] Open
Abstract
Many microRNAs participate in the development, differentiation and function preservation of the embryonic and adult inner ear, but many details still need to be elucidated regarding the numerous microRNAs in the inner ear. Based on previous investigations on the microRNA profile in the inner ear, we confirmed that several microRNAs are expressed in the inner ear, and we detected the spatial expression of these microRNAs in the neonatal mouse inner ear. Then we focused on miR-194 for its specific expression with a dynamic spatiotemporal pattern during inner ear development. Overexpression of miR-194 in cultured spiral ganglion cells significantly affected the dendrites of differentiated neurons, with more branching and obviously dispersed nerve fibres. Furthermore, the cytoskeleton of cultured cells was markedly affected, as disordered actin filaments resulting from miR-194 overexpression and enhanced filaments resulting from miR-194 knockdown were observed. Together with the bioinformatic methods, the RT-qPCR and western blot results showed that RhoB is a candidate target of miR-194 in the morphogenesis of spiral ganglion neurons. Additionally, the double luciferase reporter system was used to identify RhoB as a novel target of miR-194. Finally, the inhibition of RhoB activation by Clostridium difficile toxin B disturbed the organization of the actin filament, similar to the effects of miR-194 overexpression. In summary, we investigated microRNA expression in the mouse inner ear, and demonstrated that miR-194 is dynamically expressed during inner ear development; importantly, we found that miR-194 affects neuron morphogenesis positively through Rho B-mediated F-actin rearrangement.
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Affiliation(s)
- Jintao Du
- Department of Otorhinolaryngology Head & Neck Surgery, West China Hospital, Sichuan University, 37 Guoxue Lane, Chengdu, 610041, China
| | - Xuemei Zhang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Hui Cao
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Di Jiang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Xianren Wang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Wei Zhou
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China; Department of Otolaryngology, People's Hospital of Meishan, Meishan, Sichuan, 620010, China
| | - Kaitian Chen
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Jiao Zhou
- Department of Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongyan Jiang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China.
| | - Luo Ba
- Department of Otolaryngology, People's Hospital of the Tibet Autonomous Region, Lasha, China.
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153
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Ushakov K, Koffler-Brill T, Rom A, Perl K, Ulitsky I, Avraham KB. Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems. Sci Rep 2017; 7:8637. [PMID: 28819115 PMCID: PMC5561060 DOI: 10.1038/s41598-017-08320-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction. To help address this need, we performed a whole-genome identification of lncRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 3,239 lncRNA genes, most of which were intergenic (lincRNAs) and 721 are novel. We examined temporal and tissue specificity by analyzing the developmental profiles on embryonic day 16.5 and at birth. The spatial and temporal patterns of three lncRNAs, two of which are in proximity to genes associated with hearing and deafness, were explored further. Our findings indicate that lncRNAs are prevalent in the sensory epithelium of the mouse inner ear and are likely to play key roles in regulating critical pathways for hearing and balance.
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Affiliation(s)
- Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Kobi Perl
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.,Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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154
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Van den Ackerveken P, Mounier A, Huyghe A, Sacheli R, Vanlerberghe PB, Volvert ML, Delacroix L, Nguyen L, Malgrange B. The miR-183/ItgA3 axis is a key regulator of prosensory area during early inner ear development. Cell Death Differ 2017; 24:2054-2065. [PMID: 28777373 DOI: 10.1038/cdd.2017.127] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/15/2017] [Accepted: 06/30/2017] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs are important regulators of gene expression and are involved in cellular processes such as proliferation or differentiation, particularly during development of numerous organs including the inner ear. However, it remains unknown if miRNAs are required during the earliest stages of otocyst and cochlear duct development. Here, we report that a conditional loss of Dicer expression in the otocyst impairs the early development of the inner ear as a result of the accumulation of DNA damage that trigger p53-mediated apoptosis. Moreover, cochlear progenitors in the prosensory domain do not exit the cell cycle. Our unbiased approach identified ItgA3 as a target of miR-183, which are both enriched in the otic vesicle. We observed that the repression of integrin alpha 3 by miR-183 controls cell proliferation in the developing cochlea. Collectively, our results reveal that Dicer and miRNAs play essential roles in the regulation of early inner ear development.
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Affiliation(s)
- Priscilla Van den Ackerveken
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Anaïs Mounier
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Aurelia Huyghe
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Rosalie Sacheli
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Pierre-Bernard Vanlerberghe
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Marie-Laure Volvert
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Laurence Delacroix
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Laurent Nguyen
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
| | - Brigitte Malgrange
- GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège B-4000, Belgium
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155
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Abstract
microRNAs (miRNAs) are a small RNA species without protein-coding potential. However, they are key modulators of protein translation. Many studies have linked miRNAs with cancer initiation, progression, diagnosis, and prognosis, and recent studies have also linked them with cancer etiology and susceptibility, especially through single-nucleotide polymorphisms (SNPs). This review discusses some of the recent advances in miRNA-SNP literature-including SNPs in miRNA genes, miRNA target sites, and the processing machinery. In addition, we highlight some emerging areas of interest, including isomiRs and non-3'UTR focused miRNA-binding mechanisms that could provide further novel insight into the relationship between miR-SNPs and cancer. Finally, we note that additional epidemiological and experimental research is needed to close the gap in our understanding of the genotype-phenotype relationship between miRNA-SNPs and cancer.
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Affiliation(s)
- Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.
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156
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Role of miRNAs in development and disease: Lessons learnt from small organisms. Life Sci 2017; 185:8-14. [PMID: 28728902 DOI: 10.1016/j.lfs.2017.07.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/10/2017] [Accepted: 07/16/2017] [Indexed: 01/23/2023]
Abstract
MicroRNAs (miRNAs) constitute a class of small (18-22 nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level. Caenorhabditis elegans, Drosophila melanogaster, and many other small organisms have been instrumental in deciphering the biological functions of miRNAs. While some miRNAs from small organisms are highly conserved across the taxa, others are organism specific. The miRNAs are known to play a crucial role during development and in various cellular functions such as cell survival, cell proliferation, and differentiation. The miRNAs associated with fragile X syndrome, Parkinson's disease, Alzheimer's disease, diabetes, cancer, malaria, infectious diseases and several other human diseases have been identified from small organisms. These organisms have been used as platforms in deciphering the functions of miRNAs in the pathogenesis of human diseases and to study miRNA biogenesis. Small organisms have also been used in the development of miRNA-based diagnostic, prognostic and therapeutic strategies. The molecular techniques such as genome sequencing, northern blot analysis, and quantitative RT-PCR, have been used in deciphering the functions of miRNAs in small organisms. How miRNAs from small organisms especially those from Drosophila and C. elegans regulate development and disease pathogenesis is the focus of this review. The outstanding questions raised by our current understanding are discussed.
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157
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Huang XF, Huang ZQ, Fang XL, Chen ZJ, Cheng W, Jin ZB. Retinal miRNAs variations in a large cohort of inherited retinal disease. Ophthalmic Genet 2017; 39:175-179. [PMID: 28704127 DOI: 10.1080/13816810.2017.1329448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Although great efforts have been paid on identification of genetic predisposition in the inherited retinal disease (IRD), genetic causes of a large proportion of patients remain a mystery. This dilemma makes us attempt to speculate that genetic components other than coding genes might be an additional pool predisposing IRD. In this study, we aim to perform a mutational screening in a large cohort of IRD patients with a particular focus on retina-specific or abundant microRNAs (miRs). MATERIAL AND METHODS A total of 324 unrelated patients with IRD were recruited. Targeted next-generation sequencing (tNGS) was performed to survey genetic mutations in 32 known miRs highly expressed in the retina, followed by validation with Sanger sequencing, co-segregation analysis in each family, and computational assessments. RESULTS Novel genotype-phenotype associations have been uncovered. In total, six different variants in the miRs were identified, including four rare ones, miR-216a (n.56C>A), miR-216b (n.43_44insG), miR-7-2 (n.107C>T), and miR-7-3 (n.95G>A). The other two variants, miR-182 (n.106G>A) and miR-216a (n.105T>A), were considered as polymorphic. CONCLUSIONS We for the first time screened candidate retinal miRs in patients with IRD. Although there is no convincing evidence that these variants are responsible for the IRD, the results enhance the current knowledge of the associations between IRD and miRNAs variants.
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Affiliation(s)
- Xiu-Feng Huang
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Zhi-Qin Huang
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Xiao-Long Fang
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Zhen-Ji Chen
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Wan Cheng
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Zi-Bing Jin
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
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158
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Ebeid M, Sripal P, Pecka J, Beisel KW, Kwan K, Soukup GA. Transcriptome-wide comparison of the impact of Atoh1 and miR-183 family on pluripotent stem cells and multipotent otic progenitor cells. PLoS One 2017; 12:e0180855. [PMID: 28686713 PMCID: PMC5501616 DOI: 10.1371/journal.pone.0180855] [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: 04/07/2017] [Accepted: 06/05/2017] [Indexed: 11/18/2022] Open
Abstract
Over 5% of the global population suffers from disabling hearing loss caused by multiple factors including aging, noise exposure, genetic predisposition, or use of ototoxic drugs. Sensorineural hearing loss is often caused by the loss of sensory hair cells (HCs) of the inner ear. A barrier to hearing restoration after HC loss is the limited ability of mammalian auditory HCs to spontaneously regenerate. Understanding the molecular mechanisms orchestrating HC development is expected to facilitate cell replacement therapies. Multiple events are known to be essential for proper HC development including the expression of Atoh1 transcription factor and the miR-183 family. We have developed a series of vectors expressing the miR-183 family and/or Atoh1 that was used to transfect two different developmental cell models: pluripotent mouse embryonic stem cells (mESCs) and immortalized multipotent otic progenitor (iMOP) cells representing an advanced developmental stage. Transcriptome profiling of transfected cells show that the impact of Atoh1 is contextually dependent with more HC-specific effects on iMOP cells. miR-183 family expression in combination with Atoh1 not only appears to fine tune gene expression in favor of HC fate, but is also required for the expression of some HC-specific genes. Overall, the work provides novel insight into the combined role of Atoh1 and the miR-183 family during HC development that may ultimately inform strategies to promote HC regeneration or maintenance.
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Affiliation(s)
- Michael Ebeid
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, United States of America
| | - Prashanth Sripal
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, United States of America
| | - Jason Pecka
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, United States of America
| | - Kirk W. Beisel
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, United States of America
| | - Kelvin Kwan
- Department of Cell Biology and Neuroscience, W. M. Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Garrett A. Soukup
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, United States of America
- * E-mail:
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159
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Association of miR-938G>A Polymorphisms with Primary Ovarian Insufficiency (POI)-Related Gene Expression. Int J Mol Sci 2017; 18:ijms18061255. [PMID: 28604625 PMCID: PMC5486077 DOI: 10.3390/ijms18061255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/28/2017] [Accepted: 06/07/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) post-transcriptionally regulate gene expression in animals and plants. The aim of this study was to investigate whether polymorphisms in miR-938 are associated with the risk of primary ovarian insufficiency (POI) and POI-related target gene regulation. We identified the miR-938G>A polymorphisms within the seed sequence of mature miRNA and aligned the seed sequence with the 3′ untranslated region (UTR) of the gonadotropin-releasing hormone receptor (GnRHR) mRNA, a miR-938 target gene. We found that the binding of miR-938 to the 3′-UTR of GnRHR mRNA was significantly different between normal and variant alleles. Our data suggests that the dysregulation of miR-938G>A influences the binding to GnRHR and that miR-938G>A polymorphisms might contribute to regulation of POI-related target genes.
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160
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Sun W, Lan J, Chen L, Qiu J, Luo Z, Li M, Wang J, Zhao J, Zhang T, Long X, Chai J, Yan Z, Guo Z, Gun S. A mutation in porcine pre-miR-15b alters the biogenesis of MiR-15b\16-1 cluster and strand selection of MiR-15b. PLoS One 2017; 12:e0178045. [PMID: 28542522 PMCID: PMC5443575 DOI: 10.1371/journal.pone.0178045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in translational regulation of the messenger RNA molecules. Sequence variations in the genes encoding miRNAs could influence their biogenesis and function. MiR-15b plays an important role in cellular proliferation, apoptosis and the cell cycle. Here, we report the identification of a C58T mutation in porcine pre-miR-15b. Through in vitro and in vivo experiments, we determined that this mutation blocks the transition from pri-miRNA to pre-miRNA, alters the strand selection between miR-15b-5p and miR-15b-3p, and obstructs biogenesis of the downstream miR-16-1. These results serve to highlight the importance of miRNA mutations and their impacts on miRNA biogenesis.
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Affiliation(s)
- Wenyang Sun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Jing Lan
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Lei Chen
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Jinjie Qiu
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Zonggang Luo
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
- Department of Animal Science, Southwest University, Rongchang, Chongqing, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinyong Wang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Jiugang Zhao
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Tinghuan Zhang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Xi Long
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Jie Chai
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Zongyi Guo
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China
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161
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Abstract
MicroRNAs are a class of small non-coding RNAs that are involved in many important biological processes and the dysfunction of microRNA has been associated with many diseases. The seed region of a microRNA is of crucial importance to its target recognition. Mutations in microRNA seed regions may disrupt the binding of microRNAs to their original target genes and make them bind to new target genes. Here we use a knowledge-based computational method to systematically predict the functional effects of all the possible single nucleotide mutations in human microRNA seed regions. The result provides a comprehensive reference for the functional assessment of the impacts of possible natural and artificial single nucleotide mutations in microRNA seed regions.
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162
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Vona B, Nanda I, Shehata-Dieler W, Haaf T. Genetics of Tinnitus: Still in its Infancy. Front Neurosci 2017; 11:236. [PMID: 28533738 PMCID: PMC5421307 DOI: 10.3389/fnins.2017.00236] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/10/2017] [Indexed: 12/20/2022] Open
Abstract
Tinnitus is the perception of a phantom sound that affects between 10 and 15% of the general population. Despite this considerable prevalence, treatments for tinnitus are presently lacking. Tinnitus exhibits a diverse array of recognized risk factors and extreme clinical heterogeneity. Furthermore, it can involve an unknown number of auditory and non-auditory networks and molecular pathways. This complex combination has hampered advancements in the field. The identification of specific genetic factors has been at the forefront of several research investigations in the past decade. Nine studies have examined genes in a case-control association approach. Recently, a genome-wide association study has highlighted several potentially significant pathways that are implicated in tinnitus. Two twin studies have calculated a moderate heritability for tinnitus and disclosed a greater concordance rate in monozygotic twins compared to dizygotic twins. Despite the more recent data alluding to genetic factors in tinnitus, a strong association with any specific genetic locus is lacking and a genetic study with sufficient statistical power has yet to be designed. Future research endeavors must overcome the many inherent limitations in previous study designs. This review summarizes the previously embarked upon tinnitus genetic investigations and summarizes the hurdles that have been encountered. The identification of candidate genes responsible for tinnitus may afford gene based diagnostic approaches, effective therapy development, and personalized therapeutic intervention.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University WürzburgWürzburg, Germany
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University WürzburgWürzburg, Germany
| | - Wafaa Shehata-Dieler
- Plastic, Aesthetic and Reconstructive Surgery, Department of Otorhinolaryngology, Comprehensive Hearing Center, University Hospital WürzburgWürzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University WürzburgWürzburg, Germany
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163
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Deng Y, Luan F, Zeng L, Zhang Y, Ma K. MiR-429 suppresses the progression and metastasis of osteosarcoma by targeting ZEB1. EXCLI JOURNAL 2017; 16:618-627. [PMID: 28694763 PMCID: PMC5491908 DOI: 10.17179/excli2017-258] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/12/2017] [Indexed: 12/19/2022]
Abstract
MiR-429 functions as a tumor suppressor and has been observed in multiple types of cancer, but the effects and mechanisms of miR-429 in osteosarcoma are poorly understood. This study is performed to evaluate the functions of miR-429 in the progression of osteosarcoma. Firstly, the miR-429 expression in osteosarcoma tissues and osteosarcoma cells was detected using real time PCR, and the relationship between miR-429 expression and overall survival of osteosarcoma was analyzed. Secondly, the effects of miR-429 on the migration, invasion, proliferation and apoptosis of osteosarcoma cells were evaluated using transwell assay, wound-healing assay, CCK-8 assay and flow cytometry, respectively. Proteins related to epithelial-mesenchymal transition (EMT), E-cadherin, Vimentin, N-cadherin and Snail, were also detected using Western blot. Finally, the target gene of miR-429 in osteosarcoma was predicted and verified using dual luciferase assay and the expression correlation between them was analyzed using Pearson's correlation. MiR-429 was down-regulated in osteosarcoma tissues and osteosarcoma cells; the expression level of miR-429 was associated with the prognosis of osteosarcoma. High level of miR-429 in osteosarcoma cells significantly suppressed the migration, invasion and proliferation of cells but induced cells apoptosis. Furthermore, high level of miR-429 in osteosarcoma cells obviously increased the expression of E-cadherin protein but decreased the expression of Vimentin, N-Cadherin and Snail proteins. EMT inducer ZEB1 was the target gene of miR-429 and the expression of ZEB1 was negatively related to the miR-429 expression in osteosarcoma. In conclusion, miR-429 may functions as a tumor suppressor and be down-regulated in osteosarcoma. MiR-429 may suppress the progression and metastasis of osteosarcoma by down-regulating the ZEB1 expression.
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Affiliation(s)
- Yi Deng
- Department of Oncology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Fujun Luan
- Department of Orthopedics, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Li Zeng
- Department of Oncology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Yanjun Zhang
- Department of General Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Kunlong Ma
- Department of Orthopedics, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
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164
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Ghanbari M, Erkeland SJ, Xu L, Colijn JM, Franco OH, Dehghan A, Klaver CCW, Meester-Smoor MA. Genetic variants in microRNAs and their binding sites within gene 3'UTRs associate with susceptibility to age-related macular degeneration. Hum Mutat 2017; 38:827-838. [PMID: 28397307 DOI: 10.1002/humu.23226] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/06/2017] [Accepted: 04/06/2017] [Indexed: 01/06/2023]
Abstract
Age-related macular degeneration (AMD), the leading cause of blindness in the elderly, is a complex disease that results from multiple genetic and environmental factors. MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate target mRNAs and are frequently implicated in human diseases. Here, we investigated the association of genetic variants in miRNAs and miRNA-binding sites within gene 3'-untranslated regions (3'UTRs) with AMD using data from the largest AMD genome-wide association study. First, we identified three variants in miRNAs significantly associated with AMD. These include rs2168518:G>A in the miR-4513 seed sequence, rs41292412:C>T in pre-miR-122/miR-3591, and rs4351242:C>T in the terminal-loop of pre-miR-3135b. We demonstrated that these variants reduce expression levels of the mature miRNAs in vitro and pointed the target genes that may mediate downstream effects of these miRNAs in AMD. Second, we identified 54 variants (in 31 genes) in miRNA-binding sites associated with AMD. Based on stringent prioritization criteria, we highlighted the variants that are more likely to have an impact on the miRNA-target interactions. Further, we selected rs4151672:C>T within the CFB 3'UTR and experimentally showed that while miR-210-5p downregulates expression of CFB, the variant decreases miR-210-5p-mediated repression of CFB. Together, our findings support the notion that miRNAs may play a role in AMD.
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Affiliation(s)
- Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stefan J Erkeland
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lei Xu
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johanna M Colijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Magda A Meester-Smoor
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
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165
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Doetzlhofer A, Avraham KB. Insights into inner ear-specific gene regulation: Epigenetics and non-coding RNAs in inner ear development and regeneration. Semin Cell Dev Biol 2017; 65:69-79. [PMID: 27836639 PMCID: PMC5512292 DOI: 10.1016/j.semcdb.2016.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/14/2016] [Accepted: 11/03/2016] [Indexed: 12/12/2022]
Abstract
The vertebrate inner ear houses highly specialized sensory organs, tuned to detect and encode sound, head motion and gravity. Gene expression programs under the control of transcription factors orchestrate the formation and specialization of the non-sensory inner ear labyrinth and its sensory constituents. More recently, epigenetic factors and non-coding RNAs emerged as an additional layer of gene regulation, both in inner ear development and disease. In this review, we provide an overview on how epigenetic modifications and non-coding RNAs, in particular microRNAs (miRNAs), influence gene expression and summarize recent discoveries that highlight their critical role in the proper formation of the inner ear labyrinth and its sensory organs. Finally, we discuss recent insights into how epigenetic factors and miRNAs may facilitate, or in the case of mammals, restrict inner ear sensory hair cell regeneration.
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Affiliation(s)
- Angelika Doetzlhofer
- The Solomon H. Snyder Department of Neuroscience, the Center for Sensory Biology, the Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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166
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The Application of Next-Generation Sequencing for Mutation Detection in Autosomal-Dominant Hereditary Hearing Impairment. Otol Neurotol 2017; 38:900-903. [PMID: 28419064 DOI: 10.1097/mao.0000000000001432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Identification of the causative mutation using next-generation sequencing in autosomal-dominant hereditary hearing impairment, as mutation analysis in hereditary hearing impairment by classic genetic methods, is hindered by the high heterogeneity of the disease. PATIENTS Two Swiss families with autosomal-dominant hereditary hearing impairment. INTERVENTION Amplified DNA libraries for next-generation sequencing were constructed from extracted genomic DNA, derived from peripheral blood, and enriched by a custom-made sequence capture library. Validated, pooled libraries were sequenced on an Illumina MiSeq instrument, 300 cycles and paired-end sequencing. Technical data analysis was performed with SeqMonk, variant analysis with GeneTalk or VariantStudio. The detection of mutations in genes related to hearing loss by next-generation sequencing was subsequently confirmed using specific polymerase-chain-reaction and Sanger sequencing. MAIN OUTCOME MEASURE Mutation detection in hearing-loss-related genes. RESULTS The first family harbored the mutation c.5383+5delGTGA in the TECTA-gene. In the second family, a novel mutation c.2614-2625delCATGGCGCCGTG in the WFS1-gene and a second mutation TCOF1-c.1028G>A were identified. CONCLUSION Next-generation sequencing successfully identified the causative mutation in families with autosomal-dominant hereditary hearing impairment. The results helped to clarify the pathogenic role of a known mutation and led to the detection of a novel one. NGS represents a feasible approach with great potential future in the diagnostics of hereditary hearing impairment, even in smaller labs.
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167
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Mahmoudian-Sani MR, Mehri-Ghahfarrokhi A, Ahmadinejad F, Hashemzadeh-Chaleshtori M, Saidijam M, Jami MS. MicroRNAs: effective elements in ear-related diseases and hearing loss. Eur Arch Otorhinolaryngol 2017; 274:2373-2380. [PMID: 28224282 DOI: 10.1007/s00405-017-4470-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Abstract
miRNAs are important factors for post-transcriptional process that controls gene expression at mRNA level. Various biological processes, including growth and differentiation, are regulated by miRNAs. miRNAs have been demonstrated to play an essential role in development and progression of hearing loss. Nowadays, miRNAs are known as critical factors involved in different physiological, biological, and pathological processes, such as gene expression, progressive sensorineural hearing loss, age-related hearing loss, noise-induced hearing loss, cholesteatoma, schwannomas, and inner ear inflammation. The miR-183 family (miR-183, miR-96 and miR-182) is expressed abundantly in some types of sensory cells in inner ear specially mechanosensory hair cells that exhibit a great expression level of this family. The plasma levels of miR-24-3p, miR-16-5p, miR-185-5p, and miR-451a were upregulated during noise exposures, and increased levels of miR-21 have been found in vestibular schwannomas and human cholesteatoma. In addition, upregulation of pro-apoptotic miRNAs and downregulation of miRNAs which promote differentiation and proliferation in age-related degeneration of the organ of Corti may potentially serve as a helpful biomarker for the early detection of age-related hearing loss. This knowledge represents miRNAs as promising diagnostic and therapeutic tools in the near future.
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Affiliation(s)
- Mohammad-Reza Mahmoudian-Sani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Fereshteh Ahmadinejad
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad-Saeid Jami
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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168
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Ahmed K, LaPierre MP, Gasser E, Denzler R, Yang Y, Rülicke T, Kero J, Latreille M, Stoffel M. Loss of microRNA-7a2 induces hypogonadotropic hypogonadism and infertility. J Clin Invest 2017; 127:1061-1074. [PMID: 28218624 DOI: 10.1172/jci90031] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are negative modulators of gene expression that fine-tune numerous biological processes. miRNA loss-of-function rarely results in highly penetrant phenotypes, but rather, influences cellular responses to physiologic and pathophysiologic stresses. Here, we have reported that a single member of the evolutionarily conserved miR-7 family, miR-7a2, is essential for normal pituitary development and hypothalamic-pituitary-gonadal (HPG) function in adulthood. Genetic deletion of mir-7a2 causes infertility, with low levels of gonadotropic and sex steroid hormones, small testes or ovaries, impaired spermatogenesis, and lack of ovulation in male and female mice, respectively. We found that miR-7a2 is highly expressed in the pituitary, where it suppresses golgi glycoprotein 1 (GLG1) expression and downstream bone morphogenetic protein 4 (BMP4) signaling and also reduces expression of the prostaglandin F2a receptor negative regulator (PTGFRN), an inhibitor of prostaglandin signaling and follicle-stimulating hormone (FSH) and luteinizing hormone (LH) secretion. Our results reveal that miR-7a2 critically regulates sexual maturation and reproductive function by interconnecting miR-7 genomic circuits that regulate FSH and LH synthesis and secretion through their effects on pituitary prostaglandin and BMP4 signaling.
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169
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Franco B, Malgrange B. Concise Review: Regeneration in Mammalian Cochlea Hair Cells: Help from Supporting Cells Transdifferentiation. Stem Cells 2017; 35:551-556. [PMID: 28102558 DOI: 10.1002/stem.2554] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/16/2016] [Accepted: 11/27/2016] [Indexed: 12/28/2022]
Abstract
It is commonly assumed that mammalian cochlear cells do not regenerate. Therefore, if hair cells are lost following an injury, no recovery could occur. However, during the first postnatal week, mice harbor some progenitor cells that retain the ability to give rise to new hair cells. These progenitor cells are in fact supporting cells. Upon hair cells loss, those cells are able to generate new hair cells both by direct transdifferentiation or following cell cycle re-entry and differentiation. However, this property of supporting cells is progressively lost after birth. Here, we review the molecular mechanisms that are involved in mammalian hair cell development and regeneration. Manipulating pathways used during development constitute good candidates for inducing hair cell regeneration after injury. Despite these promising studies, there is still no evidence for a recovery following hair cells loss in adult mammals. Stem Cells 2017;35:551-556.
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Affiliation(s)
- Bénédicte Franco
- Developmental Neurobiology Unit - GIGA-Neurosciences, University of Liège, Quartier Hôpital (CHU), B-4000, Liège, Belgium
| | - Brigitte Malgrange
- Developmental Neurobiology Unit - GIGA-Neurosciences, University of Liège, Quartier Hôpital (CHU), B-4000, Liège, Belgium
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170
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The emerging roles of MicroRNAs in autism spectrum disorders. Neurosci Biobehav Rev 2016; 71:729-738. [DOI: 10.1016/j.neubiorev.2016.10.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/27/2016] [Accepted: 10/22/2016] [Indexed: 12/21/2022]
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171
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Mahmoodian Sani MR, Hashemzadeh-Chaleshtori M, Saidijam M, Jami MS, Ghasemi-Dehkordi P. MicroRNA-183 Family in Inner Ear: Hair Cell Development and Deafness. J Audiol Otol 2016; 20:131-138. [PMID: 27942598 PMCID: PMC5144812 DOI: 10.7874/jao.2016.20.3.131] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 07/09/2016] [Accepted: 09/06/2016] [Indexed: 01/19/2023] Open
Abstract
miRNAs are essential factors of an extensively conserved post-transcriptional process controlling gene expression at mRNA level. Varoius biological processes such as growth and differentiation are regulated by miRNAs. Web of Science and PubMed databases were searched using the Endnote software for the publications about the role miRNA-183 family in inner ear: hair cell development and deafness published from 2000 to 2016. A triplet of these miRNAs particularly the miR-183 family is highly expressed in vertebrate hair cells, as with some of the peripheral neurosensory cells. Point mutations in one member of this family, miR-96, underlie DFNA50 autosomal deafness in humans and lead to abnormal hair cell development and survival in mice. In zebrafish, overexpression of the miR-183 family induces extra and ectopic hair cells, while knockdown decreases the number of hair cell. The miR-183 family (miR-183, miR-96 and miR-182) is expressed abundantly in some types of sensory cell in the eye, nose and inner ear. In the inner ear, mechanosensory hair cells have a robust expression level. Despite much similarity of these miRs sequences, small differences lead to distinct targeting of messenger RNAs targets. In the near future, miRNAs are likely to be explored as potential therapeutic agents to repair or regenerate hair cells, cell reprogramming and regenerative medicine applications in animal models because they can simultaneously down-regulate dozens or even hundreds of transcripts.
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Affiliation(s)
- Mohammad Reza Mahmoodian Sani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad-Saeid Jami
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Sharekord, Iran
| | - Payam Ghasemi-Dehkordi
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Sharekord, Iran
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172
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Wang L, Wang JK, Han LX, Zhuo JS, Du X, Liu D, Yang XQ. Characterization of miRNAs involved in response to poly(I:C) in porcine airway epithelial cells. Anim Genet 2016; 48:182-190. [PMID: 27878834 DOI: 10.1111/age.12524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNA) have been implicated in a variety of pathological conditions including infectious diseases. Knowledge of the miRNAs affected by poly(I:C), a synthetic analog of viral double-stranded RNA, in porcine airway epithelial cells (PAECs) contributes to understanding the mechanisms of swine viral respiratory diseases, which bring enormous economic loss worldwide every year. In this study, we used high throughput sequencing to profile miRNA expression in PAECs treated with poly(I:C) as compared to the untreated control. This approach revealed 23 differentially expressed miRNAs (DEMs), five of which have not been implicated in viral infection before. Nineteen of the 23 miRNAs were down-regulated including members of the miR-17-92 cluster, a well-known polycistronic oncomir and extensively involved in viral infection in humans. Target genes of DEMs, predicted using bioinformatic methods and validated by luciferase reporter analysis on two representative DEMs, were significantly enriched in several pathways including transforming growth factor-β signaling. A large quantity of sequence variations (isomiRs) were found including a substitution at position 5, which was verified to redirect miRNAs to a new spectrum of targets by luciferase reporter assay together with bioinformatics analysis. Twelve novel porcine miRNAs conserved in other species were identified by homology analysis together with cloning verification. Furthermore, the expression analysis revealed the potential importance of three novel miRNAs in porcine immune response to viruses. Overall, our data contribute to clarifying the mechanisms underlying the host immune response against respiratory viruses in pigs, and enriches the repertoire of porcine miRNAs.
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Affiliation(s)
- L Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.,Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - J K Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - L X Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - J S Zhuo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - X Du
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - D Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - X Q Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
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173
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Jin T, Wu X, Yang H, Liu M, He Y, He X, Shi X, Wang F, Du S, Ma Y, Bao S, Yuan D. Association of the miR-17-5p variants with susceptibility to cervical cancer in a Chinese population. Oncotarget 2016; 7:76647-76655. [PMID: 27765929 PMCID: PMC5363537 DOI: 10.18632/oncotarget.12299] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/30/2016] [Indexed: 01/18/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression; however, the extent to which single nucleotide polymorphisms (SNPs) interfere with miRNA gene regulation and affect cervical cancer (CC) susceptibility remains largely unknown. Here, we systematically analyzed miRNA-related SNPs and their association with CC risk, and performed a case-control study of miR-17-5p SNPs and CC risk in a Chinese population. Sixteen SNPs were genotyped in 247 CC cases and 285 controls. Three were associated with CC risk (p < 0.05): the minor allele (A) of rs217727 in H19 increased risk (OR = 1.53, p = 0.002), while the minor alleles (T) of rs9931702 and (T) of rs9302648 in AKTIP decreased CC risk (p = 0.018, p = 0.014). Analysis of the SNPs after stratification based on CC clinical stage and subtype revealed that rs1048512, rs6659346, rs217727, rs9931702, and rs9302648 were associated with CC risk in clinical stages I-II; rs2862833, rs2732044, rs1030389, and rs1045935 were associated with CC risk in clinical stages III-IV; and rs217727, rs9931702, and rs9302648 were associated with CC risk in squamous carcinomas. These data could serve as a useful resource for understanding the miR-17 function, identification of miRNAs associated with CC, and development of better CC screening strategies.
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Affiliation(s)
- Tianbo Jin
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Xi'an Tiangen Precision Medical Institute, Xi'an, Shaanxi 710075, China
| | - Xiaohong Wu
- Department of Maternity care, Xi'an Maternal and Child Health Hospital, Xi'an, Shaanxi 710002, China
| | - Hua Yang
- Xi'an Tiangen Precision Medical Institute, Xi'an, Shaanxi 710075, China
| | - Ming Liu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004, China
| | - Yongjun He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Xue He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Xugang Shi
- Xi'an Tiangen Precision Medical Institute, Xi'an, Shaanxi 710075, China
| | - Fengjiao Wang
- Xi'an Tiangen Precision Medical Institute, Xi'an, Shaanxi 710075, China
| | - Shuli Du
- Xi'an Tiangen Precision Medical Institute, Xi'an, Shaanxi 710075, China
| | - Yajuan Ma
- Xi'an Tiangen Precision Medical Institute, Xi'an, Shaanxi 710075, China
| | - Shan Bao
- Clinic of Gynecology and Obstetrics, Hainan Provincial People's Hospital, Haikou, 570102, China
| | - Dongya Yuan
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
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174
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Alipoor SD, Adcock IM, Garssen J, Mortaz E, Varahram M, Mirsaeidi M, Velayati A. The roles of miRNAs as potential biomarkers in lung diseases. Eur J Pharmacol 2016; 791:395-404. [PMID: 27634639 PMCID: PMC7094636 DOI: 10.1016/j.ejphar.2016.09.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs which can act as master regulators of gene expression, modulate almost all biological process and are essential for maintaining cellular homeostasis. Dysregulation of miRNA expression has been associated with aberrant gene expression and may lead to pathological conditions. Evidence suggests that miRNA expression profiles are altered between health and disease and as such may be considered as biomarkers of disease. Evidence is increasing that miRNAs are particularly important in lung homeostasis and development and have been demonstrated to be the involved in many pulmonary diseases such as asthma, COPD, sarcoidosis, lung cancer and other smoking related diseases. Better understanding of the function of miRNA and the mechanisms underlying their action in the lung, would help to improve current diagnosis and therapeutics strategies in pulmonary diseases. Recently, some miRNA-based drugs have been introduced as possible therapeutic agents. In this review we aim to summarize the recent findings regarding the role of miRNAs in the airways and lung and emphasise their potential therapeutic roles in pulmonary diseases.
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Affiliation(s)
- Shamila D Alipoor
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran; Institute of Medical Biotechnology, Molecular Medicine Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ian M Adcock
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, UK
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands; Nutricia Research Centre for Specialized Nutrition, Utrecht, The Netherlands
| | - Esmaeil Mortaz
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, UK; Clinical Tuberculosis and Epidemiology Research Center, National Research and Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Varahram
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - Aliakbar Velayati
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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175
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Fan Y, Zhang Y, Wu R, Chen X, Zhang Y, Chen X, Zhu D. miR-431 is involved in regulating cochlear function by targeting Eya4. Biochim Biophys Acta Mol Basis Dis 2016; 1862:2119-2126. [DOI: 10.1016/j.bbadis.2016.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/15/2016] [Accepted: 08/17/2016] [Indexed: 10/21/2022]
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176
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Jiang D, Du J, Zhang X, Zhou W, Zong L, Dong C, Chen K, Chen Y, Chen X, Jiang H. miR-124 promotes the neuronal differentiation of mouse inner ear neural stem cells. Int J Mol Med 2016; 38:1367-1376. [PMID: 28025992 PMCID: PMC5065304 DOI: 10.3892/ijmm.2016.2751] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 08/08/2016] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) act as key regulators in neuronal development, synaptic morphogenesis and plasticity. However, their role in the neuronal differentiation of inner ear neural stem cells (NSCs) remains unclear. In this study, 6 miRNAs were selected and their expression patterns during the neuronal differentiation of inner ear NSCs were examined by RT-qPCR. We demonstrated that the culture of spiral ganglion stem cells present in the inner ears of newborn mice gave rise to neurons in vitro. The expression patterns of miR-124, miR-132, miR-134, miR-20a, miR-17-5p and miR-30a-5p were examined during a 14-day neuronal differentiation period. We found that miR-124 promoted the neuronal differentiation of and neurite outgrowth in mouse inner ear NSCs, and that the changes in the expression of tropomyosin receptor kinase B (TrkB) and cell division control protein 42 homolog (Cdc42) during inner ear NSC differentiation were associated with miR-124 expression. Our findings indicate that miR-124 plays a role in the neuronal differentiation of inner ear NSCs. This finding may lead to the development of novel strategies for restoring hearing in neurodegenerative diseases.
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Affiliation(s)
- Di Jiang
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Jintao Du
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Xuemei Zhang
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Wei Zhou
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Lin Zong
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Chang Dong
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Kaitian Chen
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yu Chen
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Xihui Chen
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Hongyan Jiang
- Department of Otolaryngology, The First Affiliated Hospital, and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
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177
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Liu J, Sun Y, Yang C, Zhang Y, Jiang Q, Huang J, Ju Z, Wang X, Zhong J, Wang C. Functional SNPs of INCENP Affect Semen Quality by Alternative Splicing Mode and Binding Affinity with the Target Bta-miR-378 in Chinese Holstein Bulls. PLoS One 2016; 11:e0162730. [PMID: 27669152 PMCID: PMC5036895 DOI: 10.1371/journal.pone.0162730] [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: 02/29/2016] [Accepted: 08/26/2016] [Indexed: 12/22/2022] Open
Abstract
Inner centromere protein (INCENP) plays an important role in mitosis and meiosis as the main member of chromosomal passenger protein complex (CPC). To investigate the functional markers of the INCENP gene associated with semen quality, the single nucleotide polymorphisms (SNPs) g.19970 A>G and g.34078 T>G were identified and analyzed. The new splice variant INCENP-TV is characterized by the deletion of exon 12. The g.19970 A>G in the exonic splicing enhancer (ESE) motif region results in an aberrant splice variant by constructing two minigene expression vectors using the pSPL3 exon capturing vector and transfecting vectors into MLTC-1 cells. INCENP-TV was more highly expressed than INCENP-reference in adult bull testes. The g.34078 T>G located in the binding region of bta-miR-378 could affect the expression of INCENP, which was verified by luciferase assay. To analyze comprehensively the correlation of SNPs with sperm quality, haplotype combinations constructed by g.19970 A>G and g.34078 T>G, as well as g.-692 C>T and g.-556 G>T reported in our previous studies, were analyzed. The bulls with H1H12 and H2H2 exhibited a higher ejaculate volume than those with H2H10 and H9H12, respectively (P < 0.05). Bulls with H11H11 and H2H10 exhibited higher initial sperm motility than those with H2H2 (P < 0.05). The expression levels of INCENP in bulls with H1H12 and H11H11 were significantly higher than those in bulls with H9H12 (P < 0.05), as determined by qRT-PCR. Findings suggest that g.19970 A>G and g.34078 T>G in INCENP both of which appear to change the molecular and biological characteristics of the mRNA transcribed from the locus may serve as a biomarkers of male bovine fertility by affecting alternative splicing mode and binding affinity with the target bta-miR-378.
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Affiliation(s)
- Juan Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- College of Agronomic Sciences in Shandong Agricultural University, Taian, China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- * E-mail:
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178
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MiR-182-5p protects inner ear hair cells from cisplatin-induced apoptosis by inhibiting FOXO3a. Cell Death Dis 2016; 7:e2362. [PMID: 27607577 PMCID: PMC5059852 DOI: 10.1038/cddis.2016.246] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 06/14/2016] [Accepted: 07/13/2016] [Indexed: 01/01/2023]
Abstract
Cisplatin is widely used for chemotherapy of a variety of malignancies. However, the clinical application of cisplatin is hampered by the resultant irreversible hearing loss due to hair cell apoptosis. To date, no practical regimen to resolve this has been developed. Meanwhile, the role of microRNA in protecting hair cells from cisplatin-induced apoptosis in the inner ear has not been extensively investigated. In this study, we monitored miR-183, -96, and -182 turnover in the cochlea during cisplatin treatment in vitro. We found that overexpression of miR-182, but not miR-183 and -96, improved hair cell survival after 3 μM cisplatin treatment in vitro. We demonstrated that overexpression of miR-182 repressed the intrinsic apoptotic pathway by inhibiting the translation of FOXO3a. Our study offers a new therapeutic target for alleviating cisplatin-induced hair cell apoptosis in a rapid and tissue-specific manner.
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179
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Smith ME, Rajadinakaran G. The Transcriptomics to Proteomics of Hair Cell Regeneration: Looking for a Hair Cell in a Haystack. MICROARRAYS 2016; 2. [PMID: 24416530 PMCID: PMC3886832 DOI: 10.3390/microarrays2030186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mature mammals exhibit very limited capacity for regeneration of auditory hair cells, while all non-mammalian vertebrates examined can regenerate them. In an effort to find therapeutic targets for deafness and balance disorders, scientists have examined gene expression patterns in auditory tissues under different developmental and experimental conditions. Microarray technology has allowed the large-scale study of gene expression profiles (transcriptomics) at whole-genome levels, but since mRNA expression does not necessarily correlate with protein expression, other methods, such as microRNA analysis and proteomics, are needed to better understand the process of hair cell regeneration. These technologies and some of the results of them are discussed in this review. Although there is a considerable amount of variability found between studies owing to different species, tissues and treatments, there is some concordance between cellular pathways important for hair cell regeneration. Since gene expression and proteomics data is now commonly submitted to centralized online databases, meta-analyses of these data may provide a better picture of pathways that are common to the process of hair cell regeneration and lead to potential therapeutics. Indeed, some of the proteins found to be regulated in the inner ear of animal models (e.g., IGF-1) have now gone through human clinical trials.
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Affiliation(s)
- Michael E. Smith
- Bioinformatics and Information Science Center, Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-270-745-2405; Fax: +1-270-745-6856
| | - Gopinath Rajadinakaran
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA; E-Mail:
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180
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Bhattacharya A, Cui Y. Knowledge-based analysis of functional impacts of mutations in microRNA seed regions. J Biosci 2016; 40:791-8. [PMID: 26564979 DOI: 10.1007/s12038-015-9560-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
MicroRNAs are a class of important post-transcriptional regulators. Genetic and somatic mutations in miRNAs, especially those in the seed regions, have profound and broad impacts on gene expression and physiological and pathological processes. Over 500 SNPs were mapped to the miRNA seeds, which are located at position 2-8 of the mature miRNA sequences. We found that the central positions of the miRNA seeds contain fewer genetic variants and therefore are more evolutionary conserved than the peripheral positions in the seeds. We developed a knowledgebased method to analyse the functional impacts of mutations in miRNA seed regions. We computed the gene ontology-based similarity score GOSS and the GOSS percentile score for all 517 SNPs in miRNA seeds. In addition to the annotation of SNPs for their functional effects, in the present article we also present a detailed analysis pipeline for finding the key functional changes for seed SNPs. We performed a detailed gene ontology graph-based analysis of enriched functional categories for miRNA target gene sets. In the analysis of a SNP in the seed region of hsa-miR-96 we found that two key biological processes for progressive hearing loss 'Neurotrophin TRK receptor signaling pathway' and 'Epidermal growth factor receptor signaling pathway' were significantly and differentially enriched by the two sets of allele-specific target genes of miRNA hsa-miR-96.
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Affiliation(s)
- Anindya Bhattacharya
- Department of Microbiology, Immunology and Biochemistry and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN 38163, USA,
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181
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Li H, Zhang H, Lu G, Li Q, Gu J, Song Y, Gao S, Ding Y. Mechanism analysis of colorectal cancer according to the microRNA expression profile. Oncol Lett 2016; 12:2329-2336. [PMID: 27698796 PMCID: PMC5038387 DOI: 10.3892/ol.2016.5027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/22/2016] [Indexed: 01/17/2023] Open
Abstract
The present study aimed to identify specific microRNAs (miRs) and their predicted target genes to clarify the molecular mechanisms of colorectal cancer (CRC). An miR expression profile (array ID, GSE39833), which consisted of 88 CRC samples with various tumor-necrosis-metastasis stages and 11 healthy controls, was downloaded from the Gene Expression Omnibus database. Subsequently, the differentially expressed miRs and their target genes were screened. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways of target genes were analyzed using the Database for Annotation Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of the target genes was constructed using the Search Tool for the Retrieval of Interacting Genes database. The present study identified a total of 18 differentially expressed miRs (upregulated, 8; downregulated, 10) in the sera of the CRC patients compared with the healthy controls. Of these, 3 upregulated (let-7b, miR-1290 and miR-126) and 2 downregulated (miR-16 and miR-760) differentially expressed miRs and their target genes, including cyclin D1 (CCND1), v-myc avian myelocytomatosis viral oncogene homolog (MYC), phosphoinositide-3-kinase, regulatory subunit 2 (beta) (PIK3R2) and SMAD family member 3 (SMAD3), were significantly enriched in the CRC developmental pathway. All these target genes had higher node degrees in the PPI network. In conclusion, let-7b, miR-1290, miR-126, miR-16 and miR-760 and their target genes, CCND1, MYC, PIK3R2 and SMAD3, may be important in the molecular mechanisms for the progression of CRC.
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Affiliation(s)
- Hong Li
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
| | - Huichao Zhang
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
| | - Gang Lu
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
| | - Qingjing Li
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
| | - Jifeng Gu
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
| | - Yuan Song
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
| | - Shejun Gao
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
| | - Yawen Ding
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, P.R. China
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182
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Bhajun R, Guyon L, Gidrol X. MicroRNA degeneracy and pluripotentiality within a Lavallière-tie architecture confers robustness to gene expression networks. Cell Mol Life Sci 2016; 73:2821-7. [PMID: 27038488 PMCID: PMC4937071 DOI: 10.1007/s00018-016-2186-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 02/24/2016] [Accepted: 03/18/2016] [Indexed: 11/03/2022]
Abstract
Modularity, feedback control, functional redundancy and bowtie architecture have been proposed as key factors that confer robustness to complex biological systems. MicroRNAs (miRNAs) are highly conserved but functionally dispensable. These antinomic properties suggest that miRNAs fine-tune gene expression rather than act as genetic switches. We synthesize published and unpublished data and hypothesize that miRNA pluripotentiality acts to buffer gene expression, while miRNA degeneracy tunes the expression of targets, thus providing robustness to gene expression networks. Furthermore, we propose a Lavallière-tie architecture by integrating signal transduction, miRNAs and protein expression data to model complex gene expression networks.
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Affiliation(s)
- Ricky Bhajun
- CEA, BIG, BGE, 17, rue des Martyrs, 38000, Grenoble, France
- University Grenoble Alpes, BGE, 38000, Grenoble, France
- INSERM, U1038, 38000, Grenoble, France
| | - Laurent Guyon
- CEA, BIG, BGE, 17, rue des Martyrs, 38000, Grenoble, France
- University Grenoble Alpes, BGE, 38000, Grenoble, France
- INSERM, U1038, 38000, Grenoble, France
| | - Xavier Gidrol
- CEA, BIG, BGE, 17, rue des Martyrs, 38000, Grenoble, France.
- University Grenoble Alpes, BGE, 38000, Grenoble, France.
- INSERM, U1038, 38000, Grenoble, France.
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183
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Liu Y, Bailey JC, Helwa I, Dismuke WM, Cai J, Drewry M, Brilliant MH, Budenz DL, Christen WG, Chasman DI, Fingert JH, Gaasterland D, Gaasterland T, Gordon MO, Igo RP, Kang JH, Kass MA, Kraft P, Lee RK, Lichter P, Moroi SE, Realini A, Richards JE, Ritch R, Schuman JS, Scott WK, Singh K, Sit AJ, Song YE, Vollrath D, Weinreb R, Medeiros F, Wollstein G, Zack DJ, Zhang K, Pericak-Vance MA, Gonzalez P, Stamer WD, Kuchtey J, Kuchtey RW, Allingham RR, Hauser MA, Pasquale LR, Haines JL, Wiggs JL. A Common Variant in MIR182 Is Associated With Primary Open-Angle Glaucoma in the NEIGHBORHOOD Consortium. Invest Ophthalmol Vis Sci 2016; 57:4528-4535. [PMID: 27537254 PMCID: PMC4991020 DOI: 10.1167/iovs.16-19688] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/21/2016] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Noncoding microRNAs (miRNAs) have been implicated in the pathogenesis of glaucoma. We aimed to identify common variants in miRNA coding genes (MIR) associated with primary open-angle glaucoma (POAG). METHODS Using the NEIGHBORHOOD data set (3853 cases/33,480 controls with European ancestry), we first assessed the relation between 85 variants in 76 MIR genes and overall POAG. Subtype-specific analyses were performed in high-tension glaucoma (HTG) and normal-tension glaucoma subsets. Second, we examined the expression of miR-182, which was associated with POAG, in postmortem human ocular tissues (ciliary body, cornea, retina, and trabecular meshwork [TM]), using miRNA sequencing (miRNA-Seq) and droplet digital PCR (ddPCR). Third, miR-182 expression was also examined in human aqueous humor (AH) by using miRNA-Seq. Fourth, exosomes secreted from primary human TM cells were examined for miR-182 expression by using miRNA-Seq. Fifth, using ddPCR we compared miR-182 expression in AH between five HTG cases and five controls. RESULTS Only rs76481776 in MIR182 gene was associated with POAG after adjustment for multiple comparisons (odds ratio [OR] = 1.23, 95% confidence interval [CI]: 1.11-1.42, P = 0.0002). Subtype analysis indicated that the association was primarily in the HTG subset (OR = 1.26, 95% CI: 1.08-1.47, P = 0.004). The risk allele T has been associated with elevated miR-182 expression in vitro. Data from ddPCR and miRNA-Seq confirmed miR-182 expression in all examined ocular tissues and TM-derived exosomes. Interestingly, miR-182 expression in AH was 2-fold higher in HTG patients than nonglaucoma controls (P = 0.03) without controlling for medication treatment. CONCLUSIONS Our integrative study is the first to associate rs76481776 with POAG via elevated miR-182 expression.
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Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States
- James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, Georgia, United States
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
| | - Jessica Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Inas Helwa
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States
| | - W. Michael Dismuke
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Jingwen Cai
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States
| | - Michelle Drewry
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States
| | - Murray H. Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States
| | - Donald L. Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - William G. Christen
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Daniel I. Chasman
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - John H. Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | | | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, United States
| | - Mae O. Gordon
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Robert P. Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Jae H. Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Michael A. Kass
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Peter Kraft
- School of Public Health, Harvard University, Boston, Massachusetts, United States
| | - Richard K. Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Paul Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Sayoko E. Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Anthony Realini
- Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, West Virginia, United States
| | - Julia E. Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, United States
| | - Joel S. Schuman
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - William K. Scott
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Arthur J. Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Yeunjoo E. Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Douglas Vollrath
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Robert Weinreb
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Felipe Medeiros
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Gadi Wollstein
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Donald J. Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, United States
| | - Kang Zhang
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Margaret A. Pericak-Vance
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Pedro Gonzalez
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - W. Daniel Stamer
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - John Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Rachel W. Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - R. Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael A. Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Louis R. Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Department of Ophthalmology, Mass Eye & Ear, Boston, Massachusetts, United States
| | - Jonathan L. Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Janey L. Wiggs
- Department of Ophthalmology, Mass Eye & Ear, Boston, Massachusetts, United States
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184
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Kim YR, Hong SH. Associations of MicroRNA Polymorphisms (miR-146a, miR-196a2, and miR-499) with the Risk of Hypertension in the Korean Population. Genet Test Mol Biomarkers 2016; 20:420-6. [PMID: 27379568 DOI: 10.1089/gtmb.2016.0039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AIMS Polymorphisms in microRNA (miR) genes are thought to be associated with various cancers and vascular diseases. To date, however, the effects of the miR gene polymorphisms on susceptibility to hypertension have rarely been investigated. In this study, we investigated the associations of three miR gene polymorphisms (miR-146aC>G/rs2910164, miR-196a2T>C/rs11614913, and miR-499A>G/rs3746444) with the risk of hypertension in Korean patients. METHODS A total of 855 study subjects (340 patients with hypertension and 515 healthy normotensive subjects) were included in this study. Genotyping of the three miR gene polymorphisms was accomplished by polymerase chain reaction-restriction fragment length polymorphism analyses. RESULTS Significant differences were observed in the genotype distributions of the miR-146aC>G polymorphism between the hypertensive patients and controls with the GG genotype, in both model-independent analyses, as well as in dominant (CC vs. CG+GG) and recessive (CC+CG vs. GG) models, being highly significantly associated with disease (AOR = 2.293, 95% CI: 1.466-3.586, p = 0.001; AOR = 1.727, 95% CI: 1.182-2.522, p = 0.015; AOR = 1.782, 95% CI: 1.267-2.506, p = 0.001, respectively). Neither the miR-196a2T>C nor the miR-499A>G polymorphisms were distributed significantly differently between hypertensive patients and control subjects. Several allelic combinations of the three miR polymorphisms were also associated with susceptibility to hypertension. Stratified analysis revealed that the miR-146aC>G and miR-499A>G polymorphisms are associated with a greater risk of hypertension. CONCLUSION This study suggests that the variant of miR-146aC>G polymorphism and allelic combinations, at least in Koreans, affect susceptibility to hypertension.
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Affiliation(s)
- Young Ree Kim
- 1 Department of Laboratory Medicine, School of Medicine, Jeju National University , Jeju, Republic of Korea
| | - Seung-Ho Hong
- 2 Department of Science Education, Teachers College, Jeju National University , Jeju, Republic of Korea
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Fendler W, Madzio J, Kozinski K, Patel K, Janikiewicz J, Szopa M, Tracz A, Borowiec M, Jarosz-Chobot P, Mysliwiec M, Szadkowska A, Hattersley AT, Ellard S, Malecki MT, Dobrzyn A, Mlynarski W. Differential regulation of serum microRNA expression by HNF1β and HNF1α transcription factors. Diabetologia 2016; 59:1463-1473. [PMID: 27059371 PMCID: PMC4901123 DOI: 10.1007/s00125-016-3945-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/10/2016] [Indexed: 11/29/2022]
Abstract
AIMS/HYPOTHESIS We aimed to identify microRNAs (miRNAs) under transcriptional control of the HNF1β transcription factor, and investigate whether its effect manifests in serum. METHODS The Polish cohort (N = 60) consisted of 11 patients with HNF1B-MODY, 17 with HNF1A-MODY, 13 with GCK-MODY, an HbA1c-matched type 1 diabetic group (n = 9) and ten healthy controls. Replication was performed in 61 clinically-matched British patients mirroring the groups in the Polish cohort. The Polish cohort underwent miRNA serum level profiling with quantitative real-time PCR (qPCR) arrays to identify differentially expressed miRNAs. Validation was performed using qPCR. To determine whether serum content reflects alterations at a cellular level, we quantified miRNA levels in a human hepatocyte cell line (HepG2) with small interfering RNA knockdowns of HNF1α or HNF1β. RESULTS Significant differences (adjusted p < 0.05) were noted for 11 miRNAs. Five of them differed between HNF1A-MODY and HNF1B-MODY, and, amongst those, four (miR-24, miR-27b, miR-223 and miR-199a) showed HNF1B-MODY-specific expression levels in the replication group. In all four cases the miRNA expression level was lower in HNF1B-MODY than in all other tested groups. Areas under the receiver operating characteristic curves ranged from 0.79 to 0.86, with sensitivity and specificity reaching 91.7% (miR-24) and 82.1% (miR-199a), respectively. The cellular expression pattern of miRNA was consistent with serum levels, as all were significantly higher in HNF1α- than in HNF1β-deficient HepG2 cells. CONCLUSIONS/INTERPRETATION We have shown that expression of specific miRNAs depends on HNF1β function. The impact of HNF1β deficiency was evidenced at serum level, making HNF1β-dependent miRNAs potentially applicable in the diagnosis of HNF1B-MODY.
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Affiliation(s)
- Wojciech Fendler
- Department of Paediatrics, Oncology, Haematology and Diabetology, Medical University of Lodz, Lodz, Poland.
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 36/50 Sporna Str., 91-738, Lodz, Poland.
| | - Joanna Madzio
- Department of Paediatrics, Oncology, Haematology and Diabetology, Medical University of Lodz, Lodz, Poland
- Studies in Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Kamil Kozinski
- Laboratory of Cell Signalling and Metabolic Disorders, Nencki Institute of Experimental Medicine, Polish Academy of Sciences, Warsaw, Poland
| | - Kashyap Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Justyna Janikiewicz
- Laboratory of Cell Signalling and Metabolic Disorders, Nencki Institute of Experimental Medicine, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Szopa
- Department of Metabolic Diseases, Jagiellonian University Medical College, Krakow, Poland
- University Hospital, Krakow, Poland
| | - Adam Tracz
- Department of Paediatrics, Oncology, Haematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland
| | | | - Malgorzata Mysliwiec
- Department of Paediatrics, Diabetology and Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Agnieszka Szadkowska
- Department of Paediatrics, Oncology, Haematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Maciej T Malecki
- Department of Metabolic Diseases, Jagiellonian University Medical College, Krakow, Poland
- University Hospital, Krakow, Poland
| | - Agnieszka Dobrzyn
- Laboratory of Cell Signalling and Metabolic Disorders, Nencki Institute of Experimental Medicine, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Mlynarski
- Department of Paediatrics, Oncology, Haematology and Diabetology, Medical University of Lodz, Lodz, Poland
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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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188
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Farzadfard A, Nassiri N, Moghadam TN, Paylakhi SH, Elahi E. Screening for MIR184 Mutations in Iranian Patients with Keratoconus. J Ophthalmic Vis Res 2016; 11:3-7. [PMID: 27195078 PMCID: PMC4860983 DOI: 10.4103/2008-322x.180715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Purpose: To investigate whether microRNA (MIR)-184 mutations make a substantial contribution to keratoconus (KCN) among affected Iranian patients. Methods: A total of 47 Iranian KCN patients, diagnosed based on family history, clinical examinations using slit lamp biomicroscopy, refraction and corneal topography were enrolled in this study. The pri-miR-184 encoding gene obtained from the DNAs of all participants was amplified using polymerase chain reaction and subsequently sequenced by the Sanger dideoxynucleotide protocol. The sequences were compared to MIR184 reference sequence in order to identify sequence variations. The potential effects of a single variation observed on RNA structure was predicted. Results: Only one sequence variation, +39G >T, was observed within the pri-miR-184 encoding sequence in one proband. The patient's KCN-affected sister harbored the same variation. The variation was not novel and was recently shown to be present at similar frequencies among large cohorts of KCN patients and control individuals. Conclusion: Mutations in MIR-184 are not a major cause of keratoconus among Iranian patients. The pri-miR-184 sequence needs to be screened in larger cohorts in order to establish whether mutations in the gene are present at low frequencies among Iranian patients.
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Affiliation(s)
- Azad Farzadfard
- Department of Cellular and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Nader Nassiri
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Seyed Hassan Paylakhi
- Department of Cellular and Molecular Biology, School of Biology, Damghan University, Damghan, Iran
| | - Elahe Elahi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
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189
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The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J Biomed Semantics 2016; 7:24. [PMID: 27152146 PMCID: PMC4857245 DOI: 10.1186/s13326-016-0066-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/19/2016] [Indexed: 11/17/2022] Open
Abstract
In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl.
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Riccardi S, Bergling S, Sigoillot F, Beibel M, Werner A, Leighton-Davies J, Knehr J, Bouwmeester T, Parker CN, Roma G, Kinzel B. MiR-210 promotes sensory hair cell formation in the organ of corti. BMC Genomics 2016; 17:309. [PMID: 27121005 PMCID: PMC4848794 DOI: 10.1186/s12864-016-2620-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 04/14/2016] [Indexed: 12/20/2022] Open
Abstract
Background Hearing loss is the most common sensory defect afflicting several hundred million people worldwide. In most cases, regardless of the original cause, hearing loss is related to the degeneration and death of hair cells and their associated spiral ganglion neurons. Despite this knowledge, relatively few studies have reported regeneration of the auditory system. Significant gaps remain in our understanding of the molecular mechanisms underpinning auditory function, including the factors required for sensory cell regeneration. Recently, the identification of transcriptional activators and repressors of hair cell fate has been augmented by the discovery of microRNAs (miRNAs) associated with hearing loss. As miRNAs are central players of differentiation and cell fate, identification of miRNAs and their gene targets may reveal new pathways for hair cell regeneration, thereby providing new avenues for the treatment of hearing loss. Results In order to identify new genetic elements enabling regeneration of inner ear sensory hair cells, next-generation miRNA sequencing (miRSeq) was used to identify the most prominent miRNAs expressed in the mouse embryonic inner ear cell line UB/OC-1 during differentiation towards a hair cell like phenotype. Based on these miRSeq results eight most differentially expressed miRNAs were selected for further characterization. In UB/OC-1, miR-210 silencing in vitro resulted in hair cell marker expression, whereas ectopic expression of miR-210 resulted in new hair cell formation in cochlear explants. Using a lineage tracing mouse model, transdifferentiation of supporting epithelial cells was identified as the likely mechanism for this new hair cell formation. Potential miR-210 targets were predicted in silico and validated experimentally using a miR-trap approach. Conclusion MiRSeq followed by ex vivo validation revealed miR-210 as a novel factor driving transdifferentiation of supporting epithelial cells to sensory hair cells suggesting that miR-210 might be a potential new factor for hearing loss therapy. In addition, identification of inner ear pathways regulated by miR-210 identified potential new drug targets for the treatment of hearing loss. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2620-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabrina Riccardi
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Sebastian Bergling
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Frederic Sigoillot
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Cambridge, USA
| | - Martin Beibel
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Annick Werner
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Juliet Leighton-Davies
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Judith Knehr
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Tewis Bouwmeester
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Christian N Parker
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Bernd Kinzel
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland.
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Penso-Dolfin L, Swofford R, Johnson J, Alföldi J, Lindblad-Toh K, Swarbreck D, Moxon S, Di Palma F. An Improved microRNA Annotation of the Canine Genome. PLoS One 2016; 11:e0153453. [PMID: 27119849 PMCID: PMC4847789 DOI: 10.1371/journal.pone.0153453] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
Abstract
The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions.
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Affiliation(s)
- Luca Penso-Dolfin
- Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich, United Kingdom
| | - Ross Swofford
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jessica Alföldi
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kerstin Lindblad-Toh
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - David Swarbreck
- Regulatory Genomics, The Genome Analysis Centre, Norwich, United Kingdom
| | - Simon Moxon
- Regulatory Genomics, The Genome Analysis Centre, Norwich, United Kingdom
- * E-mail: (SM); (DFP)
| | - Federica Di Palma
- Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich, United Kingdom
- * E-mail: (SM); (DFP)
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192
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Li J, Sen GL. Post-Transcriptional Mechanisms Regulating Epidermal Stem and Progenitor Cell Self-Renewal and Differentiation. J Invest Dermatol 2016; 136:746-752. [DOI: 10.1016/j.jid.2015.12.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/17/2015] [Accepted: 11/30/2015] [Indexed: 01/19/2023]
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Muraleedharan CK, McClellan SA, Barrett RP, Li C, Montenegro D, Carion T, Berger E, Hazlett LD, Xu S. Inactivation of the miR-183/96/182 Cluster Decreases the Severity of Pseudomonas aeruginosa-Induced Keratitis. Invest Ophthalmol Vis Sci 2016; 57:1506-17. [PMID: 27035623 PMCID: PMC4819431 DOI: 10.1167/iovs.16-19134] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/20/2016] [Indexed: 12/19/2022] Open
Abstract
PURPOSE The microRNA-183/96/182 cluster (miR-183/96/182) plays important roles in sensory organs. Because the cornea is replete with sensory innervation, we hypothesized that miR-183/96/182 modulates the corneal response to bacterial infection through regulation of neuroimmune interactions. METHODS Eight-week-old miR-183/96/182 knockout (ko) mice and their wild-type littermates (wt) were used. The central cornea of anesthetized mice was scarred and infected with Pseudomonas aeruginosa (PA), strain 19660. Corneal disease was graded at 1, 3, and 5 days postinfection (dpi). Corneal RNA was harvested for quantitative RT-PCR. Polymorphonuclear neutrophils (PMN) were enumerated by myeloperoxidase assays; the number of viable bacteria was determined by plate counts, and ELISA assays were performed to determine cytokine protein levels. A macrophage (Mϕ) cell line and elicited peritoneal PMN were used for in vitro functional assays. RESULTS MicroRNA-183/96/182 is expressed in the cornea, and in Mϕ and PMN of both mice and humans. Inactivation of miR-183/96/182 resulted in decreased corneal nerve density compared with wt mice. Overexpression of miR-183/96/182 in Mϕ decreased, whereas knockdown or inactivation of miR-183/96/182 in Mϕ and PMN increased their capacity for phagocytosis and intracellular killing of PA. In PA-infected corneas, ko mice showed decreased proinflammatory neuropeptides such as substance P and chemoattractant molecules, MIP-2, MCP1, and ICAM1; decreased number of PMN at 1 and 5 dpi; increased viable bacterial load at 1 dpi, but decreased at 5 dpi; and markedly decreased corneal disease. CONCLUSIONS MicroRNA-183/96/182 modulates the corneal response to bacterial infection through its regulation of corneal innervation and innate immunity.
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Affiliation(s)
- Chithra K. Muraleedharan
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University, School of Medicine, Detroit, Michigan, United States
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Sharon A. McClellan
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Ronald P. Barrett
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Cui Li
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Daniel Montenegro
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Thomas Carion
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Elizabeth Berger
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University, School of Medicine, Detroit, Michigan, United States
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Linda D. Hazlett
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University, School of Medicine, Detroit, Michigan, United States
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
| | - Shunbin Xu
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University, School of Medicine, Detroit, Michigan, United States
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States
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194
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Lewis MA, Buniello A, Hilton JM, Zhu F, Zhang WI, Evans S, van Dongen S, Enright AJ, Steel KP. Exploring regulatory networks of miR-96 in the developing inner ear. Sci Rep 2016; 6:23363. [PMID: 26988146 PMCID: PMC4796898 DOI: 10.1038/srep23363] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/24/2016] [Indexed: 12/16/2022] Open
Abstract
Mutations in the microRNA Mir96 cause deafness in mice and humans. In the diminuendo mouse, which carries a single base pair change in the seed region of miR-96, the sensory hair cells crucial for hearing fail to develop fully and retain immature characteristics, suggesting that miR-96 is important for coordinating hair cell maturation. Our previous transcriptional analyses show that many genes are misregulated in the diminuendo inner ear and we report here further misregulated genes. We have chosen three complementary approaches to explore potential networks controlled by miR-96 using these transcriptional data. Firstly, we used regulatory interactions manually curated from the literature to construct a regulatory network incorporating our transcriptional data. Secondly, we built a protein-protein interaction network using the InnateDB database. Thirdly, gene set enrichment analysis was used to identify gene sets in which the misregulated genes are enriched. We have identified several candidates for mediating some of the expression changes caused by the diminuendo mutation, including Fos, Myc, Trp53 and Nr3c1, and confirmed our prediction that Fos is downregulated in diminuendo homozygotes. Understanding the pathways regulated by miR-96 could lead to potential therapeutic targets for treating hearing loss due to perturbation of any component of the network.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Annalisa Buniello
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Fei Zhu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - William I Zhang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephanie Evans
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | | | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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195
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Bhartiya D, Scaria V. Genomic variations in non-coding RNAs: Structure, function and regulation. Genomics 2016; 107:59-68. [DOI: 10.1016/j.ygeno.2016.01.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 01/05/2016] [Accepted: 01/08/2016] [Indexed: 01/05/2023]
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196
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Bekris LM, Leverenz JB. The biomarker and therapeutic potential of miRNA in Alzheimer's disease. Neurodegener Dis Manag 2016; 5:61-74. [PMID: 25711455 DOI: 10.2217/nmt.14.52] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. Currently, a clinical diagnosis of AD is based on evidence of both cognitive and functional decline. Progression is monitored by detailed clinical evaluations over many months to years. It is increasingly clear that to advance disease-modifying therapies for AD, patients must be identified and treated early, before obvious cognitive and functional changes. In addition, better methods are needed to sensitively monitor progression of disease and therapeutic efficacy. Therefore, considerable research has focused on characterizing biomarkers that can identify the disease early as well as accurately monitor disease progression. miRNA offer a unique opportunity for biomarker development. Here, we review research focused on characterizing miRNA as potential biomarkers and as a treatment for disease.
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Affiliation(s)
- Lynn M Bekris
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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197
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Cammaerts S, Strazisar M, Smets B, Weckhuysen S, Nordin A, De Jonghe P, Adolfsson R, De Rijk P, Del Favero J. Schizophrenia-Associated MIR204 Regulates Noncoding RNAs and Affects Neurotransmitter and Ion Channel Gene Sets. PLoS One 2015; 10:e0144428. [PMID: 26714269 PMCID: PMC4695081 DOI: 10.1371/journal.pone.0144428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/18/2015] [Indexed: 11/19/2022] Open
Abstract
As regulators of gene expression, microRNAs (miRNAs) are likely to play an important role in the development of disease. In this study we present a large-scale strategy to identify miRNAs with a role in the regulation of neuronal processes. Thereby we found variant rs7861254 located near the MIR204 gene to be significantly associated with schizophrenia. This variant resulted in reduced expression of miR-204 in neuronal-like SH-SY5Y cells. Analysis of the consequences of the altered miR-204 expression on the transcriptome of these cells uncovered a new mode of action for miR-204, being the regulation of noncoding RNAs (ncRNAs), including several miRNAs, such as MIR296. Furthermore, pathway analysis showed downstream effects of miR-204 on neurotransmitter and ion channel related gene sets, potentially mediated by miRNAs regulated through miR-204.
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Affiliation(s)
- Sophia Cammaerts
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Mojca Strazisar
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Bart Smets
- University of Antwerp, Antwerp, Belgium
- Centralized Service Facility, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Sarah Weckhuysen
- University of Antwerp, Antwerp, Belgium
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Annelie Nordin
- Division of Psychiatry, Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Peter De Jonghe
- University of Antwerp, Antwerp, Belgium
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Antwerp University Hospital, Antwerp, Belgium
| | - Rolf Adolfsson
- Division of Psychiatry, Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Peter De Rijk
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Jurgen Del Favero
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Multiplicom N.V., Niel, Belgium
- * E-mail:
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198
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Zhao H, Xu J, Zhao D, Geng M, Ge H, Fu L, Zhu Z. Somatic Mutation of the SNP rs11614913 and Its Association with Increased MIR 196A2 Expression in Breast Cancer. DNA Cell Biol 2015; 35:81-7. [PMID: 26710106 DOI: 10.1089/dna.2014.2785] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Common genetic variants (single-nucleotide polymorphisms [SNPs]) in microRNA genes may alter their maturation or expression, resulting in varied functional consequences. Several studies have evaluated the association between the SNP rs11614913 and cancer risk in diverse populations and in a range of cancers, with contradictory outcomes. In this study, we examined 114 paired samples (tumor and normal tissues) from breast cancer patients to study the genotype distribution and somatic mutation of the SNP in MIR 196A2 (rs11614913 C-T). In addition, we evaluated their influence on the mature MIR 196A2 expression. We found that 14% (16/114) of tumors underwent somatic mutation of the SNP rs11614913. Moreover, the CT heterozygous and the CC homozygous states of SNP rs11614913 were more prone to mutation, while the TT homozygous state appeared to be resistant. We further detected a significant increase (p = 0.002) in mature MIR 196A2 expression in breast cancer. In particular, we found a significant association between the occurrence of SNP rs11614913 mutation and high expression (p = 0.0002). In addition, the mature MIR 196A2 expression level was significantly associated with the higher tumor grade (p = 0.004). Taken together, our results seem to demonstrate that somatic mutation of SNP rs11614913 in MIR 196A2 can have an influence on its expression. In addition, it indicated that an unknown mechanism is responsible for both the mutation of SNP rs11614913 and the dysregulation of mature MIR 196A2 expression.
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Affiliation(s)
- Huanhuan Zhao
- 1 Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin, China .,2 State Key Laboratory of Medicinal Chemical Biology, Department of Genetics and Cell Biology, College of Life Sciences, Nankai University , Tianjin, China
| | - Jingman Xu
- 3 Medical Experimental Research Center, North China University of Science and Technology , Tangshan, China
| | - Dan Zhao
- 2 State Key Laboratory of Medicinal Chemical Biology, Department of Genetics and Cell Biology, College of Life Sciences, Nankai University , Tianjin, China
| | - Meijuan Geng
- 4 Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin, China
| | - Haize Ge
- 5 Clinical Laboratory of Tianjin Third Central Hospital , Tianjin, China
| | - Li Fu
- 6 Key Laboratory of Breast Cancer Research, Department of Breast Cancer Pathology and Research Laboratory, Cancer Hospital of Tianjin Medical University , Tianjin, China
| | - Zhengmao Zhu
- 2 State Key Laboratory of Medicinal Chemical Biology, Department of Genetics and Cell Biology, College of Life Sciences, Nankai University , Tianjin, China
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199
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Genetics meets epigenetics: Genetic variants that modulate noncoding RNA in cardiovascular diseases. J Mol Cell Cardiol 2015; 89:27-34. [DOI: 10.1016/j.yjmcc.2015.10.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 12/30/2022]
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200
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Codocedo JF, Inestrosa NC. Environmental control of microRNAs in the nervous system: Implications in plasticity and behavior. Neurosci Biobehav Rev 2015; 60:121-38. [PMID: 26593111 DOI: 10.1016/j.neubiorev.2015.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/24/2015] [Accepted: 10/26/2015] [Indexed: 02/07/2023]
Abstract
The discovery of microRNAs (miRNAs) a little over 20 years ago was revolutionary given that miRNAs are essential to numerous physiological and physiopathological processes. Currently, several aspects of the biogenic process of miRNAs and of the translational repression mechanism exerted on their targets mRNAs are known in detail. In fact, the development of bioinformatics tools for predicting miRNA targets has established that miRNAs have the potential to regulate almost all known biological processes. Therefore, the identification of the signals and molecular mechanisms that regulate miRNA function is relevant to understanding the role of miRNAs in both pathological and adaptive processes. Recently, a series of studies has focused on miRNA expression in the brain, establishing that their levels are altered in response to various environmental factors (EFs), such as light, sound, odorants, nutrients, drugs and stress. In this review, we discuss how exposure to various EFs modulates the expression and function of several miRNAs in the nervous system and how this control determines adaptation to their environment, behavior and disease state.
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Affiliation(s)
- Juan F Codocedo
- Centro de Envejecimiento y Regeneración (CARE), Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nibaldo C Inestrosa
- Centro de Envejecimiento y Regeneración (CARE), Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia; Centro UC Síndrome de Down, Pontificia Universidad Católica de Chile, Santiago, Chile; Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Universidad de Magallanes, Punta Arenas, Chile.
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