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Wang Y, Wang J, Li Q, Xuan R, Guo Y, He P, Chao T. Characterization of MicroRNA expression profiles in the ovarian tissue of goats during the sexual maturity period. J Ovarian Res 2023; 16:234. [PMID: 38062510 PMCID: PMC10704810 DOI: 10.1186/s13048-023-01318-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The ovary is an important reproductive organ in mammals, and its development directly affects the sexual maturity and reproductive capacity of individuals. MicroRNAs (miRNAs) are recognized as regulators of reproductive physiological processes in various animals and have been shown to regulate ovarian development through typical targeting and translational repression. However, little is known about the regulatory role of miRNAs in ovarian tissue development during sexual maturity in goats. To comprehensively profile the different physiological stages of sexual maturation in goats, we performed small-RNA sequencing of ovarian tissue samples collected at four specific time points (1 day after birth (D1), 2 months old (M2), 4 months old (M4), and 6 months old (M6)). In addition, we used ELISAs to measure serum levels of reproductive hormones to study their temporal changes. RESULTS The results showed that serum levels of gonadotropin-releasing hormone, follicle-stimulating hormone, luteinizing hormone, oestradiol, progesterone, oxytocin, and prolactin were lower in goats at the D1 stage than at the other three developmental stages (P < 0.05). The secretion patterns of these seven hormones show a similar trend, with hormone levels reaching their peaks at 4 months of age. A total of 667 miRNAs were detected in 20 libraries, and 254 differentially expressed miRNAs and 3 groups of miRNA clusters that had unique expression patterns were identified (|log2-fold change|> 1, FDR < 0.05) in the 6 comparison groups. RT‒qPCR was employed to confirm that the expression pattern of the 15 selected miRNAs was consistent with the Illumina sequencing results. Gene ontology analyses revealed significant enrichment of GO terms such as cell proliferation regulation, epithelial cell development, and amino acid transport, as well as important signaling pathways including the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the oestrogen signaling pathway. Further miRNA‒mRNA regulation network analysis revealed that 8 differentially expressed miRNAs (chi-miR-1343, chi-miR-328-3p, chi-miR-877-3p, chi-miR-296-3p, chi-miR-128-5p, chi-miR-331-3p, chi-miR-342-5p and chi-miR-34a) have important regulatory roles in ovarian cell proliferation, hormone secretion and metabolism-related biological processes. CONCLUSIONS Overall, our study investigated the changes in serum hormone and miRNA levels in the ovaries. These data provide a valuable resource for understanding the molecular regulatory mechanisms of miRNAs in ovarian tissue during the sexual maturity period in goats.
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Affiliation(s)
- Yanyan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
| | - Qing Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yanfei Guo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
| | - Peipei He
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.
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Di Michele F, Chillón I, Feil R. Imprinted Long Non-Coding RNAs in Mammalian Development and Disease. Int J Mol Sci 2023; 24:13647. [PMID: 37686455 PMCID: PMC10487962 DOI: 10.3390/ijms241713647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic expression controls in cis the expression of protein-coding genes, often developmentally regulated. Some imprinted lncRNAs act in trans as well, controlling target gene expression elsewhere in the genome. The regulation of imprinted gene expression-including that of imprinted lncRNAs-is susceptible to stochastic and environmentally triggered epigenetic changes in the early embryo. These aberrant changes persist during subsequent development and have long-term phenotypic consequences. This review focuses on the expression and the cis- and trans-regulatory roles of imprinted lncRNAs and describes human disease syndromes associated with their perturbed expression.
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Affiliation(s)
- Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Isabel Chillón
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
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Eggermann T, Monk D, de Nanclares GP, Kagami M, Giabicani E, Riccio A, Tümer Z, Kalish JM, Tauber M, Duis J, Weksberg R, Maher ER, Begemann M, Elbracht M. Imprinting disorders. Nat Rev Dis Primers 2023; 9:33. [PMID: 37386011 DOI: 10.1038/s41572-023-00443-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Imprinting disorders (ImpDis) are congenital conditions that are characterized by disturbances of genomic imprinting. The most common individual ImpDis are Prader-Willi syndrome, Angelman syndrome and Beckwith-Wiedemann syndrome. Individual ImpDis have similar clinical features, such as growth disturbances and developmental delay, but the disorders are heterogeneous and the key clinical manifestations are often non-specific, rendering diagnosis difficult. Four types of genomic and imprinting defect (ImpDef) affecting differentially methylated regions (DMRs) can cause ImpDis. These defects affect the monoallelic and parent-of-origin-specific expression of imprinted genes. The regulation within DMRs as well as their functional consequences are mainly unknown, but functional cross-talk between imprinted genes and functional pathways has been identified, giving insight into the pathophysiology of ImpDefs. Treatment of ImpDis is symptomatic. Targeted therapies are lacking owing to the rarity of these disorders; however, personalized treatments are in development. Understanding the underlying mechanisms of ImpDis, and improving diagnosis and treatment of these disorders, requires a multidisciplinary approach with input from patient representatives.
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Affiliation(s)
- Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany.
| | - David Monk
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Guiomar Perez de Nanclares
- Rare Diseases Research Group, Molecular (Epi)Genetics Laboratory, Bioaraba Research Health Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Spain
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Eloïse Giabicani
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, APHP, Hôpital Armand Trousseau, Endocrinologie Moléculaire et Pathologies d'Empreinte, Paris, France
| | - Andrea Riccio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università della Campania Luigi Vanvitelli, Caserta, Italy
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer M Kalish
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Departments of Pediatrics and Genetics at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maithé Tauber
- Centre de Référence Maladies Rares PRADORT (syndrome de PRADer-Willi et autres Obésités Rares avec Troubles du comportement alimentaire), Hôpital des Enfants, CHU Toulouse, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse, France
| | - Jessica Duis
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Department of Paediatrics and Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Barbagallo D, Palermo CI, Barbagallo C, Battaglia R, Caponnetto A, Spina V, Ragusa M, Di Pietro C, Scalia G, Purrello M. Competing endogenous RNA network mediated by circ_3205 in SARS-CoV-2 infected cells. Cell Mol Life Sci 2022; 79:75. [PMID: 35039944 PMCID: PMC8763136 DOI: 10.1007/s00018-021-04119-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new member of the Betacoronaviridae family, responsible for the recent pandemic outbreak of COVID-19. To start exploring the molecular events that follow host cell infection, we queried VirusCircBase and identified a circular RNA (circRNA) predicted to be synthesized by SARS-CoV-2, circ_3205, which we used to probe: (i) a training cohort comprised of two pools of cells from three nasopharyngeal swabs of SARS-CoV-2 infected (positive) or uninfected (negative, UCs) individuals; (ii) a validation cohort made up of 12 positive and 3 negative samples. The expression of circRNAs, miRNAs and miRNA targets was assayed through real-time PCR. CircRNA-miRNA interactions were predicted by TarpMiR, Analysis of Common Targets for circular RNAs (ACT), and STarMir tools. Enrichment of the biological processes and the list of predicted miRNA targets were retrieved from DIANA miRPath v3.0. Our results showed that the predicted SARS-CoV-2 circ_3205 was expressed only in positive samples and its amount positively correlated with that of SARS-CoV-2 Spike (S) mRNA and the viral load (r values = 0.80952 and 0.84867, Spearman's correlation test, respectively). Human (hsa) miR-298 was predicted to interact with circ_3205 by all three predictive tools. KCNMB4 and PRKCE were predicted as hsa-miR-298 targets. Interestingly, the function of both is correlated with blood coagulation and immune response. KCNMB4 and PRKCE mRNAs were upregulated in positive samples as compared to UCs (6 and 8.1-fold, p values = 0.049 and 0.02, Student's t test, respectively) and their expression positively correlated with that of circ_3205 (r values = 0.6 and 0.25, Spearman's correlation test, respectively). We propose that our results convincingly suggest that circ_3205 is a circRNA synthesized by SARS-CoV-2 upon host cell infection and that it may behave as a competitive endogenous RNA (ceRNA), sponging hsa-miR-298 and contributing to the upregulation of KCNMB4 and PRKCE mRNAs.
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Affiliation(s)
- Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy.
| | - Concetta Ilenia Palermo
- U.O.C. Laboratory Analysis Unit, A.O.U. Policlinico‑Vittorio Emanuele, 95123, Catania, Italy
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Vittoria Spina
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123, Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Guido Scalia
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123, Catania, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
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5
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Marini F, Giusti F, Palmini G, Perigli G, Santoro R, Brandi ML. Genetics and Epigenetics of Parathyroid Carcinoma. Front Endocrinol (Lausanne) 2022; 13:834362. [PMID: 35282432 PMCID: PMC8908968 DOI: 10.3389/fendo.2022.834362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/28/2022] [Indexed: 01/12/2023] Open
Abstract
Parathyroid carcinoma (PC) is an extremely rare malignancy, accounting less than 1% of all parathyroid neoplasms, and an uncommon cause of primary hyperparathyroidism (PHPT), characterized by an excessive secretion of parathyroid hormone (PTH) and severe hypercalcemia. As opposed to parathyroid hyperplasia and adenomas, PC is associated with a poor prognosis, due to a commonly unmanageable hypercalcemia, which accounts for death in the majority of cases, and an overall survival rate of 78-85% and 49-70% at 5 and 10 years after diagnosis, respectively. No definitively effective therapies for PC are currently available. The mainly employed treatment for PC is the surgical removal of tumoral gland(s). Post-surgical persistent or recurrent disease manifest in about 50% of patients. The comprehension of genetic and epigenetic bases and molecular pathways that characterize parathyroid carcinogenesis is important to distinguish malignant PCs from benign adenomas, and to identify specific targets for novel therapies. Germline heterozygote inactivating mutations of the CDC73 tumor suppressor gene, with somatic loss of heterozygosity at 1q31.2 locus, account for about 50-75% of familial cases; over 75% of sporadic PCs harbor biallelic somatic inactivation/loss of CDC73. Recurrent mutations of the PRUNE2 gene, a recurrent mutation in the ADCK1 gene, genetic amplification of the CCND1 gene, alterations of the PI3K/AKT/mTOR signaling pathway, and modifications of microRNA expression profile and gene promoter methylation pattern have all been detected in PC. Here, we review the current knowledge on gene mutations and epigenetic changes that have been associated with the development of PC, in both familial and sporadic forms of this malignancy.
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Affiliation(s)
- Francesca Marini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
- Fondazione Italiana per la Ricerca sulle Malattie dell'Osso (F.I.R.M.O.) Italian Foundation for the Research on Bone Diseases, Florence, Italy
| | - Francesca Giusti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Gaia Palmini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Giuliano Perigli
- Department of Experimental and Clinical Medicine, University of Florence, Azienda Ospedaliero-Universitaria (AOU)-Careggi, Florence, Italy
| | - Roberto Santoro
- Department of Experimental and Clinical Medicine, University of Florence, Azienda Ospedaliero-Universitaria (AOU)-Careggi, Florence, Italy
| | - Maria Luisa Brandi
- Fondazione Italiana per la Ricerca sulle Malattie dell'Osso (F.I.R.M.O.) Italian Foundation for the Research on Bone Diseases, Florence, Italy
- *Correspondence: Maria Luisa Brandi,
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Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HES, Loux SC, Esteller-Vico A, Norris JK, Anand L, Scoggin KE, Rodriguez Lopez CM, Breen J, Bailey E, Daels P, Ball BA. Parental bias in expression and interaction of genes in the equine placenta. Proc Natl Acad Sci U S A 2021; 118:e2006474118. [PMID: 33853939 PMCID: PMC8072238 DOI: 10.1073/pnas.2006474118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a workflow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.
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Affiliation(s)
- Pouya Dini
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Theodore Kalbfleisch
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202
| | - José M Uribe-Salazar
- Department of Biochemistry and Molecular Medicine, Genome Center, Medical Investigation of Neurodevelopmental Disorders Institute, University of California, Davis, CA 95616
| | - Mariano Carossino
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, 35516, Egypt
| | - Shavahn C Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Alejandro Esteller-Vico
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Jamie K Norris
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Ernest Bailey
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Peter Daels
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Barry A Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503;
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Seasonal effects on miRNA and transcriptomic profile of oocytes and follicular cells in buffalo (Bubalus bubalis). Sci Rep 2020; 10:13557. [PMID: 32782284 PMCID: PMC7419291 DOI: 10.1038/s41598-020-70546-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
Season clearly influences oocyte competence in buffalo (Bubalus bubalis); however, changes in the oocyte molecular status in relation to season are poorly understood. This study characterizes the microRNA (miRNA) and transcriptomic profiles of oocytes (OOs) and corresponding follicular cells (FCs) from buffalo ovaries collected in the breeding (BS) and non-breeding (NBS) seasons. In the BS, cleavage and blastocyst rates are significantly higher compared to NBS. Thirteen miRNAs and two mRNAs showed differential expression (DE) in FCs between BS and NBS. DE-miRNAs target gene analysis uncovered pathways associated with transforming growth factor β (TGFβ) and circadian clock photoperiod. Oocytes cluster in function of season for their miRNA content, showing 13 DE-miRNAs between BS and NBS. Between the two seasons, 22 differentially expressed genes were also observed. Gene Ontology (GO) analysis of miRNA target genes and differentially expressed genes (DEGs) in OOs highlights pathways related to triglyceride and sterol biosynthesis and storage. Co-expression analysis of miRNAs and mRNAs revealed a positive correlation between miR-296-3p and genes related to metabolism and hormone regulation. In conclusion, season significantly affects female fertility in buffalo and impacts on oocyte transcriptomic of genes related to folliculogenesis and acquisition of oocyte competence.
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Abstract
Genomic imprinting is a parent-of-origin dependent phenomenon that restricts transcription to predominantly one parental allele. Since the discovery of the first long noncoding RNA (lncRNA), which notably was an imprinted lncRNA, a body of knowledge has demonstrated pivotal roles for imprinted lncRNAs in regulating parental-specific expression of neighboring imprinted genes. In this Review, we will discuss the multiple functionalities attributed to lncRNAs and how they regulate imprinted gene expression. We also raise unresolved questions about imprinted lncRNA function, which may lead to new avenues of investigation. This Review is dedicated to the memory of Denise Barlow, a giant in the field of genomic imprinting and functional lncRNAs. With her passion for understanding the inner workings of science, her indominable spirit and her consummate curiosity, Denise blazed a path of scientific investigation that made many seminal contributions to genomic imprinting and the wider field of epigenetic regulation, in addition to inspiring future generations of scientists.
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Affiliation(s)
- William A. MacDonald
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mellissa R. W. Mann
- Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Zamani P, Oskuee RK, Atkin SL, Navashenaq JG, Sahebkar A. MicroRNAs as important regulators of the NLRP3 inflammasome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:50-61. [PMID: 31100298 DOI: 10.1016/j.pbiomolbio.2019.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 05/13/2019] [Indexed: 12/28/2022]
Abstract
Inflammasomes are a group of cytosolic multi-protein signaling complexes that regulate maturation of the interleukin (IL)-1 family cytokines IL-1β and IL-18 through activation of inflammatory caspase-1. The NOD-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome is the best characterized and consists of several key components that are assembled and activated in response to different endogenous and exogenous signals. The NLRP3 inflammasome is common to a number of human inflammatory diseases and its targeting may lead to novel anti-inflammatory therapy. NLRP3 inflammasome activation is tightly regulated by different mechanisms especially post-transcriptional modulation via microRNAs (miRNA). MicroRNAs are small endogenous noncoding RNAs that are 21-23 nucleotides in length and control the expression of various genes through binding to the 3'-untranslated regions of the respective mRNA and subsequent post-transcriptional regulation. MicroRNAs have recently been recognized as crucial regulators of the NLRP3 inflammasome. In this review, we summarize the current understanding of the role of miRNAs in the regulation of NLRP3 inflammasome complexes and their impact on the pathogenesis of inflammatory disease processes.
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Affiliation(s)
- Parvin Zamani
- Nanotechnology Research Center, Student Research Committee, Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kazemi Oskuee
- Targeted Drug Delivery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | | | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Arslan S, Engin A, Aydemir EI, Sahin NO, Bayyurt B, Sari I, Cosgun Y, Bakir M. Identification of potential microRNA markers related to Crimean-Congo hemorrhagic fever disease. J Cell Biochem 2019; 120:15506-15517. [PMID: 31044455 DOI: 10.1002/jcb.28817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 12/21/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease caused by the arbovirus Crimean-Congo hemorrhagic fever virus (CCHFV). The CCHFV has a single-stranded RNA genome of negative sense. MicroRNAs (miRNAs) are key players in virus-host interactions and viral pathogenesis. We investigated the miRNA gene expression profiles in patients with CCHF using microarray for the first time in the world. Microarray analysis was performed using mirBase Ver 21 (Agilent Technologies, Santa Clara, CA). All statistical analyses were performed across the case-control, fatal-control, and fatal-nonfatal case groups using Genespring (Ver 3.0). Fifteen miRNAs were statistical significant in patients with CCHF compared with the controls (5 were upregulated, 10 were downregulated). Seventy-five and sixty-six miRNAs are in fatal compared with control and nonfatal case, respectively (fold change ([FC] ≥50) were statistically significant. In this study, the target genes of important miRNAs were identified and Gene Ontology analyses were performed across all groups. As a result of this study, we propose that the detection of miRNAs in patients with CCHF will allow the determination of therapeutic targets in diseases. CCHF is an important public health problem that can often be fatal. In this study, we investigated miRNA expression in case-control, fatal-control, and fatal-nonfatal case groups. Significant miRNAs associated with fatality were detected in CCHF. This study will serve as a source of data for the development of an antagomir-based therapy against CCHF using miRNAs in the future.
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Affiliation(s)
- Serdal Arslan
- Department of Medical Biology, Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkey
| | - Aynur Engin
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sivas Cumhuriyet University, School of Medicine, Sivas, Turkey
| | - Eylem Itir Aydemir
- Department of Statistic, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Nil Ozbilum Sahin
- Department of Molecular Biology and Genetic, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Burcu Bayyurt
- Department of Medical Biology, Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkey
| | - Ismail Sari
- Department of Medicinal Biochemistry, Faculty of Medicine, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Yasemin Cosgun
- Department of Microbiology Reference and Biological Products Laboratories, Ministry of Health, General Directorate of Public Health, Ankara, Turkey
| | - Mehmet Bakir
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sivas Cumhuriyet University, School of Medicine, Sivas, Turkey
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11
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Malnou EC, Umlauf D, Mouysset M, Cavaillé J. Imprinted MicroRNA Gene Clusters in the Evolution, Development, and Functions of Mammalian Placenta. Front Genet 2019; 9:706. [PMID: 30713549 PMCID: PMC6346411 DOI: 10.3389/fgene.2018.00706] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/14/2018] [Indexed: 12/27/2022] Open
Abstract
In mammals, the expression of a subset of microRNA (miRNA) genes is governed by genomic imprinting, an epigenetic mechanism that confers monoallelic expression in a parent-of-origin manner. Three evolutionarily distinct genomic intervals contain the vast majority of imprinted miRNA genes: the rodent-specific, paternally expressed C2MC located in intron 10 of the Sfmbt2 gene, the primate-specific, paternally expressed C19MC positioned at human Chr.19q13.4 and the eutherian-specific, maternally expressed miRNAs embedded within the imprinted Dlk1-Dio3 domains at human 14q32 (also named C14MC in humans). Interestingly, these imprinted miRNA genes form large clusters composed of many related gene copies that are co-expressed with a marked, or even exclusive, localization in the placenta. Here, we summarize our knowledge on the evolutionary, molecular, and physiological relevance of these epigenetically-regulated, recently-evolved miRNAs, by focusing on their roles in placentation and possibly also in pregnancy diseases (e.g., preeclampsia, intrauterine growth restriction, preterm birth).
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Affiliation(s)
- E Cécile Malnou
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - David Umlauf
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Maïlys Mouysset
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
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12
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Koohy H, Bolland DJ, Matheson LS, Schoenfelder S, Stellato C, Dimond A, Várnai C, Chovanec P, Chessa T, Denizot J, Manzano Garcia R, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE, Varga-Weisz PD. Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells. Genome Biol 2018; 19:126. [PMID: 30180872 PMCID: PMC6124017 DOI: 10.1186/s13059-018-1489-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. RESULTS Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice. Nonetheless, age-specific expression changes are observed at numerous genes, including microRNA encoding genes. Importantly, these changes are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions, and nuclear compartmentalization. Previous work has shown that differentiation is linked to changes in promoter-regulatory element interactions. We find that aging in B cell precursors is accompanied by rewiring of such interactions. We identify transcriptional downregulation of components of the insulin-like growth factor signaling pathway, in particular downregulation of Irs1 and upregulation of Let-7 microRNA expression, as a signature of the aged phenotype. These changes in expression are associated with specific alterations in H3K27me3 occupancy, suggesting that Polycomb-mediated repression plays a role in precursor B cell aging. CONCLUSIONS Changes in chromatin and 3D genome organization play an important role in shaping the altered gene expression profile of aged precursor B cells. Components of the insulin-like growth factor signaling pathways are key targets of epigenetic regulation in aging in bone marrow B cell precursors.
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Affiliation(s)
- Hashem Koohy
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | | | | | - Andrew Dimond
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Peter Chovanec
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | | | - Jeremy Denizot
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Present address: Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-, 63000, Clermont-Ferrand, France
| | | | - Steven W Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Bioinformatics, Babraham Institute, Cambridge, UK
| | - Paula Freire-Pritchett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Takashi Nagano
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Sarah Elderkin
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Functional Gene Control Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK.
| | - Patrick D Varga-Weisz
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- School of Biological Sciences, University of Essex, Colchester, UK.
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13
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Li H, Ouyang XP, Jiang T, Zheng XL, He PP, Zhao GJ. MicroRNA-296: a promising target in the pathogenesis of atherosclerosis? Mol Med 2018; 24:12. [PMID: 30134788 PMCID: PMC6016874 DOI: 10.1186/s10020-018-0012-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
Atherosclerosis has been recognized as an inflammatory disease involving the vascular wall. MicroRNAs are a group of small noncoding RNAs to regulate gene expression at the transcriptional level through mRNA degradation or translation repression. Recent studies suggest that miR-296 may play crucial roles in the regulation of angiogenesis, inflammatory response, cholesterol metabolism, hypertension, cellular proliferation and apoptosis. In this review, we primarily discussed the molecular targets of miR-296 involved in the development of atherosclerosis, which may provide a basis for future investigation and a better understanding of the biological functions of miR-296 in atherosclerosis.
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Affiliation(s)
- Heng Li
- The Clinic Medical College, Guilin Medical University, No. 1 Zhiyuan Road, Guilin, Guangxi, 541100, China
| | - Xin-Ping Ouyang
- Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, 28 West Changsheng Road, Hengyang, Hunan, 421001, China.,Department of Physiology, The Neuroscience Institute, Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Ting Jiang
- Department of Practice educational, Office of Academic Affairs, Guilin Medical University, Guilin, 541100, China
| | - Xi-Long Zheng
- Department of Biochemistry and Molecular Biology, The Libin Cardiovascular Institute of Alberta, The University of Calgary, Health Sciences Center, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada.,Key Laboratory of Molecular Targets & Clinical Pharmacology, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Ping-Ping He
- Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, 28 West Changsheng Road, Hengyang, Hunan, 421001, China. .,Nursing School, University of South China, Hengyang, Hunan, 421001, China.
| | - Guo-Jun Zhao
- Department of Biochemistry and Molecular Biology, The Libin Cardiovascular Institute of Alberta, The University of Calgary, Health Sciences Center, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada. .,Department of Histology and Embryology, Guilin Medical University, Guilin, Guangxi, 541004, China.
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14
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Wang L, Guo S, Zhang H. MiR-98 Promotes Apoptosis of Glioma Cells via Suppressing IKBKE/NF-κB Pathway. Technol Cancer Res Treat 2017; 16:1226-1234. [PMID: 29333957 PMCID: PMC5762096 DOI: 10.1177/1533034617745761] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The inhibitor of kappa B kinase epsilon is overexpressed in glioma and plays antiapoptotic role via activating nuclear factor-kappa B. microRNA-98 can suppress glioma, modulate the activities of nuclear factor-kappa B, and bind to the 3′-untranslated region of inhibitor of kappa B kinase epsilon messenger RNA. This study was aimed to investigate the modulation of inhibitor of kappa B kinase epsilon/nuclear factor-kappa B by microRNA-98 in glioma. The results indicated that microRNA-98 was downregulated in glioma cell lines and human glioma tissues. Overexpression of microRNA-98 in U87MG and T98G glioma cells significantly increased the apoptosis induced by ultraviolet irradiation and suppressed nuclear factor-kappa B luciferase activity, nuclear factor-kappa B p50 subunit expression, and B-cell lymphoma-2 (Bcl-2) expression in glioma cells. Silencing inhibitor of kappa B kinase epsilon decreased the expression of nuclear factor-kappa B p50 subunit and the luciferase activity of nuclear factor-kappa B, while the nuclear factor-kappa B activity could be significantly retrieved when inhibitor of kappa B kinase epsilon was expressed in microRNA-98-transfected cells. These findings indicated that microRNA-98 could promote apoptosis of glioma cells via inhibiting inhibitor of kappa B kinase epsilon/nuclear factor-kappa B signaling and presented a novel regulatory pathway of microRNA-98 by direct suppression of inhibitor of kappa B kinase epsilon/nuclear factor-kappa B expression in glioma cells.
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Affiliation(s)
- Lingyan Wang
- 1 The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shaolei Guo
- 1 The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Heng Zhang
- 1 The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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15
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Vaira V, Verdelli C, Forno I, Corbetta S. MicroRNAs in parathyroid physiopathology. Mol Cell Endocrinol 2017; 456:9-15. [PMID: 27816765 DOI: 10.1016/j.mce.2016.10.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/30/2016] [Accepted: 10/31/2016] [Indexed: 12/19/2022]
Abstract
Parathyroid glands regulate calcium homeostasis through synthesis and secretion of parathormone (PTH). They sense the extracellular calcium concentration through the G-protein coupled calcium sensing receptor (CASR) and release PTH in order to preserve calcium concentration in the physiological range. Tumors of the parathyroid glands are common endocrine neoplasia associated with primary or secondary/tertiary hyperparathyroidisms. Small non-coding RNAs are regulators of gene expression able to modulate hormone synthesis, hormone release and endocrine cell proliferation. In this scenario, microRNA (miRNA) expression profiles have been investigated in parathyroid tumors, while miRNAs are involved in hypocalcemia and uremia-induced PTH release from normal parathyroid cells. Here we reviewed data about the role of miRNAs in the regulation of: 1) PTH synthesis and secretion; 2) CASR expression; 3) parathyroid cell tumorigenesis. Though studies about miRNAs in parathyroid gland pathophysiology are limited, they contribute in elucidating regulatory pathways involved in PTH release and parathyroid cell tumorigenesis.
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Affiliation(s)
- V Vaira
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - C Verdelli
- Laboratory of Experimental Endocrinology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - I Forno
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - S Corbetta
- Endocrinology Service, Department of Biomedical Sciences for Health, University of Milan, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy.
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16
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Dinami R, Buemi V, Sestito R, Zappone A, Ciani Y, Mano M, Petti E, Sacconi A, Blandino G, Giacca M, Piazza S, Benetti R, Schoeftner S. Epigenetic silencing of miR-296 and miR-512 ensures hTERT dependent apoptosis protection and telomere maintenance in basal-type breast cancer cells. Oncotarget 2017; 8:95674-95691. [PMID: 29221158 PMCID: PMC5707052 DOI: 10.18632/oncotarget.21180] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 08/27/2017] [Indexed: 12/31/2022] Open
Abstract
The catalytic subunit of the telomerase complex, hTERT, ensures unlimited proliferative potential of cancer cells by maintaining telomere function and protecting from apoptosis. Using a miRNA screening approach we identified miR-296-5p and miR-512-5p as miRNAs that target hTERT in breast cancer cells. Ectopic miR-296-5p and miR-512-5p reduce telomerase activity, drive telomere shortening and cause proliferation defects by enhancing senescence and apoptosis in breast cancer cells. In line with the relevance of hTERT expression for human cancer we found that miR-296-5p and miR-512-5p expression is reduced in human breast cancer. Accordingly, high expression of miR-296-5p and miR-512-5p target genes including hTERT is linked with significantly reduced distant metastasis free survival and relapse free survival of basal type breast cancer patients. This suggests relevance of the identified miRNAs in basal type breast cancer. Epigenetic silencing of miR-296 and miR-512 encoding genes is responsible for low levels of miR-296-5p and miR-512-5p expression in basal type breast cancer cells. Disrupting gene silencing results in a dramatic upregulation of miR-296-5p and miR-512-5p levels leading to reduced hTERT expression and increased sensitivity to the induction of apoptosis. Altogether, our data suggest that epigenetic regulatory circuits in basal type breast cancer may contribute to high hTERT levels by silencing miR-296-5p and miR-512-5p expression, thereby contributing to the aggressiveness of basal type breast cancer.
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Affiliation(s)
- Roberto Dinami
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Genomic Stability Unit, Trieste 34149, Italy.,Italian National Cancer Institute, Regina Elena, Rome 00144, Italy
| | - Valentina Buemi
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Genomic Stability Unit, Trieste 34149, Italy.,Department of Life Sciences, Università degli Studi di Trieste, Trieste 34127, Italy
| | - Rosanna Sestito
- Italian National Cancer Institute, Regina Elena, Rome 00144, Italy
| | - Antonina Zappone
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Genomic Stability Unit, Trieste 34149, Italy.,Department of Life Sciences, Università degli Studi di Trieste, Trieste 34127, Italy
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Bioinformatics and Functional Genomics Unit (BFGU), Trieste 34149, Italy
| | - Miguel Mano
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Molecular Medicine Laboratory, Trieste 34149, Italy
| | - Eleonora Petti
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Genomic Stability Unit, Trieste 34149, Italy.,Italian National Cancer Institute, Regina Elena, Rome 00144, Italy.,Department of Life Sciences, Università degli Studi di Trieste, Trieste 34127, Italy
| | - Andrea Sacconi
- Italian National Cancer Institute, Regina Elena, Translational Oncogenomics Group, Rome 00144, Italy
| | - Giovanni Blandino
- Italian National Cancer Institute, Regina Elena, Translational Oncogenomics Group, Rome 00144, Italy
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Molecular Medicine Laboratory, Trieste 34149, Italy
| | - Silvano Piazza
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Bioinformatics and Functional Genomics Unit (BFGU), Trieste 34149, Italy
| | - Roberta Benetti
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Cancer Epigenetics Unit, Trieste 34149, Italy.,Department of Medical and Biological Sciences, Università degli Studi di Udine, Udine 33100, Italy
| | - Stefan Schoeftner
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (LNCIB), Genomic Stability Unit, Trieste 34149, Italy.,Italian National Cancer Institute, Regina Elena, Rome 00144, Italy.,Department of Life Sciences, Università degli Studi di Trieste, Trieste 34127, Italy
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17
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Davis JS, Sun M, Kho AT, Moore KG, Sylvia JM, Weiss ST, Lu Q, Tantisira KG. Circulating microRNAs and association with methacholine PC20 in the Childhood Asthma Management Program (CAMP) cohort. PLoS One 2017; 12:e0180329. [PMID: 28749975 PMCID: PMC5531511 DOI: 10.1371/journal.pone.0180329] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/08/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction Circulating microRNAs (miRNA) are promising biomarkers for human diseases. Our study hypothesizes that circulating miRNA would reveal candidate biomarkers related to airway hyperresponsiveness (AHR) and provide biologic insights into asthma epigenetic influences. Methods Serum samples obtained at randomization for 160 children in the Childhood Asthma Management Program were profiled using a TaqMan miRNA array set. The association of the isolated miRNA with methacholine PC20 was assessed. Network and pathway analyses were performed. Functional validation of two significant miRNAs was performed in human airway smooth muscle cells (HASMs). Results Of 155 well-detected circulating miRNAs, eight were significantly associated with PC20 with the strongest association with miR-296-5p. Pathway analysis revealed miR-16-5p as a network hub, and involvement of multiple miRNAs interacting with genes in the FoxO and Hippo signaling pathways by KEGG analysis. Functional validation of two miRNA in HASM showed effects on cell growth and diameter. Conclusion Reduced circulatory miRNA expression at baseline is associated with an increase in PC20. These miRNA provide biologic insights into, and may serve as biomarkers of, asthma severity. miR-16-5p and -30d-5p regulate airway smooth muscle phenotypes critically involved in asthma pathogenesis, supporting a mechanistic link to these findings. Functional ASM phenotypes may be directly relevant to AHR.
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Affiliation(s)
- Joshua S. Davis
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Maoyun Sun
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Alvin T. Kho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Kip G. Moore
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jody M. Sylvia
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Quan Lu
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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18
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Epigenetic Alterations in Parathyroid Cancers. Int J Mol Sci 2017; 18:ijms18020310. [PMID: 28157158 PMCID: PMC5343846 DOI: 10.3390/ijms18020310] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/27/2017] [Indexed: 02/06/2023] Open
Abstract
Parathyroid cancers (PCas) are rare malignancies representing approximately 0.005% of all cancers. PCas are a rare cause of primary hyperparathyroidism, which is the third most common endocrine disease, mainly related to parathyroid benign tumors. About 90% of PCas are hormonally active hypersecreting parathormone (PTH); consequently patients present with complications of severe hypercalcemia. Pre-operative diagnosis is often difficult due to clinical features shared with benign parathyroid lesions. Surgery provides the current best chance of cure, though persistent or recurrent disease occurs in about 50% of patients with PCas. Somatic inactivating mutations of CDC73/HRPT2 gene, encoding parafibromin, are the most frequent genetic anomalies occurring in PCas. Recently, the aberrant DNA methylation signature and microRNA expression profile have been identified in PCas, providing evidence that parathyroid malignancies are distinct entities from parathyroid benign lesions, showing an epigenetic signature resembling some embryonic aspects. The present paper reviews data about epigenetic alterations in PCas, up to now limited to DNA methylation, chromatin regulators and microRNA profile.
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19
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Lopez-Bertoni H, Lal B, Michelson N, Guerrero-Cázares H, Quiñones-Hinojosa A, Li Y, Laterra J. Epigenetic modulation of a miR-296-5p:HMGA1 axis regulates Sox2 expression and glioblastoma stem cells. Oncogene 2016; 35:4903-13. [PMID: 26898758 PMCID: PMC6151872 DOI: 10.1038/onc.2016.22] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022]
Abstract
Solid malignancies contain subsets of multipotent cells that grow as spheres and efficiently propagate tumors in xenograft models, reflecting a stem-like, self-renewing and tumor-propagating phenotype. These cancer 'stem cells (SCs)' have been shown to maintain tumor growth, contribute to resistance and drive tumor recurrence. Cancer cell stemness is dynamically influenced by epigenetic mechanisms and differentially regulated coding and noncoding RNAs. How these mechanisms specifically contribute to the generation and/or maintenance of cancer SCs remains unclear. This study identifies a novel epigenetically regulated circuit that integrates microRNA, chromatin remodeling and the reprogramming transcription factor Sox2 to regulate glioblastoma (GBM)-propagating SCs. We show that miR-296-5p expression is repressed in a DNA methylation-dependent manner under conditions that promote GBM cell stemness and that miR-296-5p inhibits GBM cell stemness and their capacity to self-renew as spheres and propagate glioma xenografts in vivo. We show that the chromatin remodeling protein HMGA1 functions as a downstream effector of these biological responses to miR-296-5p and regulates Sox2 expression, a master driver of cell stemness, by modifying chromatin architecture at the Sox2 promoter. These results show for the first time that miR-296-5p inhibits transcriptional mechanisms that support GBM SCs and identify a miR-296-5p:HMGA1:Sox2 axis as a novel regulator of GBM SCs and candidate pathway for targeting therapies directed at depleting tumors of their tumor-propagating stem cell subsets.
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Affiliation(s)
- H Lopez-Bertoni
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - B Lal
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - N Michelson
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA
| | - H Guerrero-Cázares
- Department of Neurosurgery, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - A Quiñones-Hinojosa
- Department of Neurosurgery, The Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, The Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Y Li
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - J Laterra
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, The Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
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20
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Hemmatzadeh M, Mohammadi H, Karimi M, Musavishenas MH, Baradaran B. Differential role of microRNAs in the pathogenesis and treatment of Esophageal cancer. Biomed Pharmacother 2016; 82:509-19. [PMID: 27470391 DOI: 10.1016/j.biopha.2016.05.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022] Open
Abstract
Esophageal cancer (EC) is the most invasive disease associated with inclusive poor prognosis. EC usually is found as either adenocarcinoma (EAC) or squamous cell carcinomas (ESCC). ESCC forms in squamous cells and highly occurs in the upper third of the esophagus. EAC appears in glandular cells and ordinarily develops in the lower one third of the esophagus near the stomach. Barrett's esophagus (BE) is a metaplastic precursor of EAC. There is a persistent need for improving our understanding of the molecular basis of this disease. MicroRNAs (miRNAs) demonstrate an uncovered class of small, non-coding RNAs that can negatively regulate the protein coding gene, and are associated with approximately all known physiological and pathological processes, especially cancer. MiRNAs can affect cancer pathogenesis, playing a crucial role as either oncogenes or tumor suppressors. The recent emergence of observations on the role of miRNAs in cancer and their functions has induced many investigations to examine their relevance to esophageal cancer. In esophageal cancer, miRNA dysregulation plays a crucial role in cancer prognosis and in patients' responsiveness to neo-adjuvant and adjuvant therapies. In this review, the oncogenic, tumor suppressive, and drug resistance related roles of miRNAs, and their involvement in the pathogenesis and treatment of esophageal cancer were summarized.
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Affiliation(s)
- Maryam Hemmatzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Tabriz University of Medical Sciences, International Branch (Aras), Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Karimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Tabriz University of Medical Sciences, International Branch (Aras), Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Musavishenas
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Tabriz University of Medical Sciences, International Branch (Aras), Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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MiR-298 Counteracts Mutant Androgen Receptor Toxicity in Spinal and Bulbar Muscular Atrophy. Mol Ther 2016; 24:937-45. [PMID: 26755334 PMCID: PMC4881766 DOI: 10.1038/mt.2016.13] [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: 08/24/2015] [Accepted: 01/04/2016] [Indexed: 01/18/2023] Open
Abstract
Spinal and bulbar muscular atrophy (SBMA) is a currently untreatable adult-onset neuromuscular disease caused by expansion of a polyglutamine repeat in the androgen receptor (AR). In SBMA, as in other polyglutamine diseases, a toxic gain of function in the mutant protein is an important factor in the disease mechanism; therefore, reducing the mutant protein holds promise as an effective treatment strategy. In this work, we evaluated a microRNA (miRNA) to reduce AR expression. From a list of predicted miRNAs that target human AR, we selected microRNA-298 (miR-298) for its ability to downregulate AR mRNA and protein levels when transfected in cells overexpressing wild-type and mutant AR and in SBMA patient-derived fibroblasts. We showed that miR-298 directly binds to the 3'-untranslated region of the human AR transcript, and counteracts AR toxicity in vitro. Intravenous delivery of miR-298 with adeno-associated virus serotype 9 vector resulted in efficient transduction of muscle and spinal cord and amelioration of the disease phenotype in SBMA mice. Our findings support the development of miRNAs as a therapeutic strategy for SBMA and other neurodegenerative disorders caused by toxic proteins.
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Tibbit CJ, Williamson CM, Mehta S, Ball ST, Chotalia M, Nottingham WT, Eaton SA, Quwailid MM, Teboul L, Kelsey G, Peters J. Antisense Activity across the Nesp Promoter is Required for Nespas-Mediated Silencing in the Imprinted Gnas Cluster. Noncoding RNA 2015; 1:246-265. [PMID: 29861426 PMCID: PMC5932550 DOI: 10.3390/ncrna1030246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/17/2015] [Accepted: 11/17/2015] [Indexed: 12/03/2022] Open
Abstract
Macro long non-coding RNAs (lncRNAs) play major roles in gene silencing in inprinted gene clusters. Within the imprinted Gnas cluster, the paternally expressed Nespas lncRNA downregulates its sense counterpart Nesp. To explore the mechanism of action of Nespas, we generated two new knock-in alleles to truncate Nespas upstream and downstream of the Nesp promoter. We show that Nespas is essential for methylation of the Nesp differentially methylated region (DMR), but higher levels of Nespas are required for methylation than are needed for downregulation of Nesp. Although Nespas is transcribed for over 27 kb, only Nespas transcript/transcription across a 2.6 kb region that includes the Nesp promoter is necessary for methylation of the Nesp DMR. In both mutants, the levels of Nespas were extraordinarily high, due at least in part to increased stability, an effect not seen with other imprinted lncRNAs. However, even when levels were greatly raised, Nespas remained exclusively cis-acting. We propose Nespas regulates Nesp methylation and expression to ensure appropriate levels of expression of the protein coding transcripts Gnasxl and Gnas on the paternal chromosome. Thus, Nespas mediates paternal gene expression over the entire Gnas cluster via a single gene, Nesp.
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Affiliation(s)
- Charlotte J Tibbit
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: MRC Functional Genomics Unit, Department of Physiology Anatomy & Genetics, Le Gros Clark Building, University of Oxford, South Parks Road, Oxford OX13QX, UK.
| | - Christine M Williamson
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current Address: MRC Harwell, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Stuti Mehta
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: GI Division, Their 340, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Simon T Ball
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Mita Chotalia
- Epigenetics Programme, The Babraham Institute, Cambridge CB223AT, UK.
- Current address: Genome Function Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, London W120NN, UK.
| | - Wade T Nottingham
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: West London Free School, 2 Bridge Avenue, Hammersmith, London W69JP, UK.
| | - Sally A Eaton
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Mohamed M Quwailid
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Lydia Teboul
- Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB223AT, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB23EG, UK.
| | - Jo Peters
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
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Ruhrmann S, Stridh P, Kular L, Jagodic M. Genomic imprinting: A missing piece of the Multiple Sclerosis puzzle? Int J Biochem Cell Biol 2015; 67:49-57. [PMID: 26002250 DOI: 10.1016/j.biocel.2015.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 12/14/2022]
Abstract
Evidence for parent-of-origin effects in complex diseases such as Multiple Sclerosis (MS) strongly suggests a role for epigenetic mechanisms in their pathogenesis. In this review, we describe the importance of accounting for parent-of-origin when identifying new risk variants for complex diseases and discuss how genomic imprinting, one of the best-characterized epigenetic mechanisms causing parent-of-origin effects, may impact etiology of complex diseases. While the role of imprinted genes in growth and development is well established, the contribution and molecular mechanisms underlying the impact of genomic imprinting in immune functions and inflammatory diseases are still largely unknown. Here we discuss emerging roles of imprinted genes in the regulation of inflammatory responses with a particular focus on the Dlk1 cluster that has been implicated in etiology of experimental MS-like disease and Type 1 Diabetes. Moreover, we speculate on the potential wider impact of imprinting via the action of imprinted microRNAs, which are abundantly present in the Dlk1 locus and predicted to fine-tune important immune functions. Finally, we reflect on how unrelated imprinted genes or imprinted genes together with non-imprinted genes can interact in so-called imprinted gene networks (IGN) and suggest that IGNs could partly explain observed parent-of-origin effects in complex diseases. Unveiling the mechanisms of parent-of-origin effects is therefore likely to teach us not only about the etiology of complex diseases but also about the unknown roles of this fascinating phenomenon underlying uneven genetic contribution from our parents. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pernilla Stridh
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
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Verdelli C, Forno I, Vaira V, Corbetta S. MicroRNA deregulation in parathyroid tumours suggests an embryonic signature. J Endocrinol Invest 2015; 38:383-8. [PMID: 25577262 DOI: 10.1007/s40618-014-0234-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/20/2014] [Indexed: 12/22/2022]
Abstract
Primary hyperparathyroidism is a common endocrine disorder caused by abnormal tumour parathyroid cell proliferation. Parathyroid tumours show a great variability both in clinical features, such as the severity of PTH secretion, the rate and the pattern of cell proliferation, and genetic background. Studies aiming to develop new diagnostic markers and therapeutic approaches need a deeper definition of this variability. Dysregulation of microRNAs (miRNAs) has been shown to play an essential role in the development and progression of cancer. MiRNAs are small noncoding RNAs that inhibit the translation and stability of messenger RNAs (mRNAs). Here, data about the miRNA expression pattern in parathyroid normal and tumour glands were reviewed. Though available data in parathyroid tumours are very limited, the expression pattern of a subset of specific miRNAs clearly discriminated parathyroid carcinomas from normal parathyroid glands and, more clinically relevant, from parathyroid adenomas. Investigation showed that parathyroid tumours were characterized by an embryonic expression pattern of miRNAs such as miR-296, or the miRNA clusters C19MC and miR-371-3, typically in stem cells committed to differentiation or during human embryonic development, respectively. Further, miRNA profiles were correlated with tumour aggressive behaviour. Moreover, the interaction with the oncosuppressor menin suggests that miRNAs might modulate the function of the known oncosuppressors or oncogenes involved in parathyroid tumourigenesis and thus overseeing the tumour phenotype. In conclusion, miRNAs might provide new diagnostic markers and new therapeutic approaches by developing molecular miRNA-targeted therapies for the cure of parathyroid tumours, whose unique option is surgery.
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Affiliation(s)
- C Verdelli
- Laboratory of Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, MI, Italy
| | - I Forno
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - V Vaira
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - S Corbetta
- Endocrinology and Diabetology Unit, Department of Biomedical Sciences, University of Milan, IRCCS Policlinico San Donato, Via Morandi 30, 20097, San Donato Milanese, MI, Italy.
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Fibroblasts from patients with major depressive disorder show distinct transcriptional response to metabolic stressors. Transl Psychiatry 2015; 5:e523. [PMID: 25756806 PMCID: PMC4354345 DOI: 10.1038/tp.2015.14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/12/2014] [Accepted: 12/19/2014] [Indexed: 12/13/2022] Open
Abstract
Major depressive disorder (MDD) is increasingly viewed as interplay of environmental stressors and genetic predisposition, and recent data suggest that the disease affects not only the brain, but the entire body. As a result, we aimed at determining whether patients with major depression have aberrant molecular responses to stress in peripheral tissues. We examined the effects of two metabolic stressors, galactose (GAL) or reduced lipids (RL), on the transcriptome and miRNome of human fibroblasts from 16 pairs of patients with MDD and matched healthy controls (CNTR). Our results demonstrate that both MDD and CNTR fibroblasts had a robust molecular response to GAL and RL challenges. Most importantly, a significant part (messenger RNAs (mRNAs): 26-33%; microRNAs (miRNAs): 81-90%) of the molecular response was only observed in MDD, but not in CNTR fibroblasts. The applied metabolic challenges uncovered mRNA and miRNA signatures, identifying responses to each stressor characteristic for the MDD fibroblasts. The distinct responses of MDD fibroblasts to GAL and RL revealed an aberrant engagement of molecular pathways, such as apoptosis, regulation of cell cycle, cell migration, metabolic control and energy production. In conclusion, the metabolic challenges evoked by GAL or RL in dermal fibroblasts exposed adaptive dysfunctions on mRNA and miRNA levels that are characteristic for MDD. This finding underscores the need to challenge biological systems to bring out disease-specific deficits, which otherwise might remain hidden under resting conditions.
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Perez-Nanclares G, Velayos T, Vela A, Muñoz-Torres M, Castaño L. Pseudohypoparathyroidism type Ib associated with novel duplications in the GNAS locus. PLoS One 2015; 10:e0117691. [PMID: 25710380 PMCID: PMC4339194 DOI: 10.1371/journal.pone.0117691] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 12/30/2014] [Indexed: 12/18/2022] Open
Abstract
Context Pseudohypoparathyroidism type 1b (PHP-Ib) is characterized by renal resistance to PTH (and, sometimes, a mild resistance to TSH) and absence of any features of Albright's hereditary osteodystrophy. Patients with PHP-Ib suffer of defects in the methylation pattern of the complex GNAS locus. PHP-Ib can be either sporadic or inherited in an autosomal dominant pattern. Whereas familial PHP-Ib is well characterized at the molecular level, the genetic cause of sporadic PHP-Ib cases remains elusive, although some molecular mechanisms have been associated with this subtype. Objective The aim of the study was to investigate the molecular and imprinting defects in the GNAS locus in two unrelated patients with PHP-Ib. Design We have analyzed the GNAS locus by direct sequencing, Methylation-Specific Multiplex Ligation-dependent Probe Amplification, microsatellites, Quantitative Multiplex PCR of Short Fluorescent fragments and array-Comparative Genomic Hybridization studies in order to characterize two unrelated families with clinical features of PHP-Ib. Results We identified two duplications in the GNAS region in two patients with PHP-Ib: one of them, comprising ∼320 kb, occurred ‘de novo’ in the patient, whereas the other one, of ∼179 kb in length, was inherited from the maternal allele. In both cases, no other known genetic cause was observed. Conclusion In this article, we describe the to-our-knowledge biggest duplications reported so far in the GNAS region. Both are associated to PHP-Ib, one of them occurring ‘de novo’ and the other one being maternally inherited.
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Affiliation(s)
- Gustavo Perez-Nanclares
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
| | - Teresa Velayos
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
| | - Amaya Vela
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
| | - Manuel Muñoz-Torres
- Clinical Management Unit of Endocrinology and Nutrition, Hospital Universitario San Cecilio, Instituto de Investigacion Biosanitaria de Granada, Granada, Spain
| | - Luis Castaño
- Endocrinology and Diabetes Research Group, Hospital Universitario Cruces, BioCruces, CIBERER, CIBERDEM, UPV-EHU, Barakaldo, Basque Country, Spain
- * E-mail:
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27
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Miozzo M, Vaira V, Sirchia SM. Epigenetic alterations in cancer and personalized cancer treatment. Future Oncol 2015; 11:333-48. [DOI: 10.2217/fon.14.237] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT Based on the pivotal importance of epigenetics for transcription regulation, it is not surprising that cancer is characterized by several epigenetic abnormalities. Conversely to genetic alterations, epigenetic changes are not permanent, thus represent opportunities for therapeutic strategies designed to reverse transcriptional abnormalities, and cancer is the first disease in which epigenetic therapies with chromatin remodeling agents were introduced. The role of miRNAs in gene regulation supports their potential as innovative therapeutic strategy. Recent evidences have proven that the environment can profoundly influence the epigenome: diet, smoking and alcohol consumption can negatively impact the expression profile. Given the plasticity of epigenetic marks, it is challenging the idea that the epigenetic alterations are ‘druggable’ sites using specific food components.
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Affiliation(s)
- Monica Miozzo
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Istituto Nazionale di Genetica Molecolare ‘Romeo ed Enrica Invernizzi’, Integrative Biology Unit, Milano, Italy
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Kobayashi H. Imprinting genes associated with endometriosis. EXCLI JOURNAL 2014; 13:252-64. [PMID: 26417259 PMCID: PMC4464490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/19/2014] [Indexed: 11/30/2022]
Abstract
PURPOSE Much work has been carried out to investigate the genetic and epigenetic basis of endometriosis and proposed that endometriosis has been described as an epigenetic disease. The purpose of this study was to extract the imprinting genes that are associated with endometriosis development. METHODS The information on the imprinting genes can be accessed publicly from a web-based interface at http://www.geneimprint.com/site/genes-by-species. RESULTS In the current version, the database contains 150 human imprinted genes derived from the literature. We searched gene functions and their roles in particular biological processes or events, such as development and pathogenesis of endometriosis. From the genomic imprinting database, we picked 10 genes that were highly associated with female reproduction; prominent among them were paternally expressed genes (DIRAS3, BMP8B, CYP1B1, ZFAT, IGF2, MIMT1, or MIR296) and maternally expressed genes (DVL1, FGFRL1, or CDKN1C). These imprinted genes may be associated with reproductive biology such as endometriosis, pregnancy loss, decidualization process and preeclampsia. DISCUSSION This study supports the possibility that aberrant epigenetic dysregulation of specific imprinting genes may contribute to endometriosis predisposition.
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Affiliation(s)
- Hiroshi Kobayashi
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
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29
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Kobayashi H, Higashiura Y, Koike N, Akasaka J, Uekuri C, Iwai K, Niiro E, Morioka S, Yamada Y. Genes Downregulated in Endometriosis Are Located Near the Known Imprinting Genes. Reprod Sci 2014; 21:966-972. [PMID: 24615936 DOI: 10.1177/1933719114526473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
There is now accumulating evidence that endometriosis is a disease associated with an epigenetic disorder. Genomic imprinting is an epigenetic phenomenon known to regulate DNA methylation of either maternal or paternal alleles. We hypothesize that hypermethylated endometriosis-associated genes may be enriched at imprinted gene loci. We sought to determine whether downregulated genes associated with endometriosis susceptibility are associated with chromosomal location of the known paternally and maternally expressed imprinting genes. Gene information has been gathered from National Center for Biotechnology Information database geneimprint.com. Several researchers have identified specific loci with strong DNA methylation in eutopic endometrium and ectopic lesion with endometriosis. Of the 29 hypermethylated genes in endometriosis, 19 genes were located near 45 known imprinted foci. There may be an association of the genomic location between genes specifically downregulated in endometriosis and epigenetically imprinted genes.
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Affiliation(s)
- Hiroshi Kobayashi
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Yumi Higashiura
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Natsuki Koike
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Juria Akasaka
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Chiharu Uekuri
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Kana Iwai
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Emiko Niiro
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Sachiko Morioka
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
| | - Yuki Yamada
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
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Abstract
Genomic imprinting affects a subset of genes in mammals and results in a monoallelic, parental-specific expression pattern. Most of these genes are located in clusters that are regulated through the use of insulators or long noncoding RNAs (lncRNAs). To distinguish the parental alleles, imprinted genes are epigenetically marked in gametes at imprinting control elements through the use of DNA methylation at the very least. Imprinted gene expression is subsequently conferred through lncRNAs, histone modifications, insulators, and higher-order chromatin structure. Such imprints are maintained after fertilization through these mechanisms despite extensive reprogramming of the mammalian genome. Genomic imprinting is an excellent model for understanding mammalian epigenetic regulation.
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Affiliation(s)
- Denise P Barlow
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, CeMM, 1090 Vienna, Austria
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31
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Tran DA, Bai AY, Singh P, Wu X, Szabó PE. Characterization of the imprinting signature of mouse embryo fibroblasts by RNA deep sequencing. Nucleic Acids Res 2013; 42:1772-83. [PMID: 24217910 PMCID: PMC3919614 DOI: 10.1093/nar/gkt1042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mouse embryo fibroblasts (MEFs) are convenient sources for biochemical studies when cell number in mouse embryos is limiting. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we performed strand- and allele-specific RNA deep sequencing. We used sequenom allelotyping in embryo and adult organs to verify parental allele-specific expression. Thirty-two known ubiquitously imprinted genes displayed correct parental allele-specific transcripts in MEFs. Our analysis did not reveal any novel imprinted genes, but detected extended parental allele-specific transcripts in several known imprinted domains: maternal allele-specific transcripts downstream of Grb10 and downstream of Meg3, Rtl1as and Rian in the Dlk1-Dio3 cluster, an imprinted domain implicated in development and pluripotency. We detected paternal allele-specific transcripts downstream of Nespas, Peg3, Peg12 and Snurf/Snrpn. These imprinted transcript extensions were not unique to MEFs, but were also present in other somatic cells. The 5′ end points of the imprinted transcript extensions did not carry opposing chromatin marks or parental allele-specific DNA methylation, suggesting that their parental allele-specific transcription is under the control of the extended imprinted genes. Based on the imprinting signature of MEFs, these cells provide valid models for understanding the biochemical aspects of genomic imprinting.
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Affiliation(s)
- Diana A Tran
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA, Eugene and Ruth Roberts Summer Academy, City of Hope National Medical Center, Duarte, CA 91010, USA and Department of Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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32
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Menigatti M, Staiano T, Manser CN, Bauerfeind P, Komljenovic A, Robinson M, Jiricny J, Buffoli F, Marra G. Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions. Oncogenesis 2013; 2:e56. [PMID: 23857251 PMCID: PMC3740287 DOI: 10.1038/oncsis.2013.21] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/10/2013] [Accepted: 05/15/2013] [Indexed: 12/15/2022] Open
Abstract
Epigenetic silencing of protein-encoding genes is common in early-stage colorectal tumorigenesis. Less is known about the methylation-mediated silencing of genes encoding microRNAs (miRNAs), which are also important epigenetic modulators of gene expression. Using quantitative PCR, we identified 56 miRNAs that were expressed in normal colorectal mucosa and in HT29 colorectal cancer cells treated with demethylating agents but not in untreated HT29 cells, suggesting that they probably undergo methylation-induced silencing during colorectal tumorigenesis. One of these, miR-195, had recently been reported to be underexpressed in colorectal cancers and to exert tumor-suppressor effects in colorectal cancer cells. We identified the transcription start site (TSS) for primary miRNA (pri-miR)-497/195, the primary precursor that yields miR-195 and another candidate on our list, miR-497, and a single CpG island upstream to the TSS, which controls expression of both miRNAs. Combined bisulfite restriction analysis and bisulfite genomic sequencing studies revealed monoallelic methylation of this island in normal colorectal mucosa (50/50 samples) and full methylation in most colorectal adenomas (38/50; 76%). The hypermethylated precancerous lesions displayed significantly downregulated expression of both miRNAs. Similar methylation patterns were observed at two known imprinted genes, MEG3 and GNAS-AS1, which encode several of the 56 miRNAs on our list. Imprinting at these loci was lost in over half the adenomas (62% at MEG3 and 52% at GNAS-AS1). Copy-number alterations at MEG3, GNAS-AS1 and pri-miR-497/195, which are frequent in colorectal cancers, were less common in adenomas and confined to tumors displaying differential methylation at the involved locus. Our data show that somatically acquired, epigenetic changes at monoallelically methylated regions encoding miRNAs are relatively frequent in sporadic colorectal adenomas and might contribute to the onset and progression of these tumors.
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Affiliation(s)
- M Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - T Staiano
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - C N Manser
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - P Bauerfeind
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - A Komljenovic
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - M Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - J Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - F Buffoli
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - G Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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Lee JT, Bartolomei MS. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 2013; 152:1308-23. [PMID: 23498939 DOI: 10.1016/j.cell.2013.02.016] [Citation(s) in RCA: 498] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Indexed: 12/22/2022]
Abstract
X chromosome inactivation and genomic imprinting are classic epigenetic processes that cause disease when not appropriately regulated in mammals. Whereas X chromosome inactivation evolved to solve the problem of gene dosage, the purpose of genomic imprinting remains controversial. Nevertheless, the two phenomena are united by allelic control of large gene clusters, such that only one copy of a gene is expressed in every cell. Allelic regulation poses significant challenges because it requires coordinated long-range control in cis and stable propagation over time. Long noncoding RNAs have emerged as a common theme, and their contributions to diseases of imprinting and the X chromosome have become apparent. Here, we review recent advances in basic biology, the connections to disease, and preview potential therapeutic strategies for future development.
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Affiliation(s)
- Jeannie T Lee
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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Human microRNA hsa-miR-296-5p suppresses enterovirus 71 replication by targeting the viral genome. J Virol 2013; 87:5645-56. [PMID: 23468506 DOI: 10.1128/jvi.02655-12] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Enterovirus 71 (EV71) has emerged as a major cause of neurological disease following the near eradication of poliovirus. Accumulating evidence suggests that mammalian microRNAs (miRNAs), a class of noncoding RNAs of 18 to 23 nucleotides (nt) with important regulatory roles in many cellular processes, participate in host antiviral defenses. However, the roles of miRNAs in EV71 infection and pathogenesis are still unclear. Here, hsa-miR-296-5p expression was significantly increased in EV71-infected human cells. As determined by virus titration, quantitative real-time PCR (qRT-PCR), and Western blotting, overexpression of hsa-miR-296-5p inhibited, while inhibition of endogenous hsa-miR-296-5p facilitated, EV71 infection. Additionally, two potential hsa-miR-296-5p targets (nt 2115 to 2135 and nt 2896 to 2920) located in the EV71 genome (strain BrCr) were bioinformatically predicted and validated by luciferase reporter assays and Western blotting. Genomic alignment of various EV71 strains revealed synonymous mutations in hsa-miR-296-5p target sequences. Furthermore, the introduction of synonymous mutations into the EV71 BrCr genome by site-directed mutagenesis impaired the viral inhibitory effects of hsa-miR-296-5p and facilitated mutant virus infection. Meanwhile, compensatory mutations in corresponding hsa-miR-296-5p target sequences of the EV71 HeN strain (GenBank accession number JN256064) restored the inhibitory effects of the miRNA. These results indicate that hsa-miR-296-5p inhibits EV71 replication by targeting the viral genome. Our findings support the notion that cellular miRNAs can inhibit virus infection and that the virus mutates to escape suppression by cellular miRNAs.
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Barbagallo D, Piro S, Condorelli AG, Mascali LG, Urbano F, Parrinello N, Monello A, Statello L, Ragusa M, Rabuazzo AM, Di Pietro C, Purrello F, Purrello M. miR-296-3p, miR-298-5p and their downstream networks are causally involved in the higher resistance of mammalian pancreatic α cells to cytokine-induced apoptosis as compared to β cells. BMC Genomics 2013; 14:62. [PMID: 23360399 PMCID: PMC3571888 DOI: 10.1186/1471-2164-14-62] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/26/2013] [Indexed: 01/03/2023] Open
Abstract
Background The molecular bases of mammalian pancreatic α cells higher resistance than β to proinflammatory cytokines are very poorly defined. MicroRNAs are master regulators of cell networks, but only scanty data are available on their transcriptome in these cells and its alterations in diabetes mellitus. Results Through high-throughput real-time PCR, we analyzed the steady state microRNA transcriptome of murine pancreatic α (αTC1-6) and β (βTC1) cells: their comparison demonstrated significant differences. We also characterized the alterations of αTC1-6 cells microRNA transcriptome after treatment with proinflammatory cytokines. We focused our study on two microRNAs, miR-296-3p and miR-298-5p, which were: (1) specifically expressed at steady state in αTC1-6, but not in βTC1 or INS-1 cells; (2) significantly downregulated in αTC1-6 cells after treatment with cytokines in comparison to untreated controls. These microRNAs share more targets than expected by chance and were co-expressed in αTC1-6 during a 6–48 h time course treatment with cytokines. The genes encoding them are physically clustered in the murine and human genome. By exploiting specific microRNA mimics, we demonstrated that experimental upregulation of miR-296-3p and miR-298-5p raised the propensity to apoptosis of transfected and cytokine-treated αTC1-6 cells with respect to αTC1-6 cells, treated with cytokines after transfection with scramble molecules. Both microRNAs control the expression of IGF1Rβ, its downstream targets phospho-IRS-1 and phospho-ERK, and TNFα. Our computational analysis suggests that MAFB (a transcription factor exclusively expressed in pancreatic α cells within adult rodent islets of Langerhans) controls the expression of miR-296-3p and miR-298-5p. Conclusions Altogether, high-throughput microRNA profiling, functional analysis with synthetic mimics and molecular characterization of modulated pathways strongly suggest that specific downregulation of miR-296-3p and miR-298-5p, coupled to upregulation of their targets as IGF1Rβ and TNFα, is a major determinant of mammalian pancreatic α cells resistance to apoptosis induction by cytokines.
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Affiliation(s)
- Davide Barbagallo
- Dipartimento Gian Filippo Ingrassia, Unità di BioMedicina Molecolare Genomica e dei Sistemi Complessi, Genetica, Biologia Computazionale, Università di Catania, Catania, EU 95123, Italy
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Girardot M, Cavaillé J, Feil R. Small regulatory RNAs controlled by genomic imprinting and their contribution to human disease. Epigenetics 2012; 7:1341-8. [PMID: 23154539 PMCID: PMC3528689 DOI: 10.4161/epi.22884] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
More than a hundred protein-coding genes are controlled by genomic imprinting in humans. These atypical genes are organized in chromosomal domains, each of which is controlled by a differentially methylated "imprinting control region" (ICR). How ICRs mediate the parental allele-specific expression of close-by genes is now becoming understood. At several imprinted domains, this epigenetic mechanism involves the action of long non-coding RNAs. It is less well appreciated that imprinted gene domains also transcribe hundreds of microRNA and small nucleolar RNA genes and that these represent the densest clusters of small RNA genes in mammalian genomes. The evolutionary reasons for this remarkable enrichment of small regulatory RNAs at imprinted domains remain unclear. However, recent studies show that imprinted small RNAs modulate specific functions in development and metabolism and also are frequently perturbed in cancer. Here, we review our current understanding of imprinted small RNAs in the human genome and discuss how perturbation of their expression contributes to disease.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics, CNRS and the University of Montpellier, Montpellier, France.
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Hong L, Han Y, Lu Q, Zhang H, Zhao Q, Wu K, Fan D. Drug resistance-related microRNAs in esophageal cancer. Expert Opin Biol Ther 2012; 12:1487-94. [PMID: 22827640 DOI: 10.1517/14712598.2012.711309] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Drug resistance has been the main obstacle in cancer therapy. A number of drug resistance-related molecules are under investigation but no one agent has already been used in clinical practice. The research on drug resistance-related microRNAs (miRNAs) may eventually lead to improved clinical strategies and outcomes for patients with esophageal cancer (EC). AREAS COVERED This review summarizes the recent advances in drug resistance-related miRNAs in EC, and also analyzes the clinical and therapeutic applications they provide. The authors envisage future developments in the molecular mechanisms of these miRNAs and their potential applications to cancer treatment. EXPERT OPINION Drug resistance-related miRNAs can be used as a useful therapeutic tool for EC. More investigations should be performed to promote the success of therapeutic-clinical use of miRNAs in cancer.
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Affiliation(s)
- Liu Hong
- Fourth Military Medical University, Xijing Hospital of Digestive Diseases, State Key Laboratory of Cancer Biology, Xi'an, 710032, Shaanxi Province, China.
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