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Iskusnykh IY, Fattakhov N, Li Y, Bihannic L, Kirchner MK, Steshina EY, Northcott PA, Chizhikov VV. Lmx1a is a master regulator of the cortical hem. eLife 2023; 12:e84095. [PMID: 37725078 PMCID: PMC10508884 DOI: 10.7554/elife.84095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
Development of the nervous system depends on signaling centers - specialized cellular populations that produce secreted molecules to regulate neurogenesis in the neighboring neuroepithelium. In some cases, signaling center cells also differentiate to produce key types of neurons. The formation of a signaling center involves its induction, the maintenance of expression of its secreted molecules, and cell differentiation and migration events. How these distinct processes are coordinated during signaling center development remains unknown. By performing studies in mice, we show that Lmx1a acts as a master regulator to orchestrate the formation and function of the cortical hem (CH), a critical signaling center that controls hippocampus development. Lmx1a co-regulates CH induction, its Wnt signaling, and the differentiation and migration of CH-derived Cajal-Retzius neurons. Combining RNAseq, genetic, and rescue experiments, we identified major downstream genes that mediate distinct Lmx1a-dependent processes. Our work revealed that signaling centers in the mammalian brain employ master regulatory genes and established a framework for analyzing signaling center development.
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Affiliation(s)
- Igor Y Iskusnykh
- Department of Anatomy and Neurobiology, University of Tennessee Health Science CenterMemphisUnited States
| | - Nikolai Fattakhov
- Department of Anatomy and Neurobiology, University of Tennessee Health Science CenterMemphisUnited States
| | - Yiran Li
- Department of Developmental Neurobiology, St. Jude Children's Research HospitalMemphisUnited States
| | - Laure Bihannic
- Department of Developmental Neurobiology, St. Jude Children's Research HospitalMemphisUnited States
| | - Matthew K Kirchner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science CenterMemphisUnited States
| | - Ekaterina Y Steshina
- Department of Anatomy and Neurobiology, University of Tennessee Health Science CenterMemphisUnited States
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research HospitalMemphisUnited States
| | - Victor V Chizhikov
- Department of Anatomy and Neurobiology, University of Tennessee Health Science CenterMemphisUnited States
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2
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Hitit M, Kose M, Kaya MS, Kırbas M, Dursun S, Alak I, Atli MO. Circulating miRNAs in maternal plasma as potential biomarkers of early pregnancy in sheep. Front Genet 2022; 13:929477. [PMID: 36061213 PMCID: PMC9428447 DOI: 10.3389/fgene.2022.929477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNA (miRNA) plays an important role in the control of gene expression and is implied in many biological functions, including embryo implantation and development. The aim was to assess plasma miRNA profiles during the peri-implantation and ascertain potential candidate miRNA markers for early pregnancy diagnosis in ovine plasma. The plasma samples were obtained from a total of 24 ewes on days 12 (pre-implantation; P12, n = 4), 16 (implantation; P16, n = 4) and 22 (post-implantation; P22, n = 4) after mating, and on their corresponding days of 12 (Pre-C; C12, n = 4), 16 (Imp-C; C16, n = 4) and 22 (Post-C; C22, n = 4) of the estrous cycle. The miRNA profiles in plasma were assessed by microarray technology. We detected the presence of 60 ovine-specific miRNAs in plasma samples. Of these miRNAs, 22 demonstrated a differential expression pattern, especially between the estrous cycle and early pregnancy, and targeted 521 genes. Two miRNAs (oar-miR-218a and oar-miR-1185-3p) were confirmed using RT-qPCR in the ovine plasma samples. Protein-protein interaction (PPI) network of target genes established six functional modules, of which modules 1 and 3 were enriched in the common GO terms, such as inflammatory response, defense response, and regulation of immune response. In contrast, module 2 was enriched in the developmental process involved in reproduction, embryo development, embryonic morphogenesis, and regulation of the developmental process. The results indicate that miRNAs profiles of plasma seemed to be modulated during the peri-implantation stage of pregnancy in ewes. Circulating miRNAs could be promising candidates for diagnosis in early ovine pregnancy.
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Affiliation(s)
- Mustafa Hitit
- Department of Genetics, Faculty of Veterinary Medicine, Kastamonu University, Kastamonu, Turkey
- *Correspondence: Mustafa Hitit, ; Mehmet Osman Atli,
| | - Mehmet Kose
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Dicle University, Diyarbakir, Turkey
| | - Mehmet Salih Kaya
- Department of Physiology, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Mesut Kırbas
- Bahri Dagdas International Agricultural Research Institute, Konya, Turkey
| | - Sukru Dursun
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Aksaray University, Aksaray, Turkey
| | - Ilyas Alak
- Department of Animal Sciences, Vocational School of Technical Sciences, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Mehmet Osman Atli
- Department of Reproduction and Artificial Insemination, Faculty of Veterinary Medicine, Harran University, Sanliurfa, Turkey
- *Correspondence: Mustafa Hitit, ; Mehmet Osman Atli,
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Prieto-Colomina A, Fernández V, Chinnappa K, Borrell V. MiRNAs in early brain development and pediatric cancer: At the intersection between healthy and diseased embryonic development. Bioessays 2021; 43:e2100073. [PMID: 33998002 DOI: 10.1002/bies.202100073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022]
Abstract
The size and organization of the brain are determined by the activity of progenitor cells early in development. Key mechanisms regulating progenitor cell biology involve miRNAs. These small noncoding RNA molecules bind mRNAs with high specificity, controlling their abundance and expression. The role of miRNAs in brain development has been studied extensively, but their involvement at early stages remained unknown until recently. Here, recent findings showing the important role of miRNAs in the earliest phases of brain development are reviewed, and it is discussed how loss of specific miRNAs leads to pathological conditions, particularly adult and pediatric brain tumors. Let-7 miRNA downregulation and the initiation of embryonal tumors with multilayered rosettes (ETMR), a novel link recently discovered by the laboratory, are focused upon. Finally, it is discussed how miRNAs may be used for the diagnosis and therapeutic treatment of pediatric brain tumors, with the hope of improving the prognosis of these devastating diseases.
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Affiliation(s)
- Anna Prieto-Colomina
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Virginia Fernández
- Neurobiology of miRNA, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Kaviya Chinnappa
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
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4
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Abstract
Among the large, diverse set of mammalian long noncoding RNAs (lncRNAs), long noncoding primary microRNAs (lnc-pri-miRNAs) are those that host miRNAs. Whether lnc-pri-miRNA loci have important biological function independent of their cognate miRNAs is poorly understood. From a genome-scale lncRNA screen, lnc-pri-miRNA loci were enriched for function in cell proliferation, and in glioblastoma (i.e., GBM) cells with DGCR8 or DROSHA knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied LOC646329 (also known as MIR29HG), which hosts the miR-29a/b1 cluster. In GBM cells, LOC646329 knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster (LOC646329-miR29Δ) did not decrease cell growth, while knockdown of LOC646329-miR29Δ transcripts reduced cell proliferation. The miR-29a/b1-independent activity of LOC646329 corresponded to enhancer-like activation of a neighboring oncogene (MKLN1), regulating cell propagation. The LOC646329 locus interacts with the MKLN1 promoter, and antisense oligonucleotide knockdown of the lncRNA disrupts these interactions and reduces the enhancer-like activity. More broadly, analysis of genome-wide data from multiple human cell types showed that lnc-pri-miRNA loci are significantly enriched for DNA looping interactions with gene promoters as well as genomic and epigenetic characteristics of transcriptional enhancers. Functional studies of additional lnc-pri-miRNA loci demonstrated cognate miRNA-independent enhancer-like activity. Together, these data demonstrate that lnc-pri-miRNA loci can regulate cell biology via both miRNA-dependent and miRNA-independent mechanisms.
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Pöstyéni E, Kovács-Valasek A, Urbán P, Czuni L, Sétáló G, Fekete C, Gabriel R. Analysis of mir-9 Expression Pattern in Rat Retina during Postnatal Development. Int J Mol Sci 2021; 22:ijms22052577. [PMID: 33806574 PMCID: PMC7961372 DOI: 10.3390/ijms22052577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 12/31/2022] Open
Abstract
It is well established that miR-9 contributes to retinal neurogenesis. However, little is known about its presence and effects in the postnatal period. To expand our knowledge, miRNA-small RNA sequencing and in situ hybridization supported by RT-qPCR measurement were carried out. Mir-9 expression showed two peaks in the first three postnatal weeks in Wistar rats. The first peak was detected at postnatal Day 3 (P3) and the second at P10, then the expression gradually decreased until P21. Furthermore, we performed in silico prediction and established that miR-9 targets OneCut2 or synaptotagmin-17. Another two microRNAs (mir-135, mir-218) were found from databases which also target these proteins. They showed a similar tendency to mir-9; their lowest expression was at P7 and afterwards, they showed increase. We revealed that miR-9 is localized mainly in the inner retina. Labeling was observed in ganglion and amacrine cells. Additionally, horizontal cells were also marked. By dual miRNA-in situ hybridization/immunocytochemistry and qPCR, we revealed alterations in their temporal and spatial expression. Our results shed light on the significance of mir-9 regulation during the first three postnatal weeks in rat retina and suggest that miRNA could act on their targets in a stage-specific manner.
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Affiliation(s)
- Etelka Pöstyéni
- Department of Experimental Zoology and Neurobiology, University of Pécs, 7624 Pécs, Hungary;
| | - Andrea Kovács-Valasek
- Department of Experimental Zoology and Neurobiology, University of Pécs, 7624 Pécs, Hungary;
- Correspondence: (A.K.-V.); (R.G.)
| | - Péter Urbán
- János Szentágothai Research Centre, 7624 Pécs, Hungary; (P.U.); (L.C.); (C.F.)
| | - Lilla Czuni
- János Szentágothai Research Centre, 7624 Pécs, Hungary; (P.U.); (L.C.); (C.F.)
| | - György Sétáló
- Department of Medical Biology, Medical School, University of Pécs, 7624 Pécs, Hungary;
| | - Csaba Fekete
- János Szentágothai Research Centre, 7624 Pécs, Hungary; (P.U.); (L.C.); (C.F.)
| | - Robert Gabriel
- Department of Experimental Zoology and Neurobiology, University of Pécs, 7624 Pécs, Hungary;
- Department of Medical Biology, Medical School, University of Pécs, 7624 Pécs, Hungary;
- Correspondence: (A.K.-V.); (R.G.)
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6
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García-Moreno F, Molnár Z. Variations of telencephalic development that paved the way for neocortical evolution. Prog Neurobiol 2020; 194:101865. [PMID: 32526253 PMCID: PMC7656292 DOI: 10.1016/j.pneurobio.2020.101865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022]
Abstract
Charles Darwin stated, "community in embryonic structure reveals community of descent". Thus, to understand how the neocortex emerged during mammalian evolution we need to understand the evolution of the development of the pallium, the source of the neocortex. In this article, we review the variations in the development of the pallium that enabled the production of the six-layered neocortex. We propose that an accumulation of subtle modifications from very early brain development accounted for the diversification of vertebrate pallia and the origin of the neocortex. Initially, faint differences of expression of secretable morphogens promote a wide variety in the proportions and organization of sectors of the early pallium in different vertebrates. It prompted different sectors to host varied progenitors and distinct germinative zones. These cells and germinative compartments generate diverse neuronal populations that migrate and mix with each other through radial and tangential migrations in a taxon-specific fashion. Together, these early variations had a profound influence on neurogenetic gradients, lamination, positioning, and connectivity. Gene expression, hodology, and physiological properties of pallial neurons are important features to suggest homologies, but the origin of cells and their developmental trajectory are fundamental to understand evolutionary changes. Our review compares the development of the homologous pallial sectors in sauropsids and mammals, with a particular focus on cell lineage, in search of the key changes that led to the appearance of the mammalian neocortex.
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Affiliation(s)
- Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain; IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013, Bilbao, Spain; Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain.
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, Sherrington Building, University of Oxford, Oxford, OX1 3QX, UK.
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Pascale E, Divisato G, Palladino R, Auriemma M, Ngalya EF, Caiazzo M. Noncoding RNAs and Midbrain DA Neurons: Novel Molecular Mechanisms and Therapeutic Targets in Health and Disease. Biomolecules 2020; 10:biom10091269. [PMID: 32899172 PMCID: PMC7563414 DOI: 10.3390/biom10091269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
Midbrain dopamine neurons have crucial functions in motor and emotional control and their degeneration leads to several neurological dysfunctions such as Parkinson’s disease, addiction, depression, schizophrenia, and others. Despite advances in the understanding of specific altered proteins and coding genes, little is known about cumulative changes in the transcriptional landscape of noncoding genes in midbrain dopamine neurons. Noncoding RNAs—specifically microRNAs and long noncoding RNAs—are emerging as crucial post-transcriptional regulators of gene expression in the brain. The identification of noncoding RNA networks underlying all stages of dopamine neuron development and plasticity is an essential step to deeply understand their physiological role and also their involvement in the etiology of dopaminergic diseases. Here, we provide an update about noncoding RNAs involved in dopaminergic development and metabolism, and the related evidence of these biomolecules for applications in potential treatments for dopaminergic neurodegeneration.
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Affiliation(s)
- Emilia Pascale
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (G.D.); (R.P.); (M.A.); (E.F.N.)
| | - Giuseppina Divisato
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (G.D.); (R.P.); (M.A.); (E.F.N.)
| | - Renata Palladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (G.D.); (R.P.); (M.A.); (E.F.N.)
| | - Margherita Auriemma
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (G.D.); (R.P.); (M.A.); (E.F.N.)
| | - Edward Faustine Ngalya
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (G.D.); (R.P.); (M.A.); (E.F.N.)
| | - Massimiliano Caiazzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (G.D.); (R.P.); (M.A.); (E.F.N.)
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
- Correspondence:
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8
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Dori M, Cavalli D, Lesche M, Massalini S, Alieh LHA, de Toledo BC, Khudayberdiev S, Schratt G, Dahl A, Calegari F. MicroRNA profiling of mouse cortical progenitors and neurons reveals miR-486-5p as a regulator of neurogenesis. Development 2020; 147:dev.190520. [PMID: 32273274 DOI: 10.1242/dev.190520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/26/2020] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are short (∼22 nt) single-stranded non-coding RNAs that regulate gene expression at the post-transcriptional level. Over recent years, many studies have extensively characterized the involvement of miRNA-mediated regulation in neurogenesis and brain development. However, a comprehensive catalog of cortical miRNAs expressed in a cell-specific manner in progenitor types of the developing mammalian cortex is still missing. Overcoming this limitation, here we exploited a double reporter mouse line previously validated by our group to allow the identification of the transcriptional signature of neurogenic commitment and provide the field with the complete atlas of miRNA expression in proliferating neural stem cells, neurogenic progenitors and newborn neurons during corticogenesis. By extending the currently known list of miRNAs expressed in the mouse brain by over twofold, our study highlights the power of cell type-specific analyses for the detection of transcripts that would otherwise be diluted out when studying bulk tissues. We further exploited our data by predicting putative miRNAs and validated the power of our approach by providing evidence for the involvement of miR-486 in brain development.
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Affiliation(s)
- Martina Dori
- CRTD - Center for Regenerative Therapies Dresden, School of Medicine, TU Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
| | - Daniel Cavalli
- CRTD - Center for Regenerative Therapies Dresden, School of Medicine, TU Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
| | - Mathias Lesche
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
| | - Simone Massalini
- CRTD - Center for Regenerative Therapies Dresden, School of Medicine, TU Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
| | - Leila Haj Abdullah Alieh
- CRTD - Center for Regenerative Therapies Dresden, School of Medicine, TU Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
| | - Beatriz Cardoso de Toledo
- CRTD - Center for Regenerative Therapies Dresden, School of Medicine, TU Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
| | - Sharof Khudayberdiev
- Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg, Philipps-University of Marburg, Karl-von-Frisch-Strasse 2, 35043 Marburg, Germany
| | - Gerhard Schratt
- Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg, Philipps-University of Marburg, Karl-von-Frisch-Strasse 2, 35043 Marburg, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
| | - Federico Calegari
- CRTD - Center for Regenerative Therapies Dresden, School of Medicine, TU Dresden, Fetcherstrasse 105, 01307 Dresden, Germany
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9
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Stamou M, Ng SY, Brand H, Wang H, Plummer L, Best L, Havlicek S, Hibberd M, Khor CC, Gusella J, Balasubramanian R, Talkowski M, Stanton LW, Crowley WF. A Balanced Translocation in Kallmann Syndrome Implicates a Long Noncoding RNA, RMST, as a GnRH Neuronal Regulator. J Clin Endocrinol Metab 2020; 105:5601163. [PMID: 31628846 PMCID: PMC7112981 DOI: 10.1210/clinem/dgz011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/20/2019] [Indexed: 12/16/2022]
Abstract
CONTEXT Kallmann syndrome (KS) is a rare, genetically heterogeneous Mendelian disorder. Structural defects in KS patients have helped define the genetic architecture of gonadotropin-releasing hormone (GnRH) neuronal development in this condition. OBJECTIVE Examine the functional role a novel structural defect affecting a long noncoding RNA (lncRNA), RMST, found in a KS patient. DESIGN Whole genome sequencing, induced pluripotent stem cells and derived neural crest cells (NCC) from the KS patient were contrasted with controls. SETTING The Harvard Reproductive Sciences Center, Massachusetts General Hospital Center for Genomic Medicine, and Singapore Genome Institute. PATIENT A KS patient with a unique translocation, t(7;12)(q22;q24). INTERVENTIONS/MAIN OUTCOME MEASURE/RESULTS A novel translocation was detected affecting the lncRNA, RMST, on chromosome 12 in the absence of any other KS mutations. Compared with controls, the patient's induced pluripotent stem cells and NCC provided functional information regarding RMST. Whereas RMST expression increased during NCC differentiation in controls, it was substantially reduced in the KS patient's NCC coincident with abrogated NCC morphological development and abnormal expression of several "downstream" genes essential for GnRH ontogeny (SOX2, PAX3, CHD7, TUBB3, and MKRN3). Additionally, an intronic single nucleotide polymorphism in RMST was significantly implicated in a genome-wide association study associated with age of menarche. CONCLUSIONS A novel deletion in RMST implicates the loss of function of a lncRNA as a unique cause of KS and suggests it plays a critical role in the ontogeny of GnRH neurons and puberty.
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Affiliation(s)
- Maria Stamou
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital, Boston
| | - Shi-Yan Ng
- Institute of Molecular & Cell Biology, Singapore
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
- Neurology, Psychiatry, & Pathology Departments, Massachusetts General Hospital, Boston
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA
| | - Harold Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
| | - Lacey Plummer
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital, Boston
| | - Lyle Best
- Turtle Mountain Community College, Belcourt, ND
- Family Medicine Department, University of North Dakota, Grand Forks, ND
| | | | - Martin Hibberd
- London School of Hygiene & Tropical Medicine, Keppel Street, London
- Genome Institute of Singapore, Singapore
| | | | - James Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
| | | | - Michael Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
- Neurology, Psychiatry, & Pathology Departments, Massachusetts General Hospital, Boston
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA
| | - Lawrence W Stanton
- Genome Institute of Singapore, Singapore
- Qatar Biomedical Research Institute (QBRI), Hamad BIn Khalifa University (HBRI), Doha, Qatar
| | - William F Crowley
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital, Boston
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
- Correspondence and Reprint Requests: William F. Crowley, Jr., M.D., Center for Genomic Medicine CPZN-6.6312 - 185 Cambridge Street, Boston, MA 02114. E-mail:
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10
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Yi Z, Pu Y, Gou R, Chen Y, Ren X, Liu W, Dong P. Silencing of RIPK4 inhibits epithelial‑mesenchymal transition by inactivating the Wnt/β‑catenin signaling pathway in osteosarcoma. Mol Med Rep 2020; 21:1154-1162. [PMID: 32016450 PMCID: PMC7002986 DOI: 10.3892/mmr.2020.10939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/29/2019] [Indexed: 12/17/2022] Open
Abstract
Receptor interacting protein kinase 4 (RIPK4) is a serine/threonine kinase that plays an important role in the regulation of cell proliferation, invasion and metastasis in several malignancies; however, its clinical significance and biological function in osteosarcoma (OS) remains unknown. In the present study, the RIPK4 expression level was significantly upregulated in OS tissues and cell lines. High RIPK4 expression was positively associated with larger sized tumors, advanced Enneking stage and poor prognosis in patients with OS. Furthermore, the results revealed that RIPK4 knockdown in the OS cell lines MG‑63 and U2OS reduced cell migration and invasion via the inhibition of epithelial‑mesenchymal transition (EMT) process, whereby E‑cadherin expression was increased and N‑cadherin and vimentin expression decreased. Mechanistically, RIPK4 knockdown inhibited EMT by inactivating the Wnt/β‑catenin signaling pathway. These findings suggest that RIPK4 may be a novel potential therapeutic target for the treatment of metastases in patients with OS.
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Affiliation(s)
- Zhigang Yi
- Department of Pediatric Orthopedics and Pediatrics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yanchuan Pu
- Department of Orthopedics, Wuwei City People's Hospital, Wuwei, Gansu 733000, P.R. China
| | - Ruoyan Gou
- Department of Pediatric Orthopedics and Pediatrics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yonggang Chen
- Department of Pediatric Orthopedics and Pediatrics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xiaojun Ren
- Department of Pediatric Orthopedics and Pediatrics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Wenzhong Liu
- Department of Pediatric Orthopedics and Pediatrics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Ping Dong
- Department of Pediatric Orthopedics and Pediatrics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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11
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Pons-Espinal M, Gasperini C, Marzi MJ, Braccia C, Armirotti A, Pötzsch A, Walker TL, Fabel K, Nicassio F, Kempermann G, De Pietri Tonelli D. MiR-135a-5p Is Critical for Exercise-Induced Adult Neurogenesis. Stem Cell Reports 2019; 12:1298-1312. [PMID: 31130358 PMCID: PMC6565832 DOI: 10.1016/j.stemcr.2019.04.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/15/2022] Open
Abstract
Physical exercise stimulates adult hippocampal neurogenesis and is considered a relevant strategy for preventing age-related cognitive decline in humans. The underlying mechanisms remains controversial. Here, we show that exercise increases proliferation of neural precursor cells (NPCs) of the mouse dentate gyrus (DG) via downregulation of microRNA 135a-5p (miR-135a). MiR-135a inhibition stimulates NPC proliferation leading to increased neurogenesis, but not astrogliogenesis, in DG of resting mice, and intriguingly it re-activates NPC proliferation in aged mice. We identify 17 proteins (11 putative targets) modulated by miR-135 in NPCs. Of note, inositol 1,4,5-trisphosphate (IP3) receptor 1 and inositol polyphosphate-4-phosphatase type I are among the modulated proteins, suggesting that IP3 signaling may act downstream miR-135. miR-135 is the first noncoding RNA essential modulator of the brain's response to physical exercise. Prospectively, the miR-135-IP3 axis might represent a novel target of therapeutic intervention to prevent pathological brain aging.
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Affiliation(s)
| | - Caterina Gasperini
- Neurobiology of miRNA, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Clarissa Braccia
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Alexandra Pötzsch
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Tara L Walker
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Klaus Fabel
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany; CRTD - Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
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12
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Antagonizing Increased miR-135a Levels at the Chronic Stage of Experimental TLE Reduces Spontaneous Recurrent Seizures. J Neurosci 2019; 39:5064-5079. [PMID: 31015341 DOI: 10.1523/jneurosci.3014-18.2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/31/2019] [Accepted: 04/16/2019] [Indexed: 01/01/2023] Open
Abstract
Mesial temporal lobe epilepsy (mTLE) is a chronic neurological disease characterized by recurrent seizures. The antiepileptic drugs currently available to treat mTLE are ineffective in one-third of patients and lack disease-modifying effects. miRNAs, a class of small noncoding RNAs which control gene expression at the post-transcriptional level, play a key role in the pathogenesis of mTLE and other epilepsies. Although manipulation of miRNAs at acute stages has been reported to reduce subsequent spontaneous seizures, it is uncertain whether targeting miRNAs at chronic stages of mTLE can also reduce seizures. Furthermore, the functional role and downstream targets of most epilepsy-associated miRNAs remain poorly understood. Here, we show that miR-135a is selectively upregulated within neurons in epileptic brain and report that targeting miR-135a in vivo using antagomirs after onset of spontaneous recurrent seizures can reduce seizure activity at the chronic stage of experimental mTLE in male mice. Further, by using an unbiased approach combining immunoprecipitation and RNA sequencing, we identify several novel neuronal targets of miR-135a, including Mef2a Mef2 proteins are key regulators of excitatory synapse density. Mef2a and miR-135a show reciprocal expression regulation in human (of both sexes) and experimental TLE, and miR-135a regulates dendritic spine number and type through Mef2. Together, our data show that miR-135a is target for reducing seizure activity in chronic epilepsy, and that deregulation of miR-135a in epilepsy may alter Mef2a expression and thereby affect synaptic function and plasticity.SIGNIFICANCE STATEMENT miRNAs are post-transcriptional regulators of gene expression with roles in the pathogenesis of epilepsy. However, the precise mechanism of action and therapeutic potential of most epilepsy-associated miRNAs remain poorly understood. Our study reveals dramatic upregulation of the key neuronal miRNA miR-135a in both experimental and human mesial temporal lobe epilepsy. Silencing miR-135a in experimental temporal lobe epilepsy reduces seizure activity at the spontaneous recurrent seizure stage. These data support the exciting possibility that miRNAs can be targeted to combat seizures after spontaneous seizure activity has been established. Further, by using unbiased approaches novel neuronal targets of miR-135a, including members of the Mef2 protein family, are identified that begin to explain how deregulation of miR-135a may contribute to epilepsy.
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13
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Lin HP, Oksuz I, Svaren J, Awatramani R. Egr2-dependent microRNA-138 is dispensable for peripheral nerve myelination. Sci Rep 2018; 8:3817. [PMID: 29491350 PMCID: PMC5830491 DOI: 10.1038/s41598-018-22010-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/14/2018] [Indexed: 12/27/2022] Open
Abstract
Recent studies have elucidated the crucial role for microRNAs in peripheral nerve myelination by ablating components of the microRNA synthesis machinery. Few studies have focused on the role of individual microRNAs. To fill this gap, we focused this study on miR-138, which was shown to be drastically reduced in Dicer1 and Dgcr8 knockout mice with hypomyelinating phenotypes and to potentially target the negative regulators of Schwann cell differentiation. Here, we show that of two miR-138 encoding loci, mir-138-1 is the predominant locus transcribed in Schwann cells. mir-138-1 is transcriptionally upregulated during myelination and downregulated upon nerve injury. EGR2 is required for mir-138-1 transcription during development, and both SOX10 and EGR2 bind to an active enhancer near the mir-138-1 locus. Based on expression analyses, we hypothesized that miR-138 facilitates the transition between undifferentiated Schwann cells and myelinating Schwann cells. However, in conditional knockouts, we could not detect significant changes in Schwann cell proliferation, cell cycle exit, or myelination. Overall, our results demonstrate that miR-138 is an Egr2-dependent microRNA but is dispensable for Schwann cell myelination.
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Affiliation(s)
- Hsin-Pin Lin
- Department of Neurology and Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Idil Oksuz
- Department of Neurology and Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - John Svaren
- Waisman Center and Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Rajeshwar Awatramani
- Department of Neurology and Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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14
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Su Z, Zhang Y, Liao B, Zhong X, Chen X, Wang H, Guo Y, Shan Y, Wang L, Pan G. Antagonism between the transcription factors NANOG and OTX2 specifies rostral or caudal cell fate during neural patterning transition. J Biol Chem 2018; 293:4445-4455. [PMID: 29386354 DOI: 10.1074/jbc.m117.815449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 01/29/2018] [Indexed: 01/08/2023] Open
Abstract
During neurogenesis, neural patterning is a critical step during which neural progenitor cells differentiate into neurons with distinct functions. However, the molecular determinants that regulate neural patterning remain poorly understood. Here we optimized the "dual SMAD inhibition" method to specifically promote differentiation of human pluripotent stem cells (hPSCs) into forebrain and hindbrain neural progenitor cells along the rostral-caudal axis. We report that neural patterning determination occurs at the very early stage in this differentiation. Undifferentiated hPSCs expressed basal levels of the transcription factor orthodenticle homeobox 2 (OTX2) that dominantly drove hPSCs into the "default" rostral fate at the beginning of differentiation. Inhibition of glycogen synthase kinase 3β (GSK3β) through CHIR99021 application sustained transient expression of the transcription factor NANOG at early differentiation stages through Wnt signaling. Wnt signaling and NANOG antagonized OTX2 and, in the later stages of differentiation, switched the default rostral cell fate to the caudal one. Our findings have uncovered a mutual antagonism between NANOG and OTX2 underlying cell fate decisions during neural patterning, critical for the regulation of early neural development in humans.
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Affiliation(s)
- Zhenghui Su
- From the School of Life Sciences, University of Science and Technology of China, 230027 Hefei, China.,the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China.,the Hefei Institute of Stem Cell and Regenerative Medicine, 230088 Hefei, China
| | - Yanqi Zhang
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Baojian Liao
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China.,the Hefei Institute of Stem Cell and Regenerative Medicine, 230088 Hefei, China
| | - Xiaofen Zhong
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Xin Chen
- the School of Automation, Guangdong University of Technology, 510006 Guangzhou, China, and
| | - Haitao Wang
- From the School of Life Sciences, University of Science and Technology of China, 230027 Hefei, China
| | - Yiping Guo
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Yongli Shan
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Lihui Wang
- the Department of Pathology, Medical College, Jinan University, 510632 Guangzhou, China
| | - Guangjin Pan
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China, .,the Hefei Institute of Stem Cell and Regenerative Medicine, 230088 Hefei, China
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15
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Clark BS, Blackshaw S. Understanding the Role of lncRNAs in Nervous System Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:253-282. [PMID: 28815543 DOI: 10.1007/978-981-10-5203-3_9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of lncRNAs has expanded within mammals in tandem with the evolution of increased brain complexity, suggesting that lncRNAs play an integral role in this process. In this chapter, we will highlight the identification and characterization of lncRNAs in nervous system development. We discuss the potential role of lncRNAs in nervous system and brain evolution, along with efforts to create comprehensive catalogues that analyze spatial and temporal changes in lncRNA expression during nervous system development. Additionally, we focus on recent endeavors that attempt to assign function to lncRNAs during nervous system development. We highlight discrepancies that have been observed between in vitro and in vivo studies of lncRNA function and the challenges facing researchers in conducting mechanistic analyses of lncRNAs in the developing nervous system. Altogether, this chapter highlights the emerging role of lncRNAs in the developing brain and sheds light on novel, RNA-mediated mechanisms by which nervous system development is controlled.
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Affiliation(s)
- Brian S Clark
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seth Blackshaw
- Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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16
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An Image-Based miRNA Screen Identifies miRNA-135s As Regulators of CNS Axon Growth and Regeneration by Targeting Krüppel-like Factor 4. J Neurosci 2017; 38:613-630. [PMID: 29196317 DOI: 10.1523/jneurosci.0662-17.2017] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/24/2017] [Accepted: 10/29/2017] [Indexed: 01/08/2023] Open
Abstract
During embryonic development, axons extend over long distances to establish functional connections. In contrast, axon regeneration in the adult mammalian CNS is limited in part by a reduced intrinsic capacity for axon growth. Therefore, insight into the intrinsic control of axon growth may provide new avenues for enhancing CNS regeneration. Here, we performed one of the first miRNome-wide functional miRNA screens to identify miRNAs with robust effects on axon growth. High-content screening identified miR-135a and miR-135b as potent stimulators of axon growth and cortical neuron migration in vitro and in vivo in male and female mice. Intriguingly, both of these developmental effects of miR-135s relied in part on silencing of Krüppel-like factor 4 (KLF4), a well known intrinsic inhibitor of axon growth and regeneration. These results prompted us to test the effect of miR-135s on axon regeneration after injury. Our results show that intravitreal application of miR-135s facilitates retinal ganglion cell (RGC) axon regeneration after optic nerve injury in adult mice in part by repressing KLF4. In contrast, depletion of miR-135s further reduced RGC axon regeneration. Together, these data identify a novel neuronal role for miR-135s and the miR-135-KLF4 pathway and highlight the potential of miRNAs as tools for enhancing CNS axon regeneration.SIGNIFICANCE STATEMENT Axon regeneration in the adult mammalian CNS is limited in part by a reduced intrinsic capacity for axon growth. Therefore, insight into the intrinsic control of axon growth may provide new avenues for enhancing regeneration. By performing an miRNome-wide functional screen, our studies identify miR-135s as stimulators of axon growth and neuron migration and show that intravitreal application of these miRNAs facilitates CNS axon regeneration after nerve injury in adult mice. Intriguingly, these developmental and regeneration-promoting effects rely in part on silencing of Krüppel-like factor 4 (KLF4), a well known intrinsic inhibitor of axon regeneration. Our data identify a novel neuronal role for the miR-135-KLF4 pathway and support the idea that miRNAs can be used for enhancing CNS axon regeneration.
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17
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Wang Q, Wang N, Cai R, Zhao F, Xiong Y, Li X, Wang A, Lin P, Jin Y. Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window. Oncotarget 2017; 8:84360-84372. [PMID: 29137430 PMCID: PMC5663602 DOI: 10.18632/oncotarget.21031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/06/2017] [Indexed: 12/17/2022] Open
Abstract
Establishment of the receptive uterus is a crucial step for embryo implantation. In this study, the expression profiles and characterization of long non-coding RNAs (lncRNAs) in pregnant mouse uteri on day 4, day 5 at implantation sites and inter-implantation sites were conducted using RNA-seq. A total of 7,764 putative lncRNA transcripts were identified, including 6,179 known lncRNA transcripts and 1,585 novel lncRNA transcripts. Bioinformatics analysis of the cis and trans lncRNA targets showed that the differentially expressed lncRNAs were mainly involved in tissue remodelling, immune response and metabolism-related processes, indicating that lncRNAs could be involved in the regulation of embryo implantation. We also discovered that differentially expressed lncRNAs might regulate multiple signalling pathways that play an important role in the regulation of embryo implantation. In addition, nine known lncRNAs and four novel lncRNAs were randomly selected and validated by qRT-PCR. The expression of Tug1, Neat1, Gas5, Malat1, H19 and Rmst were significantly regulated in the mouse uterus during the implantation window. Our results are the first to systematically identify lncRNAs in the mouse uterus and provide a catalogue of lncRNAs for further understanding their functions in pregnant mouse uteri during the implantation window.
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Affiliation(s)
- Qi Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Nan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Rui Cai
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fan Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongjie Xiong
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
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18
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Wang P, Mokhtari R, Pedrosa E, Kirschenbaum M, Bayrak C, Zheng D, Lachman HM. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells. Mol Autism 2017; 8:11. [PMID: 28321286 PMCID: PMC5357816 DOI: 10.1186/s13229-017-0124-1] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/15/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND CHD8 (chromodomain helicase DNA-binding protein 8), which codes for a member of the CHD family of ATP-dependent chromatin-remodeling factors, is one of the most commonly mutated genes in autism spectrum disorders (ASD) identified in exome-sequencing studies. Loss of function mutations in the gene have also been found in schizophrenia (SZ) and intellectual disabilities and influence cancer cell proliferation. We previously reported an RNA-seq analysis carried out on neural progenitor cells (NPCs) and monolayer neurons derived from induced pluripotent stem (iPS) cells that were heterozygous for CHD8 knockout (KO) alleles generated using CRISPR-Cas9 gene editing. A significant number of ASD and SZ candidate genes were among those that were differentially expressed in a comparison of heterozygous KO lines (CHD8+/-) vs isogenic controls (CHD8+/-), including the SZ and bipolar disorder (BD) candidate gene TCF4, which was markedly upregulated in CHD8+/- neuronal cells. METHODS In the current study, RNA-seq was carried out on CHD8+/- and isogenic control (CHD8+/+) cerebral organoids, which are 3-dimensional structures derived from iPS cells that model the developing human telencephalon. RESULTS TCF4 expression was, again, significantly upregulated. Pathway analysis carried out on differentially expressed genes (DEGs) revealed an enrichment of genes involved in neurogenesis, neuronal differentiation, forebrain development, Wnt/β-catenin signaling, and axonal guidance, similar to our previous study on NPCs and monolayer neurons. There was also significant overlap in our CHD8+/- DEGs with those found in a transcriptome analysis carried out by another group using cerebral organoids derived from a family with idiopathic ASD. Remarkably, the top DEG in our respective studies was the non-coding RNA DLX6-AS1, which was markedly upregulated in both studies; DLX6-AS1 regulates the expression of members of the DLX (distal-less homeobox) gene family. DLX1 was also upregulated in both studies. DLX genes code for transcription factors that play a key role in GABAergic interneuron differentiation. Significant overlap was also found in a transcriptome study carried out by another group using iPS cell-derived neurons from patients with BD, a condition characterized by dysregulated WNT/β-catenin signaling in a subgroup of affected individuals. CONCLUSIONS Overall, the findings show that distinct ASD, SZ, and BD candidate genes converge on common molecular targets-an important consideration for developing novel therapeutics in genetically heterogeneous complex traits.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
| | - Ryan Mokhtari
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Michael Kirschenbaum
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Can Bayrak
- Erciyes University School of Medicine, Kayseri, Turkey
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
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19
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Nouri N, Awatramani R. A novel floor plate boundary defined by adjacent En1 and Dbx1 microdomains distinguishes midbrain dopamine and hypothalamic neurons. Development 2017; 144:916-927. [PMID: 28174244 DOI: 10.1242/dev.144949] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
The mesodiencephalic floor plate (mdFP) is the source of diverse neuron types. Yet, how this structure is compartmentalized has not been clearly elucidated. Here, we identify a novel boundary subdividing the mdFP into two microdomains, defined by engrailed 1 (En1) and developing brain homeobox 1 (Dbx1). Utilizing simultaneous dual and intersectional fate mapping, we demonstrate that this boundary is precisely formed with minimal overlap between En1 and Dbx1 microdomains, unlike many other boundaries. We show that the En1 microdomain gives rise to dopaminergic (DA) neurons, whereas the Dbx1 microdomain gives rise to subthalamic (STN), premammillary (PM) and posterior hypothalamic (PH) populations. To determine whether En1 is sufficient to induce DA neuron production beyond its normal limit, we generated a mouse strain that expresses En1 in the Dbx1 microdomain. In mutants, we observed ectopic production of DA neurons derived from the Dbx1 microdomain, at the expense of STN and PM populations. Our findings provide new insights into subdivisions in the mdFP, and will impact current strategies for the conversion of stem cells into DA neurons.
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Affiliation(s)
- Navid Nouri
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rajeshwar Awatramani
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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20
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Triozzi PL, Achberger S, Aldrich W, Crabb JW, Saunthararajah Y, Singh AD. Association of tumor and plasma microRNA expression with tumor monosomy-3 in patients with uveal melanoma. Clin Epigenetics 2016; 8:80. [PMID: 27453764 PMCID: PMC4957327 DOI: 10.1186/s13148-016-0243-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/04/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Epigenetic events mediated by methylation and histone modifications have been associated with the development of metastasis in patients with uveal melanoma. The role of epigenetic events mediated by microRNA (miR) is less clear. Tumor and plasma miR expression was examined in patients with primary uveal melanoma with tumor monosomy-3, a predictor of metastasis. RESULTS miR profiling of tumors by microarray found six miRs over-expressed and 19 under-expressed in 33 tumors with monosomy-3 compared to 22 without. None of the miRs differentially expressed in tumors with and without monosomy-3 was differentially expressed in tumors with and without tumor infiltrating lymphocytes. Tumors manifesting monosomy-3 were also characterized by higher levels of TARBP2 and DDX17 and by lower levels of XPO5 and HIWI, miR biogenesis factors. miR profiling of plasma by a quantitative nuclease protection assay found elevated levels of 11 miRs and reduction in four in patients with tumor monosomy-3. Only three miRs differentially expressed in the tumor arrays were detectable in plasma. miRs implicated in uveal melanoma development were not differentially expressed. Elevated plasma levels in patients with tumor monosomy-3 of miR-92b, identified in the tumor array, and of miR-199-5p and miR-223, identified in the plasma array, were confirmed by quantitative real-time polymerase chain reaction. Levels were also higher in patients compared to normal controls. CONCLUSIONS These results support a role for epigenetic mechanisms in the development of metastasis in patients with uveal melanoma and the analysis of miRs as biomarkers of metastatic risk. They also suggest that potentially useful blood miRs may be derived from the host response as well as the tumor.
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Affiliation(s)
- Pierre L Triozzi
- Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH USA ; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157 USA
| | - Susan Achberger
- Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH USA
| | - Wayne Aldrich
- Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH USA
| | - John W Crabb
- Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH USA
| | | | - Arun D Singh
- Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH USA
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