1
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Iwaya C, Yu S, Iwata J. Genes Related to Frontonasal Malformations Are Regulated by miR-338-5p, miR-653-5p, and miR-374-5p in O9-1 Cells. J Dev Biol 2024; 12:19. [PMID: 39051201 PMCID: PMC11270360 DOI: 10.3390/jdb12030019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
Frontonasal malformations are caused by a failure in the growth of the frontonasal prominence during development. Although genetic studies have identified genes that are crucial for frontonasal development, it remains largely unknown how these genes are regulated during this process. Here, we show that microRNAs, which are short non-coding RNAs capable of targeting their target mRNAs for degradation or silencing their expression, play a crucial role in the regulation of genes related to frontonasal development in mice. Using the Mouse Genome Informatics (MGI) database, we curated a total of 25 mouse genes related to frontonasal malformations, including frontonasal hypoplasia, frontonasal dysplasia, and hypotelorism. MicroRNAs regulating the expression of these genes were predicted through bioinformatic analysis. We then experimentally evaluated the top three candidate miRNAs (miR-338-5p, miR-653-5p, and miR-374c-5p) for their effect on cell proliferation and target gene regulation in O9-1 cells, a neural crest cell line. Overexpression of these miRNAs significantly inhibited cell proliferation, and the genes related to frontonasal malformations (Alx1, Lrp2, and Sirt1 for miR-338-5p; Alx1, Cdc42, Sirt1, and Zic2 for miR-374c-5p; and Fgfr2, Pgap1, Rdh10, Sirt1, and Zic2 for miR-653-5p) were directly regulated by these miRNAs in a dose-dependent manner. Taken together, our results highlight miR-338-5p, miR-653-5p, and miR-374c-5p as pathogenic miRNAs related to the development of frontonasal malformations.
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Affiliation(s)
- Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (C.I.); (S.Y.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Sunny Yu
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (C.I.); (S.Y.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (C.I.); (S.Y.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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2
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Feiner N, Yang W, Bunikis I, While GM, Uller T. Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards. SCIENCE ADVANCES 2024; 10:eadk9315. [PMID: 38569035 PMCID: PMC10990284 DOI: 10.1126/sciadv.adk9315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The joint expression of particular colors, morphologies, and behaviors is a common feature of adaptation, but the genetic basis for such "phenotypic syndromes" remains poorly understood. Here, we identified a complex genetic architecture associated with a sexually selected syndrome in common wall lizards, by capitalizing on the adaptive introgression of coloration and morphology into a distantly related lineage. Consistent with the hypothesis that the evolution of phenotypic syndromes in vertebrates is facilitated by developmental linkage through neural crest cells, most of the genes associated with the syndrome are involved in neural crest cell regulation. A major locus was a ~400-kb region, characterized by standing structural genetic variation and previously implied in the evolutionary innovation of coloration and beak size in birds. We conclude that features of the developmental and genetic architecture contribute to maintaining trait integration, facilitating the extensive and rapid introgressive spread of suites of sexually selected characters.
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Affiliation(s)
| | - Weizhao Yang
- Department of Biology, Lund University, Lund, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Geoffrey M. While
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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3
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Pai C, Sengupta R, Heuckeroth RO. Sequencing Reveals miRNAs Enriched in the Developing Mouse Enteric Nervous System. Noncoding RNA 2023; 10:1. [PMID: 38250801 PMCID: PMC10801555 DOI: 10.3390/ncrna10010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/01/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024] Open
Abstract
The enteric nervous system (ENS) is an essential network of neurons and glia in the bowel wall. Defects in ENS development can result in Hirschsprung disease (HSCR), a life-threatening condition characterized by severe constipation, abdominal distention, bilious vomiting, and failure to thrive. A growing body of literature connects HSCR to alterations in miRNA expression, but there are limited data on the normal miRNA landscape in the developing ENS. We sequenced small RNAs (smRNA-seq) and messenger RNAs (mRNA-seq) from ENS precursor cells of mid-gestation Ednrb-EGFP mice and compared them to aggregated RNA from all other cells in the developing bowel. Our smRNA-seq results identified 73 miRNAs that were significantly enriched and highly expressed in the developing ENS, with miR-9, miR-27b, miR-124, miR-137, and miR-488 as our top 5 miRNAs that are conserved in humans. However, contrary to prior reports, our follow-up analyses of miR-137 showed that loss of Mir137 in Nestin-cre, Wnt1-cre, Sox10-cre, or Baf53b-cre lineage cells had no effect on mouse survival or ENS development. Our data provide important context for future studies of miRNAs in HSCR and other ENS diseases and highlight open questions about facility-specific factors in development.
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Affiliation(s)
- Christopher Pai
- The Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA;
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajarshi Sengupta
- American Association for Cancer Research, Philadelphia, PA 19106, USA;
| | - Robert O. Heuckeroth
- The Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA;
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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4
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Bagci O, Tumer S, Altungoz O. Chromosome 1p status in neuroblastoma correlates with higher expression levels of miRNAs targeting neuronal differentiation pathway. In Vitro Cell Dev Biol Anim 2023; 59:100-108. [PMID: 36800078 DOI: 10.1007/s11626-023-00750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
Neuroblastoma (NB) is characterized by acquired segmental and numerical chromosome aberrations. Although deletions of distal 1p and 11q are frequent alterations, no candidate tumor suppressor gene residing in these chromosomal sites could be identified so far. In the present study, we detected the genomic imbalances of six neuroblastoma cell lines using the multiplex ligation-dependent probe amplification (MLPA) technique and the microRNA (miRNA) expression profiles of the cell lines by a microarray study. According to MLPA results, we aimed to assess the miRNA expression profiles of the cell lines harboring 11q and 1p deletions. The cell lines with 1p deletions revealed statistically significant higher levels of expression for 29 miRNAs in contrast to the cell lines without 1p deletion in microarray study. We also performed GO enrichment analysis for predicted targets of the differentially expressed miRNAs. According to GO enrichment analysis, miRNAs that showed the high change in expression was associated with neuronal differentiation. We showed that hsa-miR-494, hsa-miR-495, and hsa-miR-543 target most of mRNAs in neuronal differentiation pathway. Although limited to the cell lines, our results highly suggest that NBs with different segmental chromosome abnormalities may have different dysregulated miRNA expression signatures that target the genes involved in neuronal differentiation.
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Affiliation(s)
- Ozkan Bagci
- Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylul University, 35340, Balcova, Izmir, Turkey.,Department of Medical Genetics, School of Medicine, Selcuk University, Konya, Turkey
| | - Sait Tumer
- Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylul University, 35340, Balcova, Izmir, Turkey.,Acibadem Genetic Diagnosis Center, Istanbul, Turkey
| | - Oguz Altungoz
- Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylul University, 35340, Balcova, Izmir, Turkey.
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5
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Iwaya C, Suzuki A, Iwata J. MicroRNAs and Gene Regulatory Networks Related to Cleft Lip and Palate. Int J Mol Sci 2023; 24:3552. [PMID: 36834963 PMCID: PMC9958963 DOI: 10.3390/ijms24043552] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cleft lip and palate is one of the most common congenital birth defects and has a complex etiology. Either genetic or environmental factors, or both, are involved at various degrees, and the type and severity of clefts vary. One of the longstanding questions is how environmental factors lead to craniofacial developmental anomalies. Recent studies highlight non-coding RNAs as potential epigenetic regulators in cleft lip and palate. In this review, we will discuss microRNAs, a type of small non-coding RNAs that can simultaneously regulate expression of many downstream target genes, as a causative mechanism of cleft lip and palate in humans and mice.
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Affiliation(s)
- Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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6
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Li X, Jin DS, Eadara S, Caterina MJ, Meffert MK. Regulation by noncoding RNAs of local translation, injury responses, and pain in the peripheral nervous system. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2023; 13:100119. [PMID: 36798094 PMCID: PMC9926024 DOI: 10.1016/j.ynpai.2023.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Neuropathic pain is a chronic condition arising from damage to somatosensory pathways that results in pathological hypersensitivity. Persistent pain can be viewed as a consequence of maladaptive plasticity which, like most enduring forms of cellular plasticity, requires altered expression of specific gene programs. Control of gene expression at the level of protein synthesis is broadly utilized to directly modulate changes in activity and responsiveness in nociceptive pathways and provides an effective mechanism for compartmentalized regulation of the proteome in peripheral nerves through local translation. Levels of noncoding RNAs (ncRNAs) are commonly impacted by peripheral nerve injury leading to persistent pain. NcRNAs exert spatiotemporal regulation of local proteomes and affect signaling cascades supporting altered sensory responses that contribute to hyperalgesia. This review discusses ncRNAs found in the peripheral nervous system (PNS) that are dysregulated following nerve injury and the current understanding of their roles in pathophysiological pain-related responses including neuroimmune interactions, neuronal survival and axon regeneration, Schwann cell dedifferentiation and proliferation, intercellular communication, and the generation of ectopic action potentials in primary afferents. We review progress in the field beyond cataloging, with a focus on the relevant target transcripts and mechanisms underlying pain modulation by ncRNAs.
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Affiliation(s)
- Xinbei Li
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
| | - Daniel S. Jin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
| | - Sreenivas Eadara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
| | - Michael J. Caterina
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
- Department of Neurosurgery and Neurosurgery Pain Research Institute, Johns Hopkins University School of Medicine, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, United States
| | - Mollie K. Meffert
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, United States
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7
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Yan S, Peng Y, Lu J, Shakil S, Shi Y, Crossman DK, Johnson WH, Liu S, Rokosh DG, Lincoln J, Wang Q, Jiao K. Differential requirement for DICER1 activity during the development of mitral and tricuspid valves. J Cell Sci 2022; 135:jcs259783. [PMID: 35946425 PMCID: PMC9482344 DOI: 10.1242/jcs.259783] [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: 01/17/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mitral and tricuspid valves are essential for unidirectional blood flow in the heart. They are derived from similar cell sources, and yet congenital dysplasia affecting both valves is clinically rare, suggesting the presence of differential regulatory mechanisms underlying their development. Here, we specifically inactivated Dicer1 in the endocardium during cardiogenesis and found that Dicer1 deletion caused congenital mitral valve stenosis and regurgitation, whereas it had no impact on other valves. We showed that hyperplastic mitral valves were caused by abnormal condensation and extracellular matrix (ECM) remodeling. Our single-cell RNA sequencing analysis revealed impaired maturation of mesenchymal cells and abnormal expression of ECM genes in mutant mitral valves. Furthermore, expression of a set of miRNAs that target ECM genes was significantly lower in tricuspid valves compared to mitral valves, consistent with the idea that the miRNAs are differentially required for mitral and tricuspid valve development. We thus reveal miRNA-mediated gene regulation as a novel molecular mechanism that differentially regulates mitral and tricuspid valve development, thereby enhancing our understanding of the non-association of inborn mitral and tricuspid dysplasia observed clinically.
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Affiliation(s)
- Shun Yan
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Yin Peng
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jin Lu
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Saima Shakil
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Yang Shi
- Department of Population Health Science, and Department of Neuroscience & Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - David K. Crossman
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Walter H. Johnson
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shanrun Liu
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Donald G. Rokosh
- Division of Cardiovascular Disease, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joy Lincoln
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- The Herma Heart Institute, Division of Pediatric Cardiology, Children's Wisconsin, Milwaukee, WI 53226, USA
| | - Qin Wang
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia at Augusta University, August, GA 30912, USA
| | - Kai Jiao
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
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8
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Abstract
Neural crest cells (NCCs) are a dynamic, multipotent, vertebrate-specific population of embryonic stem cells. These ectodermally-derived cells contribute to diverse tissue types in developing embryos including craniofacial bone and cartilage, the peripheral and enteric nervous systems and pigment cells, among a host of other cell types. Due to their contribution to a significant number of adult tissue types, the mechanisms that drive their formation, migration and differentiation are highly studied. NCCs have a unique ability to transition from tightly adherent epithelial cells to mesenchymal and migratory cells by altering their polarity, expression of cell-cell adhesion molecules and gaining invasive abilities. In this Review, we discuss classical and emerging factors driving NCC epithelial-to-mesenchymal transition and migration, highlighting the role of signaling and transcription factors, as well as novel modifying factors including chromatin remodelers, small RNAs and post-translational regulators, which control the availability and longevity of major NCC players.
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Affiliation(s)
| | - Crystal D. Rogers
- Department of Anatomy, Physiology, and Cell Biology, UC Davis School of Veterinary Medicine, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
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9
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Yoshioka H, Suzuki A, Iwaya C, Iwata J. Suppression of microRNA 124-3p and microRNA 340-5p ameliorates retinoic acid-induced cleft palate in mice. Development 2022; 149:275062. [PMID: 35420127 PMCID: PMC9148563 DOI: 10.1242/dev.200476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/25/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex, with genetic and epigenetic, as well as environmental, contributing factors. Recent studies suggest that fetal development is affected by maternal conditions through microRNAs (miRNAs), a group of short noncoding RNAs. Here, we show that miR-129-5p and miR-340-5p suppress cell proliferation in both primary mouse embryonic palatal mesenchymal cells and O9-1 cells, a neural crest cell line, through the regulation of Sox5 and Trp53 by miR-129-5p, and the regulation of Chd7, Fign and Tgfbr1 by miR-340-5p. Notably, miR-340-5p, but not miR-129-5p, was upregulated following all-trans retinoic acid (atRA; tretinoin) administration, and a miR-340-5p inhibitor rescued the cleft palate (CP) phenotype in 47% of atRA-induced CP mice. We have previously reported that a miR-124-3p inhibitor can also partially rescue the CP phenotype in atRA-induced CP mouse model. In this study, we found that a cocktail of miR-124-3p and miR-340-5p inhibitors rescued atRA-induced CP with almost complete penetrance. Taken together, our results suggest that normalization of pathological miRNA expression can be a preventive intervention for CP.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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10
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Antonaci M, Wheeler GN. MicroRNAs in neural crest development and neurocristopathies. Biochem Soc Trans 2022; 50:965-974. [PMID: 35383827 PMCID: PMC9162459 DOI: 10.1042/bst20210828] [Citation(s) in RCA: 5] [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: 10/18/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022]
Abstract
The neural crest (NC) is a vertebrate-specific migratory population of multipotent stem cells that originate during late gastrulation in the region between the neural and non-neural ectoderm. This population of cells give rise to a range of derivatives, such as melanocytes, neurons, chondrocytes, chromaffin cells, and osteoblasts. Because of this, failure of NC development can cause a variety of pathologies, often syndromic, that are globally called neurocristopathies. Many genes are known to be involved in NC development, but not all of them have been identified. In recent years, attention has moved from protein-coding genes to non-coding genes, such as microRNAs (miRNA). There is increasing evidence that these non-coding RNAs are playing roles during embryogenesis by regulating the expression of protein-coding genes. In this review, we give an introduction to miRNAs in general and then focus on some miRNAs that may be involved in NC development and neurocristopathies. This new direction of research will give geneticists, clinicians, and molecular biologists more tools to help patients affected by neurocristopathies, as well as broadening our understanding of NC biology.
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Affiliation(s)
- Marco Antonaci
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR7 7TJ, U.K
| | - Grant N. Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR7 7TJ, U.K
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11
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Godden AM, Antonaci M, Ward NJ, van der Lee M, Abu-Daya A, Guille M, Wheeler GN. An efficient miRNA knockout approach using CRISPR-Cas9 in Xenopus. Dev Biol 2022; 483:66-75. [PMID: 34968443 PMCID: PMC8865746 DOI: 10.1016/j.ydbio.2021.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022]
Abstract
In recent years CRISPR-Cas9 knockouts (KO) have become increasingly ultilised to study gene function. MicroRNAs (miRNAs) are short non-coding RNAs, 20-22 nucleotides long, which affect gene expression through post-transcriptional repression. We previously identified miRNAs-196a and -219 as implicated in the development of Xenopus neural crest (NC). The NC is a multipotent stem-cell population, specified during early neurulation. Following EMT, NC cells migrate to various points in the developing embryo where they give rise to a number of tissues including parts of the peripheral nervous system, pigment cells and craniofacial skeleton. Dysregulation of NC development results in many diseases grouped under the term neurocristopathies. As miRNAs are so small, it is difficult to design CRISPR sgRNAs that reproducibly lead to a KO. We have therefore designed a novel approach using two guide RNAs to effectively 'drop out' a miRNA. We have knocked out miR-196a and miR-219 and compared the results to morpholino knockdowns (KD) of the same miRNAs. Validation of efficient CRISPR miRNA KO and phenotype analysis included use of whole-mount in situ hybridization of key NC and neural plate border markers such as Pax3, Xhe2, Sox10 and Snail2, q-RT-PCR and Sanger sequencing. To show specificity we have also rescued the knockout phenotype using miRNA mimics. MiRNA-219 and miR-196a KO's both show loss of NC, altered neural plate and hatching gland phenotypes. Tadpoles show gross craniofacial and pigment phenotypes.
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Affiliation(s)
- Alice M Godden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Marco Antonaci
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Nicole J Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Michael van der Lee
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Anita Abu-Daya
- King Henry Building, King Henry I St, Portsmouth, PO1 2DY, United Kingdom
| | - Matthew Guille
- King Henry Building, King Henry I St, Portsmouth, PO1 2DY, United Kingdom
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.
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12
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Seelan RS, Pisano MM, Greene RM. MicroRNAs as epigenetic regulators of orofacial development. Differentiation 2022; 124:1-16. [DOI: 10.1016/j.diff.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 11/03/2022]
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13
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Yu X, Li M, Guo C, Wu Y, Zhao L, Shi Q, Song J, Song B. Therapeutic Targeting of Cancer: Epigenetic Homeostasis. Front Oncol 2021; 11:747022. [PMID: 34765551 PMCID: PMC8576334 DOI: 10.3389/fonc.2021.747022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
A large number of studies have revealed that epigenetics plays an important role in cancer development. However, the currently-developed epigenetic drugs cannot achieve a stable curative effect. Thus, it may be necessary to redefine the role of epigenetics in cancer development. It has been shown that embryonic development and tumor development share significant similarities in terms of biological behavior and molecular expression patterns, and epigenetics may be the link between them. Cell differentiation is likely a manifestation of epigenetic homeostasis at the cellular level. In this article, we introduced the importance of epigenetic homeostasis in cancer development and analyzed the shortcomings of current epigenetic treatment regimens. Understanding the dynamic process of epigenetic homeostasis in organ development can help us characterize cancer according to its differentiation stages, explore new targets for cancer treatment, and improve the clinical prognosis of patients with cancer.
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Affiliation(s)
- Xiaoyuan Yu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Menglu Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Chunyan Guo
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuesheng Wu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Li Zhao
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Qinying Shi
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianbo Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Bin Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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14
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Yoshioka H, Li A, Suzuki A, Ramakrishnan SS, Zhao Z, Iwata J. Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice. Hum Mol Genet 2021; 30:1881-1893. [PMID: 34104955 PMCID: PMC8444451 DOI: 10.1093/hmg/ddab151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/17/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
The etiology of cleft lip with/without cleft palate (CL/P), one of the most frequent craniofacial birth defects worldwide, is complicated by contributions of both genetic and environmental factors. Understanding the etiology of these conditions is essential for developing preventive strategies. This study thus aims to identify regulatory networks of microRNAs (miRNAs), transcriptional factors (TFs) and non-TF genes associated with cleft lip (CL) that are conserved in humans and mice. Notably, we found that miR-27b, miR-133b, miR-205, miR-376b and miR-376c were involved in the regulation of CL-associated gene expression in both humans and mice. Among the candidate miRNAs, the overexpression of miR-27b, miR-133b and miR-205, but not miR-376b and miR-376c, significantly inhibited cell proliferation through suppression of CL-associated genes (miR-27b suppressed PAX9 and RARA; miR-133b suppressed FGFR1, PAX7, and SUMO1; and miR-205 suppressed PAX9 and RARA) in cultured human and mouse lip mesenchymal cells. Taken together, our results suggest that elevated expression of miR-27b, miR-133b and miR-205 may play a crucial role in CL through the suppression of genes associated with CL.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Sai Shankar Ramakrishnan
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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15
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Expression of R-spondins/Lgrs in development of movable craniofacial organs. Gene Expr Patterns 2021; 41:119195. [PMID: 34126267 DOI: 10.1016/j.gep.2021.119195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/26/2021] [Accepted: 06/02/2021] [Indexed: 01/26/2023]
Abstract
Wnt signaling plays a critical role in the development of many organs, including the major movable craniofacial organs tongue, lip, and eyelid. Four members of the R-spondin family (Rspo1-4) bind to Lgr4/5/6 to regulate the activation of Wnt signaling. However, it is not fully understood how Rspos/Lgrs regulate Wnt signaling during the development of movable craniofacial organs. To address this question, we examined the expression of Rspos, Lgrs, and Axin2 (major mediator of canonical Wnt signaling) during tongue, lip, and eyelid development. The expression of Axin2, Rspos and Lgrs was observed in many similar regions, suggesting that Rspos likely activate canonical Wnt signaling through the Lgr-dependent pathway in these regions. Lgr expression was not detected in regions where Axin2 and Rspos were expressed, suggesting that Rspos might activate canonical Wnt signaling through the Lgr-independent pathway in these regions. In addition, the expression of Rspos and Lgrs were observed in some other regions where Axin2 was not expressed, suggesting the possibility that Rspos and/or Lgrs are involved in non-canonical Wnt signaling or the Wnt-independent pathway. Thus, we identified a dynamic spatiotemporal expression pattern of Rspos and Lgrs during the development of the eyelid, tongue, and lip.
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16
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Individual and joint effects of genetic polymorphisms in microRNA-machinery genes on congenital heart disease susceptibility. Cardiol Young 2021; 31:965-968. [PMID: 33423710 DOI: 10.1017/s1047951120004874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Single-nucleotide polymorphisms in miRNA-machinery genes may alter the biogenesis of miRNAs affecting disease susceptibility. In this case-control study, we aimed to evaluate the impact of three single-nucleotide polymorphisms (DICER rs1057035, DROSHA rs10719, and XPO5 rs11077) and their combined effect in a genetic risk score model on congenital heart disease (CHD) risk. A total of 639 participants was recruited, including 125 patients with CHD (65 males; age 9.2 ± 10 years) and 514 healthy controls (289 males; age 15.8 ± 18 years). Genotyping of polymorphisms in miRNA-machinery genes was performed using a TaqMan®SNP genotyping assay. A genetic risk score was calculated by summing the number of risk alleles of selected single-nucleotide polymorphisms. There was a significantly increased risk of CHD in patients with XPO5 rs11077 CC genotype as compared to AC heterozygote and AA homozygote patients (ORadjusted = 1.7; 95% CI: 1.1-2.8; p = 0.018). A clear tendency to significance was also found for DROSHA rs10719 AA genotype and CHD risk for both codominant and recessive models (ORadjusted = 1.8; 95% CI: 0.91-3.8; p = 0.09 and ORadjusted = 1.9; 95% CI: 0.92-4; p = 0.08, respectively). The resulting genetic risk score predicted a 1.73 risk for CHD per risk allele (95% CI: 1.2-2.5; p = 0.002). Subjects in the top tertile of genetic risk score were estimated to have more than three-fold increased risk of CHD compared with those in the bottom tertile (ORadjusted = 3.52; 95% CI: 1.4-9; p = 0.009). Our findings show that the genetic variants in miRNA-machinery genes might participate in the development of CHD.
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17
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Trakanant S, Nihara J, Nagai T, Kawasaki M, Kawasaki K, Ishida Y, Meguro F, Kudo T, Yamada A, Maeda T, Saito I, Ohazama A. MicroRNAs regulate distal region of mandibular development through Hh signaling. J Anat 2021; 238:711-719. [PMID: 33011977 PMCID: PMC7855062 DOI: 10.1111/joa.13328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 11/29/2022] Open
Abstract
Mandibular anomalies are often seen in various congenital diseases, indicating that mandibular development is under strict molecular control. Therefore, it is crucial to understand the molecular mechanisms involved in mandibular development. MicroRNAs (miRNAs) are noncoding small single-stranded RNAs that play a critical role in regulating the level of gene expression. We found that the mesenchymal conditional deletion of miRNAs arising from a lack of Dicer (an essential molecule for miRNA processing, Dicerfl/fl ;Wnt1Cre), led to an abnormal groove formation at the distal end of developing mandibles. At E10.5, when the region forms, inhibitors of Hh signaling, Ptch1 and Hhip1 showed increased expression at the region in Dicer mutant mandibles, while Gli1 (a major mediator of Hh signaling) was significantly downregulated in mutant mandibles. These suggest that Hh signaling was downregulated at the distal end of Dicer mutant mandibles by increased inhibitors. To understand whether the abnormal groove formation inDicer mutant mandibles was caused by the downregulation of Hh signaling, mice with a mesenchymal deletion of Hh signaling activity arising from a lack of Smo (an essential molecule for Hh signaling activation, Smofl/fl ;Wnt1Cre) were examined. Smofl/fl ;Wnt1Cre mice showed a similar phenotype in the distal region of their mandibles to those in Dicerfl/fl ;Wnt1Cre mice. We also found that approximately 400 miRNAs were expressed in wild-type mandibular mesenchymes at E10.5, and six microRNAs were identified as miRNAs with binding potential against both Ptch1 and Hhip1. Their expressions at the distal end of the mandible were confirmed by in situ hybridization. This indicates that microRNAs regulate the distal part of mandibular formation at an early stage of development by involving Hh signaling activity through controlling its inhibitor expression level.
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Affiliation(s)
- Supaluk Trakanant
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan,Division of OrthodonticsFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Jun Nihara
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan,Division of OrthodonticsFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Takahiro Nagai
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Maiko Kawasaki
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Katsushige Kawasaki
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan,Center for Advanced Oral ScienceFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Yoko Ishida
- Center for Advanced Oral ScienceFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Fumiya Meguro
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Takehisa Kudo
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan,Division of OrthodonticsFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Akane Yamada
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Takeyasu Maeda
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Isao Saito
- Division of OrthodonticsFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Atsushi Ohazama
- Division of Oral AnatomyFaculty of Dentistry and Graduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
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18
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Yoshioka H, Ramakrishnan SS, Suzuki A, Iwata J. Phenytoin Inhibits Cell Proliferation through microRNA-196a-5p in Mouse Lip Mesenchymal Cells. Int J Mol Sci 2021; 22:1746. [PMID: 33572377 PMCID: PMC7916186 DOI: 10.3390/ijms22041746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/22/2023] Open
Abstract
Cleft lip (CL) is one of the most common birth defects. It is caused by either genetic mutations or environmental factors. Recent studies suggest that environmental factors influence the expression of noncoding RNAs [e.g., microRNA (miRNA)], which can regulate the expression of genes crucial for cellular functions. In this study, we examined which miRNAs are associated with CL. Among 10 candidate miRNAs (miR-98-3p, miR-101a-3p, miR-101b-3p, miR-141-3p, miR-144-3p, miR-181a-5p, miR-196a-5p, miR-196b-5p, miR-200a-3p, and miR-710) identified through our bioinformatic analysis of CL-associated genes, overexpression of miR-181a-5p, miR-196a-5p, miR-196b-5p, and miR-710 inhibited cell proliferation through suppression of genes associated with CL in cultured mouse embryonic lip mesenchymal cells (MELM cells) and O9-1 cells, a mouse cranial neural crest cell line. In addition, we found that phenytoin, an inducer of CL, decreased cell proliferation through miR-196a-5p induction. Notably, treatment with a specific inhibitor for miR-196a-5p restored cell proliferation through normalization of expression of CL-associated genes in the cells treated with phenytoin. Taken together, our results suggest that phenytoin induces CL through miR-196a-5p induction, which suppresses the expression of CL-associated genes.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Sai Shankar Ramakrishnan
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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19
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Kang YN, Fung C, Vanden Berghe P. Gut innervation and enteric nervous system development: a spatial, temporal and molecular tour de force. Development 2021; 148:148/3/dev182543. [PMID: 33558316 DOI: 10.1242/dev.182543] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During embryonic development, the gut is innervated by intrinsic (enteric) and extrinsic nerves. Focusing on mammalian ENS development, in this Review we highlight how important the different compartments of this innervation are to assure proper gut function. We specifically address the three-dimensional architecture of the innervation, paying special attention to the differences in development along the longitudinal and circumferential axes of the gut. We review recent information about the formation of both intrinsic innervation, which is fairly well-known, as well as the establishment of the extrinsic innervation, which, despite its importance in gut-brain signaling, has received much less attention. We further discuss how external microbial and nutritional cues or neuroimmune interactions may influence development of gut innervation. Finally, we provide summary tables, describing the location and function of several well-known molecules, along with some newer factors that have more recently been implicated in the development of gut innervation.
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Affiliation(s)
- Yi-Ning Kang
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
| | - Candice Fung
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
| | - Pieter Vanden Berghe
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
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20
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Iwata J. Gene-Environment Interplay and MicroRNAs in Cleft Lip and Cleft Palate. ORAL SCIENCE INTERNATIONAL 2021; 18:3-13. [PMID: 36855534 PMCID: PMC9969970 DOI: 10.1002/osi2.1072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cleft lip (CL) with/without cleft palate (CP) (hereafter CL/P) is the second most common congenital birth defect, affecting 7.94 to 9.92 children per 10,000 live births worldwide, followed by Down syndrome. An increasing number of genes have been identified as affecting susceptibility and/or as causative genes for CL/P in mouse genetic and chemically-induced CL and CP studies, as well as in human genome-wide association studies and linkage analysis. While marked progress has been made in the identification of genetic and environmental risk factors for CL/P, the interplays between these factors are not yet fully understood. This review aims to summarize our current knowledge of CL and CP from genetically engineered mouse models and environmental factors that have been studied in mice. Understanding the regulatory mechanism(s) of craniofacial development may not only advance our understanding of craniofacial developmental biology, but could also provide approaches for the prevention of birth defects and for tissue engineering in craniofacial tissue regeneration.
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Affiliation(s)
- Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, Texas, 77054 USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, Texas, 77054 USA.,Pediatric Research Center, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, 77030 USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, 77030 USA
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21
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Yoshioka H, Mikami Y, Ramakrishnan SS, Suzuki A, Iwata J. MicroRNA-124-3p Plays a Crucial Role in Cleft Palate Induced by Retinoic Acid. Front Cell Dev Biol 2021; 9:621045. [PMID: 34178974 PMCID: PMC8219963 DOI: 10.3389/fcell.2021.621045] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/05/2021] [Indexed: 01/13/2023] Open
Abstract
Cleft lip with/without cleft palate (CL/P) is one of the most common congenital birth defects, showing the complexity of both genetic and environmental contributions [e.g., maternal exposure to alcohol, cigarette, and retinoic acid (RA)] in humans. Recent studies suggest that epigenetic factors, including microRNAs (miRs), are altered by various environmental factors. In this study, to investigate whether and how miRs are involved in cleft palate (CP) induced by excessive intake of all-trans RA (atRA), we evaluated top 10 candidate miRs, which were selected through our bioinformatic analyses, in mouse embryonic palatal mesenchymal (MEPM) cells as well as in mouse embryos treated with atRA. Among them, overexpression of miR-27a-3p, miR-27b-3p, and miR-124-3p resulted in the significant reduction of cell proliferation in MEPM cells through the downregulation of CP-associated genes. Notably, we found that excessive atRA upregulated the expression of miR-124-3p, but not of miR-27a-3p and miR-27b-3p, in both in vivo and in vitro. Importantly, treatment with a specific inhibitor for miR-124-3p restored decreased cell proliferation through the normalization of target gene expression in atRA-treated MEPM cells and atRA-exposed mouse embryos, resulting in the rescue of CP in mice. Taken together, our results indicate that atRA causes CP through the induction of miR-124-3p in mice.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Yurie Mikami
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Sai Shankar Ramakrishnan
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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22
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Post-transcriptional tuning of FGF signaling mediates neural crest induction. Proc Natl Acad Sci U S A 2020; 117:33305-33316. [PMID: 33376218 DOI: 10.1073/pnas.2009997117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Ectodermal patterning is required for the establishment of multiple components of the vertebrate body plan. Previous studies have demonstrated that precise combinations of extracellular signals induce distinct ectodermal cell populations, such as the neural crest and the neural plate. Yet, we still lack understanding of how the response to inductive signals is modulated to generate the proper transcriptional output in target cells. Here we show that posttranscriptional attenuation of fibroblast growth factor (FGF) signaling is essential for the establishment of the neural crest territory. We found that neural crest progenitors display elevated expression of DICER, which promotes enhanced maturation of a set of cell-type-specific miRNAs. These miRNAs collectively target components of the FGF signaling pathway, a central player in the process of neural induction in amniotes. Inactivation of this posttranscriptional circuit results in a fate switch, in which neural crest cells are converted into progenitors of the central nervous system. Thus, the posttranscriptional attenuation of signaling systems is a prerequisite for proper segregation of ectodermal cell types. These findings demonstrate how posttranscriptional repression may alter the activity of signaling systems to generate distinct spatial domains of progenitor cells.
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23
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Richbourg HA, Hu DP, Xu Y, Barczak AJ, Marcucio RS. miR-199 family contributes to regulation of sonic hedgehog expression during craniofacial development. Dev Dyn 2020; 249:1062-1076. [PMID: 32391617 DOI: 10.1002/dvdy.191] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The frontonasal ectodermal zone (FEZ) is a signaling center that regulates patterned development of the upper jaw, and Sonic hedgehog (SHH) mediates FEZ activity. Induction of SHH expression in the FEZ results from SHH-dependent signals from the brain and neural crest cells. Given the role of miRNAs in modulating gene expression, we investigated the extent to which miRNAs regulate SHH expression and FEZ signaling. RESULTS In the FEZ, the miR-199 family appears to be regulated by SHH-dependent signals from the brain; expression of this family increased from HH18 to HH22, and upon activation of SHH signaling in the brain. However, the miR-199 family is more broadly expressed in the mesenchyme of the frontonasal process and adjacent neuroepithelium. Downregulating the miR-199 genes expanded SHH expression in the FEZ, resulting in wider faces, while upregulating miR-199 genes resulted in decreased SHH expression and narrow faces. Hypoxia inducible factor 1 alpha (HIF1A) and mitogen-activated protein kinase kinase kinase 4 (MAP3K4) appear to be potential targets of miR-199b. Reduction of MAP3K4 altered beak development but increased apoptosis, while reducing HIF1A reduced expression of SHH in the FEZ and produced malformations independent of apoptosis. CONCLUSIONS Our results demonstrate that this miRNA family appears to participate in regulating SHH expression in the FEZ; however, specific molecular mechanisms remain unknown.
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Affiliation(s)
- Heather A Richbourg
- Department of Orthopaedic Surgery, San Francisco General Hospital, University of California, San Francisco, San Francisco, California, USA
| | - Diane P Hu
- Department of Orthopaedic Surgery, San Francisco General Hospital, University of California, San Francisco, San Francisco, California, USA
| | - Yanhua Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Zhejiang University Life Sciences Institute, Hangzhou, China
| | - Andrea J Barczak
- Functional Genomics Core, University of California, San Francisco, San Francisco, California, USA
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, San Francisco General Hospital, University of California, San Francisco, San Francisco, California, USA
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24
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Cardiac Neural Crest Cells: Their Rhombomeric Specification, Migration, and Association with Heart and Great Vessel Anomalies. Cell Mol Neurobiol 2020; 41:403-429. [PMID: 32405705 DOI: 10.1007/s10571-020-00863-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/05/2020] [Indexed: 02/06/2023]
Abstract
Outflow tract abnormalities are the most frequent congenital heart defects. These are due to the absence or dysfunction of the two main cell types, i.e., neural crest cells and secondary heart field cells that migrate in opposite directions at the same stage of development. These cells directly govern aortic arch patterning and development, ascending aorta dilatation, semi-valvular and coronary artery development, aortopulmonary septation abnormalities, persistence of the ductus arteriosus, trunk and proximal pulmonary arteries, sub-valvular conal ventricular septal/rotational defects, and non-compaction of the left ventricle. In some cases, depending on the functional defects of these cells, additional malformations are found in the expected spatial migratory area of the cells, namely in the pharyngeal arch derivatives and cervico-facial structures. Associated non-cardiovascular anomalies are often underestimated, since the multipotency and functional alteration of these cells can result in the modification of multiple neural, epidermal, and cervical structures at different levels. In most cases, patients do not display the full phenotype of abnormalities, but congenital cardiac defects involving the ventricular outflow tract, ascending aorta, aortic arch and supra-aortic trunks should be considered as markers for possible impaired function of these cells. Neural crest cells should not be considered as a unique cell population but on the basis of their cervical rhombomere origins R3-R5 or R6-R7-R8 and specific migration patterns: R3-R4 towards arch II, R5-R6 arch III and R7-R8 arch IV and VI. A better understanding of their development may lead to the discovery of unknown associated abnormalities, thereby enabling potential improvements to be made to the therapeutic approach.
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25
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Cerrizuela S, Vega-Lopez GA, Aybar MJ. The role of teratogens in neural crest development. Birth Defects Res 2020; 112:584-632. [PMID: 31926062 DOI: 10.1002/bdr2.1644] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/11/2019] [Accepted: 12/22/2019] [Indexed: 12/13/2022]
Abstract
The neural crest (NC), discovered by Wilhelm His 150 years ago, gives rise to a multipotent migratory embryonic cell population that generates a remarkably diverse and important array of cell types during the development of the vertebrate embryo. These cells originate in the neural plate border (NPB), which is the ectoderm between the neural plate and the epidermis. They give rise to the neurons and glia of the peripheral nervous system, melanocytes, chondrocytes, smooth muscle cells, odontoblasts and neuroendocrine cells, among others. Neurocristopathies are a class of congenital diseases resulting from the abnormal induction, specification, migration, differentiation or death of NC cells (NCCs) during embryonic development and have an important medical and societal impact. In general, congenital defects affect an appreciable percentage of newborns worldwide. Some of these defects are caused by teratogens, which are agents that negatively impact the formation of tissues and organs during development. In this review, we will discuss the teratogens linked to the development of many birth defects, with a strong focus on those that specifically affect the development of the NC, thereby producing neurocristopathies. Although increasing attention is being paid to the effect of teratogens on embryonic development in general, there is a strong need to critically evaluate the specific role of these agents in NC development. Therefore, increased understanding of the role of these factors in NC development will contribute to the planning of strategies aimed at the prevention and treatment of human neurocristopathies, whose etiology was previously not considered.
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Affiliation(s)
- Santiago Cerrizuela
- Área Biología Experimental, Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Guillermo A Vega-Lopez
- Área Biología Experimental, Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Manuel J Aybar
- Área Biología Experimental, Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
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26
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Gajera M, Desai N, Suzuki A, Li A, Zhang M, Jun G, Jia P, Zhao Z, Iwata J. MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip. BMC Med Genomics 2019; 12:70. [PMID: 31122291 PMCID: PMC6533741 DOI: 10.1186/s12920-019-0535-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Background The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex and involves the contribution of genetic and environmental factors. Although many candidate genes have been identified, the regulation and interaction of these genes in CL/P remain unclear. In addition, the contribution of microRNAs (miRNAs), non-coding RNAs that regulate the expression of multiple genes, to the etiology of CL/P is largely unknown. Methods To identify the signatures of causative biological pathways for human CL/P, we conducted a systematic literature review for human CL/P candidate genes and subsequent bioinformatics analyses. Functional enrichment analyses of the candidate CL/P genes were conducted using the pathway databases GO and KEGG. The miRNA-mediated post-transcriptional regulation of the CL/P candidate genes was analyzed with miRanda, PITA, and TargetScan, and miRTarbase. Genotype-phenotype association analysis was conducted using GWAS. The functional significance of the candidate miRNAs was evaluated experimentally in cell proliferation and target gene regulation assays in human lip fibroblasts. Results Through an extensive search of the main biomedical databases, we mined 177 genes with mutations or association/linkage reported in individuals with CL/P, and considered them as candidate genes for human CL/P. The genotype-phenotype association study revealed that mutations in 12 genes (ABCA4, ADAM3A, FOXE1, IRF6, MSX2, MTHFR, NTN1, PAX7, TP63, TPM1, VAX1, and WNT9B) were significantly associated with CL/P. In addition, our bioinformatics analysis predicted 16 microRNAs (miRNAs) to be post-transcriptional regulators of CL/P genes. To validate the bioinformatics results, the top six candidate miRNAs (miR-124-3p, miR-369-3p, miR-374a-5p, miR-374b-5p, miR-497-5p, and miR-655-3p) were evaluated by cell proliferation/survival assays and miRNA-gene regulation assays in cultured human lip fibroblasts. We found that miR-497-5p and miR-655-3p significantly suppressed cell proliferation in these cells. Furthermore, the expression of the predicted miRNA-target genes was significantly downregulated by either miR-497-5p or miR-655-3p mimic. Conclusion Expression of miR-497-5p and miR-655-3p suppresses cell proliferation through the regulation of human CL/P-candidate genes. This study provides insights into the role of miRNAs in the etiology of CL/P and suggests possible strategies for the diagnosis of CL/P. Electronic supplementary material The online version of this article (10.1186/s12920-019-0535-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mona Gajera
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Neha Desai
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Musi Zhang
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Goo Jun
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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27
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Weiner AMJ, Scampoli NL, Steeman TJ, Dooley CM, Busch-Nentwich EM, Kelsh RN, Calcaterra NB. Dicer1 is required for pigment cell and craniofacial development in zebrafish. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:472-485. [PMID: 30840854 DOI: 10.1016/j.bbagrm.2019.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 12/22/2022]
Abstract
The multidomain RNase III endoribonuclease DICER is required for the generation of most functional microRNAs (miRNAs). Loss of Dicer affects developmental processes at different levels. Here, we characterized the zebrafish Dicer1 mutant, dicer1sa9205, which has a single point mutation induced by N-ethyl-N-nitrosourea mutagenesis. Heterozygous dicer1sa9205 developed normally, being phenotypically indistinguishable from wild-type siblings. Homozygous dicer1sa9205 mutants display smaller eyes, abnormal craniofacial development and aberrant pigmentation. Reduced numbers of both iridophores and melanocytes were observed in the head and ventral trunk of dicer1sa9205 homozygotes; the effect on melanocytes was stronger and detectable earlier in development. The expression of microphthalmia-associated transcription factor a (mitfa), the master gene for melanocytes differentiation, was enhanced in dicer1-depleted fish. Similarly, the expression of SRY-box containing gene 10 (sox10), required for mitfa activation, was higher in mutants than in wild types. In silico and in vivo analyses of either sox10 or mitfa 3'UTRs revealed conserved potential miRNA binding sites likely involved in the post-transcriptional regulation of both genes. Based on these findings, we propose that dicer1 participates in the gene regulatory network governing zebrafish melanocyte differentiation by controlling the expression of mitfa and sox10.
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Affiliation(s)
- Andrea M J Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina.
| | - Nadia L Scampoli
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina
| | - Tomás J Steeman
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina
| | - Christopher M Dooley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Robert N Kelsh
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina.
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Reynolds K, Kumari P, Sepulveda Rincon L, Gu R, Ji Y, Kumar S, Zhou CJ. Wnt signaling in orofacial clefts: crosstalk, pathogenesis and models. Dis Model Mech 2019; 12:12/2/dmm037051. [PMID: 30760477 PMCID: PMC6398499 DOI: 10.1242/dmm.037051] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Diverse signaling cues and attendant proteins work together during organogenesis, including craniofacial development. Lip and palate formation starts as early as the fourth week of gestation in humans or embryonic day 9.5 in mice. Disruptions in these early events may cause serious consequences, such as orofacial clefts, mainly cleft lip and/or cleft palate. Morphogenetic Wnt signaling, along with other signaling pathways and transcription regulation mechanisms, plays crucial roles during embryonic development, yet the signaling mechanisms and interactions in lip and palate formation and fusion remain poorly understood. Various Wnt signaling and related genes have been associated with orofacial clefts. This Review discusses the role of Wnt signaling and its crosstalk with cell adhesion molecules, transcription factors, epigenetic regulators and other morphogenetic signaling pathways, including the Bmp, Fgf, Tgfβ, Shh and retinoic acid pathways, in orofacial clefts in humans and animal models, which may provide a better understanding of these disorders and could be applied towards prevention and treatments.
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Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Priyanka Kumari
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Lessly Sepulveda Rincon
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Ran Gu
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Santosh Kumar
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA .,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
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29
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Epigenetics, cardiovascular disease, and cellular reprogramming. J Mol Cell Cardiol 2019; 128:129-133. [PMID: 30690032 DOI: 10.1016/j.yjmcc.2019.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 12/29/2022]
Abstract
Under the seeming disorder of "junk" sequences the last decade has seen developments in our understanding of non-coding RNA's (ncRNAs). It's a complex revised order and nowhere is this more relevant than in the developing heart whereby old rules have been set aside to make room for new ones. The development of the mammalian heart has been studied at the genetic and cellular level for several decades because these areas were considered ideal control points. As such, detailed mechanisms governing cell lineages are well described. Emerging evidence suggests a complex new order regulated by epigenetic mechanisms mark cardiac cell lineage. Indeed, molecular cardiologists are in the process of shedding light on the roles played by ncRNAs, nucleic acid methylation and histone/chromatin modifications in specific pathologies of the heart. The aim of this article is to discuss some of the recent advances in the field of cardiovascular epigenetics that are related to direct cell reprogramming and repair. As such, we explore ncRNAs as nodes regulating signaling networks and attempt to make sense of regulatory disorder by reinforcing the importance of epigenetic components in the developmental program.
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30
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Nagai T, Trakanant S, Kawasaki M, Kawasaki K, Yamada Y, Watanabe M, Blackburn J, Otsuka-Tanaka Y, Hishinuma M, Kitatmura A, Meguro F, Yamada A, Kodama Y, Maeda T, Zhou Q, Saijo Y, Yasue A, Sharpe PT, Hindges R, Takagi R, Ohazama A. MicroRNAs control eyelid development through regulating Wnt signaling. Dev Dyn 2019; 248:201-210. [PMID: 30653268 DOI: 10.1002/dvdy.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/08/2018] [Accepted: 01/08/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The timing, location, and level of gene expression are crucial for normal organ development, because morphogenesis requires strict genetic control. MicroRNAs (miRNAs) are noncoding small single-stranded RNAs that play a critical role in regulating gene expression level. Although miRNAs are known to be involved in many biological events, the role of miRNAs in organogenesis is not fully understood. Mammalian eyelids fuse and separate during development and growth. In mice, failure of this process results in the eye-open at birth (EOB) phenotype. RESULTS It has been shown that conditional deletion of mesenchymal Dicer (an essential protein for miRNA processing; Dicer fl/fl ;Wnt1Cre) leads to the EOB phenotype with full penetrance. Here, we identified that the up-regulation of Wnt signaling resulted in the EOB phenotype in Dicer mutants. Down-regulation of Fgf signaling observed in Dicer mutants was caused by an inverse relationship between Fgf and Wnt signaling. Shh and Bmp signaling were down-regulated as the secondary effects in Dicer fl/fl ;Wnt1Cre mice. Wnt, Shh, and Fgf signaling were also found to mediate the epithelial-mesenchymal interactions in eyelid development. CONCLUSIONS miRNAs control eyelid development through Wnt. Developmental Dynamics 248:201-210, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Takahiro Nagai
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Division of Oral and Maxillofacial Surgery, Department of Health Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Supaluk Trakanant
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Maiko Kawasaki
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Department of Craniofacial Development and Stem Cell Biology, Dental Institute, Kings College London, London, United Kingdom
| | - Katsushige Kawasaki
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Department of Craniofacial Development and Stem Cell Biology, Dental Institute, Kings College London, London, United Kingdom.,Oral Life Science, Research Center for Advanced Oral Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yurie Yamada
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Oral Life Science, Research Center for Advanced Oral Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Momoko Watanabe
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - James Blackburn
- Department of Craniofacial Development and Stem Cell Biology, Dental Institute, Kings College London, London, United Kingdom
| | - Yoko Otsuka-Tanaka
- Department of Craniofacial Development and Stem Cell Biology, Dental Institute, Kings College London, London, United Kingdom.,Department of Special Needs Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo, Japan
| | - Mitsue Hishinuma
- Department of Special Needs Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo, Japan
| | - Atsushi Kitatmura
- Division of Oral and Maxillofacial Surgery, Department of Health Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Fumiya Meguro
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akane Yamada
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Division of Oral and Maxillofacial Surgery, Department of Health Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yasumitsu Kodama
- Division of Oral and Maxillofacial Surgery, Department of Health Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takeyasu Maeda
- Oral Life Science, Research Center for Advanced Oral Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Faculty of Dental Medicine, University of Airlangga, Surabaya, Indonesia
| | - Qiliang Zhou
- Department of Medical Oncology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yasuo Saijo
- Department of Medical Oncology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akihiro Yasue
- Department of Orthodontics and Dentofacial Orthopedics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima City, Tokushima, Japan
| | - Paul T Sharpe
- Department of Craniofacial Development and Stem Cell Biology, Dental Institute, Kings College London, London, United Kingdom
| | - Robert Hindges
- MRC Centre for Developmental Neurobiology, King's College London, New Hunt's House, Guy's Campus, London, United Kingdom
| | - Ritsuo Takagi
- Division of Oral and Maxillofacial Surgery, Department of Health Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Atsushi Ohazama
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Department of Craniofacial Development and Stem Cell Biology, Dental Institute, Kings College London, London, United Kingdom
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Schoen C, Glennon JC, Abghari S, Bloemen M, Aschrafi A, Carels CEL, Von den Hoff JW. Differential microRNA expression in cultured palatal fibroblasts from infants with cleft palate and controls. Eur J Orthod 2018; 40:90-96. [PMID: 28486694 DOI: 10.1093/ejo/cjx034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background The role of microRNAs (miRNAs) in animal models of palatogenesis has been shown, but only limited research has been carried out in humans. To date, no miRNA expression study on tissues or cells from cleft palate patients has been published. We compared miRNA expression in palatal fibroblasts from cleft palate patients and age-matched controls. Material and Methods Cultured palatal fibroblasts from 10 non-syndromic cleft lip and palate patients (nsCLP; mean age: 18 ± 2 months), 5 non-syndromic cleft palate only patients (nsCPO; mean age: 17 ± 2 months), and 10 controls (mean age: 24 ± 5 months) were analysed with next-generation small RNA sequencing. All subjects are from Western European descent. Sequence reads were bioinformatically processed and the differentially expressed miRNAs were technically validated using quantitative reverse-transcription polymerase chain reaction (RT-qPCR). Results Using RNA sequencing, three miRNAs (hsa-miR-93-5p, hsa-miR-18a-5p, and hsa-miR-92a-3p) were up-regulated and six (hsa-miR-29c-5p, hsa-miR-549a, hsa-miR-3182, hsa-miR-181a-5p, hsa-miR-451a, and hsa-miR-92b-5p) were down-regulated in nsCPO fibroblasts. One miRNA (hsa-miR-505-3p) was down-regulated in nsCLP fibroblasts. Of these, hsa-miR-505-3p, hsa-miR-92a, hsa-miR-181a, and hsa-miR-451a were also differentially expressed using RT-PCR with a higher fold change than in RNAseq. Limitations The small sample size may limit the value of the data. In addition, interpretation of the data is complicated by the fact that biopsy samples are taken after birth, while the origin of the cleft lies in the embryonic period. This, together with possible effects of the culture medium, implies that only cell-autonomous genetic and epigenetic differences might be detected. Conclusions For the first time, we have shown that several miRNAs appear to be dysregulated in palatal fibroblasts from patients with nsCLP and nsCPO. Furthermore, large-scale genomic and expression studies are needed to validate these findings.
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Affiliation(s)
- Christian Schoen
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeffrey C Glennon
- Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Shaghayegh Abghari
- Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjon Bloemen
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institute of Health, Bethesda, USA
| | - Carine E L Carels
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Oral Health Sciences, KU Leuven, University Hospitals, Belgium.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johannes W Von den Hoff
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
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Croizier S, Park S, Maillard J, Bouret SG. Central Dicer-miR-103/107 controls developmental switch of POMC progenitors into NPY neurons and impacts glucose homeostasis. eLife 2018; 7:40429. [PMID: 30311908 PMCID: PMC6203430 DOI: 10.7554/elife.40429] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
Proopiomelanocortin (POMC) neurons are major negative regulators of energy balance. A distinct developmental property of POMC neurons is that they can adopt an orexigenic neuropeptide Y (NPY) phenotype. However, the mechanisms underlying the differentiation of Pomc progenitors remain unknown. Here, we show that the loss of the microRNA (miRNA)-processing enzyme Dicer in POMC neurons causes metabolic defects, an age-dependent decline in the number of PomcmRNA-expressing cells, and an increased proportion of Pomc progenitors acquiring a NPY phenotype. miRNome microarray screening further identified miR-103/107 as candidates that may be involved in the maturation of Pomc progenitors. In vitro inhibition of miR-103/107 causes a reduction in the number of Pomc-expressing cells and increases the proportion of Pomc progenitors differentiating into NPY neurons. Moreover, in utero silencing of miR-103/107 causes perturbations in glucose homeostasis. Together, these data suggest a role for prenatal miR-103/107 in the maturation of Pomc progenitors and glucose homeostasis.
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Affiliation(s)
- Sophie Croizier
- The Saban Research Institute, Developmental Neuroscience Program, Diabetes and Obesity Program, Center for Endocrinology, Diabetes and Metabolism, Children's Hospital Los Angeles, Los Angeles, United States.,Pediatrics, University of Southern California, Los Angeles, California
| | - Soyoung Park
- The Saban Research Institute, Developmental Neuroscience Program, Diabetes and Obesity Program, Center for Endocrinology, Diabetes and Metabolism, Children's Hospital Los Angeles, Los Angeles, United States.,Pediatrics, University of Southern California, Los Angeles, California
| | - Julien Maillard
- The Saban Research Institute, Developmental Neuroscience Program, Diabetes and Obesity Program, Center for Endocrinology, Diabetes and Metabolism, Children's Hospital Los Angeles, Los Angeles, United States.,Pediatrics, University of Southern California, Los Angeles, California.,Jean-Pierre Aubert Research Center, Inserm U1172, Lille 2 University of Health and Law, Lille, France
| | - Sebastien G Bouret
- The Saban Research Institute, Developmental Neuroscience Program, Diabetes and Obesity Program, Center for Endocrinology, Diabetes and Metabolism, Children's Hospital Los Angeles, Los Angeles, United States.,Pediatrics, University of Southern California, Los Angeles, California.,Jean-Pierre Aubert Research Center, Inserm U1172, Lille 2 University of Health and Law, Lille, France
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Sox Genes Show Spatiotemporal Expression during Murine Tongue and Eyelid Development. Int J Dent 2018; 2018:1601363. [PMID: 30402101 PMCID: PMC6198611 DOI: 10.1155/2018/1601363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/03/2018] [Accepted: 08/27/2018] [Indexed: 11/17/2022] Open
Abstract
The tongue is a critical organ, involved in functions such as speaking, swallowing, mastication, and degustation. Although Sox genes are known to play critical roles in many biological processes, including organogenesis, the expression of the Sox family members during tongue development remains unclear. We therefore performed a comparative in situ hybridization analysis of 17 Sox genes (Sox1–14, 17, 18, and 21) during murine tongue development. Sox2, 4, 6, 8, 9, 10, 11, 12, and 21 were found to be expressed in the tongue epithelium, whereas Sox2, 4–6, 8–11, 13, and 21 showed expression in the mesenchyme of the developing tongue. Expression of Sox1, 4, 6, 8–12, and 21 were observed in the developing tongue muscle. Sox5 and 13 showed expression only at E12, while Sox1 expression was observed only on E18. Sox6, 8, 9, and 12 showed expression at several stages. Although the expression of Sox2, 4, 10, 11, and 21 was detected during all the four stages of tongue development, their expression patterns differed among the stages. We thus identified a dynamic spatiotemporal expression pattern of the Sox genes during murine tongue development. To understand whether Sox genes are involved in the development of other craniofacial organs through similar roles to those in tongue development, we also examined the expression of Sox genes in eyelid primordia, which also contain epithelium, mesenchyme, and muscle. However, expression patterns and timing of Sox genes differed between tongue and eyelid development. Sox genes are thus related to organogenesis through different functions in each craniofacial organ.
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34
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Weiner AMJ. MicroRNAs and the neural crest: From induction to differentiation. Mech Dev 2018; 154:98-106. [PMID: 29859253 DOI: 10.1016/j.mod.2018.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 01/06/2023]
Abstract
MicroRNAs are small noncoding RNAs that can control gene expression by base pairing to partially complementary mRNAs. Regulation by microRNAs plays essential roles in diverse biological processes such as neural crest formation during embryonic development. The neural crest is a multipotent cell population that develops from the dorsal neural fold of vertebrate embryos in order to migrate extensively and differentiate into a variety of tissues. Gene regulatory networks that coordinate neural crest cell specification and differentiation have been considerably studied so far. Although it is known that microRNAs play important roles in neural crest development, posttranscriptional regulation by microRNAs has not been deeply characterized yet. This review is focused on the microRNAs identified so far in order to regulate gene expression of neural crest cells during vertebrate development.
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Affiliation(s)
- Andrea M J Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina.
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Salivary microRNAs as new molecular markers in cleft lip and palate: a new frontier in molecular medicine. Oncotarget 2018; 9:18929-18938. [PMID: 29721173 PMCID: PMC5922367 DOI: 10.18632/oncotarget.24838] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding RNAs of about twenty-two nucleotides that regulate gene expression through post-transcriptional control. The purpose of the present study was to identify and describe the salivary miRNAs in cleft lip and palate (CLP) patients comparing them with a control healthy group. Twelve patients (mean age 11.9 ± 2.42 years; 6M/6F) formed the study group. The control group was created selecting twelve healthy subjects matched for age and sex with study group. We recorded differences in miRNA expression profile between the saliva of CLP patients and the control group. Specifically, miR-141, miR-223, and miR-324-3p were mostly deregulated between the study and control groups. Interestingly, these three miRNAs are the regulators of the following genes correlated to cleft palate and lip development: MTHFR, SATB2, PVRL1. The present study showed that collecting saliva samples is a non-invasive procedure and is well accepted by CLP patients. MiRNAs can be easily isolated and identified. The differences in regulation of miR-141, miR-223 and miR-324-3p between the two groups of salivary samples suggest that these molecules are valid prognostic biomarkers and therapy dynamic response indicators, also for the accuracy and non-invasive sampling and dosing system.
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Kumari P, Singh SK, Raman R. A novel non-coding RNA within an intron of CDH2 and association of its SNP with non-syndromic cleft lip and palate. Gene 2018. [PMID: 29524576 DOI: 10.1016/j.gene.2018.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Genome-wide linkage analysis and whole genome sequencing in a Van der Woude syndrome (VWS) family revealed that the SNP, rs539075, within intron 2 of the cadherin 2 gene (CDH2) co-segregated with the disease phenotype. RESULTS A study with nonsyndromic cleft lip with or without cleft palate (NSCL ± P) cases (N = 292) and controls (N = 287) established association of this SNP with NSCL ± P as a risk factor. RT-PCR based expression analysis of the SNP-harbouring region of intron 2 of CDH2 in the clefted lip and/or palate tissues of 16 patients revealed that the mutant allele expressed in all those individuals having it (hetero-/homozygous), whereas the wild type allele expressed in <50% of the samples in which it was present. The intronic transcript was also present in the prospective lip and palate region of 13.5 dpc mouse embryo, detected by RNA in situ hybridization and RT-PCR. CONCLUSIONS These results including the in silico, characterization of the ~200 nt-intronic transcript showed that conformationally it fits best with noncoding small RNA, possibly a precursor of miRNA. Its function in the orofacial organogenesis remains to be elucidated which will enable us to define the role of this mutant ncRNA in the clefting of lip and palate.
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Affiliation(s)
- Priyanka Kumari
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Subodh Kumar Singh
- G. S. Memorial Plastic Surgery Hospital and Trauma Center, Varanasi 221010, Uttar Pradesh, India
| | - Rajiva Raman
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India.
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Functional Redundancy of DICER Cofactors TARBP2 and PRKRA During Murine Embryogenesis Does Not Involve miRNA Biogenesis. Genetics 2018; 208:1513-1522. [PMID: 29467169 PMCID: PMC5887145 DOI: 10.1534/genetics.118.300791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/10/2018] [Indexed: 12/21/2022] Open
Abstract
Several in vitro studies have suggested that canonical microRNA (miRNA) biogenesis requires the DICER cofactors TARBP2 and PRKRA for processing of pre-miRNAs to mature miRNAs. To investigate the roles of TARBP2 and PRKRA in miRNA biogenesis in vivo, and to determine possible functional redundancy, we first compared the phenotypes of Tarbp2 and Prkra single and double mutants. In contrast to Dicer −/− embryos, which die by embryonic day 7.5 (E7.5), single Tarbp2 −/− and Prkra −/− mice survive beyond E7.5 and either die perinatally or survive and exhibit cranial/facial abnormalities, respectively. In contrast, only a few Tarbp2 −/−; Prkra −/− double mutants survived beyond E12.5, suggesting genetic redundancy between Tarbp2 and Prkra during embryonic development. Sequencing of miRNAs from single-mutant embryos at E15.5 revealed changes in abundance and isomiR type in Tarbp2 −/−, but not Prkra −/−, embryos, demonstrating that TARBP2, but not PRKRA, functions in miRNA biogenesis of a subclass of miRNAs, and suggesting that functional redundancy between TARBP2 and PRKRA does not involve miRNA biogenesis.
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Ward NJ, Green D, Higgins J, Dalmay T, Münsterberg A, Moxon S, Wheeler GN. microRNAs associated with early neural crest development in Xenopus laevis. BMC Genomics 2018; 19:59. [PMID: 29347911 PMCID: PMC5774138 DOI: 10.1186/s12864-018-4436-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in order to migrate and differentiate throughout the developing embryo. The derivative cell types give rise to multiple tissues, including the craniofacial skeleton, peripheral nervous system and skin pigment cells. Several well-studied gene regulatory networks underpin NC development, which when disrupted can lead to various neurocristopathies such as craniofrontonasal dysplasia, DiGeorge syndrome and some forms of cancer. Small RNAs, such as microRNAs (miRNAs) are non-coding RNA molecules important in post-transcriptional gene silencing and critical for cellular regulation of gene expression. RESULTS To uncover novel small RNAs in NC development we used high definition adapters and next generation sequencing of libraries derived from ectodermal explants of Xenopus laevis embryos induced to form neural and NC tissue. Ectodermal and blastula animal pole (blastula) stage tissues were also sequenced. We show that miR-427 is highly abundant in all four tissue types though in an isoform specific manner and we define a set of 11 miRNAs that are enriched in the NC. In addition, we show miR-301a and miR-338 are highly expressed in both the NC and blastula suggesting a role for these miRNAs in maintaining the stem cell-like phenotype of NC cells. CONCLUSION We have characterised the miRNAs expressed in Xenopus embryonic explants treated to form ectoderm, neural or NC tissue. This has identified novel tissue specific miRNAs and highlighted differential expression of miR-427 isoforms.
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Affiliation(s)
- Nicole J. Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Janet Higgins
- Regulatory Genomics, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Andrea Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Grant N. Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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Peng C, Furlan A, Zhang MD, Su J, Lübke M, Lönnerberg P, Abdo H, Sontheimer J, Sundström E, Ernfors P. Termination of cell-type specification gene programs by miR-183 cluster determines the population sizes of low threshold mechanosensitive neurons. Development 2018; 145:dev.165613. [DOI: 10.1242/dev.165613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/03/2018] [Indexed: 01/03/2023]
Abstract
Touch and mechanical sensations require the development of several different kinds of sensory neurons dedicated to respond to certain types of mechanical stimuli. The transcription factor Shox2 (short stature homeobox 2) is involved in the generation of TRKB+ low-threshold mechanoreceptors (LTMRs), but mechanisms terminating this program and allowing for alternative fates are unknown. Here, we show that the conditional loss of miR-183-96-182 cluster leads to a failure of extinction of Shox2 during development and an increase in the proportion of Aδ LTMRs (TRKB+/NECAB2+) neurons at the expense of Aβ slowly adapting (SA)-LTMRs (TRKC+/Runx3−) neurons. Conversely, overexpression of miR-183 cluster that represses Shox2 expression, or loss of Shox2, both increases the Aβ SA-LTMRs population at expense of Aδ LTMRs. Our results suggest that the miR-183 cluster determines the timing of Shox2 expression by direct targeting during development, and through this determines the population sizes of Aδ LTMRs and Aβ SA-LTMRs.
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Affiliation(s)
- Changgeng Peng
- The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, 200029 Shanghai, China
| | - Alessandro Furlan
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Ming-Dong Zhang
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jie Su
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Moritz Lübke
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Peter Lönnerberg
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Hind Abdo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jana Sontheimer
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Erik Sundström
- Department of Neurobiology, Care Sciences and Society. Karolinska Institutet, 171777 Stockholm, Sweden
| | - Patrik Ernfors
- Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden
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40
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Duncan KM, Mukherjee K, Cornell RA, Liao EC. Zebrafish models of orofacial clefts. Dev Dyn 2017; 246:897-914. [PMID: 28795449 DOI: 10.1002/dvdy.24566] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/06/2017] [Accepted: 07/31/2017] [Indexed: 12/12/2022] Open
Abstract
Zebrafish is a model organism that affords experimental advantages toward investigating the normal function of genes associated with congenital birth defects. Here we summarize zebrafish studies of genes implicated in orofacial cleft (OFC). The most common use of zebrafish in this context has been to explore the normal function an OFC-associated gene product in craniofacial morphogenesis by inhibiting expression of its zebrafish ortholog. The most frequently deployed method has been to inject embryos with antisense morpholino oligonucleotides targeting the desired transcript. However, improvements in targeted mutagenesis strategies have led to widespread adoption of CRISPR/Cas9 technology. A second application of zebrafish has been for functional assays of gene variants found in OFC patients; such in vivo assays are valuable because the success of in silico methods for testing allele severity has been mixed. Finally, zebrafish have been used to test the tissue specificity of enhancers that harbor single nucleotide polymorphisms associated with risk for OFC. We review examples of each of these approaches in the context of genes that are implicated in syndromic and non-syndromic OFC. Developmental Dynamics 246:897-914, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kaylia M Duncan
- Department of Anatomy and Cell Biology, Molecular and Cell Biology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Kusumika Mukherjee
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, Molecular and Cell Biology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Eric C Liao
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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Xu M, Ma L, Lou S, Du Y, Yin X, Zhang C, Fan L, Wang H, Wang Z, Zhang W, Wang L, Pan Y. Genetic variants of microRNA processing genes and risk of non-syndromic orofacial clefts. Oral Dis 2017; 24:422-428. [PMID: 28833944 DOI: 10.1111/odi.12741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 12/21/2022]
Abstract
OBJECTIVE MicroRNA (miRNA) processing genes play important roles in the craniofacial development. The aim of this study was to explore the associations between single nucleotide polymorphisms (SNPs) of miRNA processing genes with the risk of non-syndromic orofacial clefts (NSOC). METHODS We genotyped 12 potentially functional SNPs from seven miRNA processing genes (GEMIN3, DROSHA, DGCR8, GEMIN4, PIWIL1, XPO5, and DICER) in a case-control study of 602 NSOC cases and 605 controls. RESULTS Two SNPs were associated with the susceptibility of CL/P: rs10719 in DROSHA led to an increased risk of cleft lip with or without palate (CL/P) (GA/AA: p = .024, OR = 1.33, 95% CI = [1.04, 1.70]; GG + GA/AA: p = .037, OR = 1.29, 95% CI = [1.02, 1.63]), while rs493760 in DROSHA (CC/TT: p = .049, OR = 0.58, 95% CI = [0.34, 0.99]) could reduce the risk of CL/P. In addition, rs10719 (A)-rs493760 (C) haplotype contributed to a decreased risk of CL/P (OR = 0.77, 95% CI = [0.63, 0.94]), whereas the rs10719 (G)-rs493760 (C) haplotype contributed to the increased risk of cleft palate only (CPO) (OR = 2.70, 95% CI = [1.15, 6.35]). However, there was no difference observed in these SNPs after the Bonferroni correction. CONCLUSION Taken together, our results provided the potential evidence that rs10719 and rs493760 might contribute to the risk of CL/P and suggested potential genetic basis and mechanisms of CL/P. The lack of association between these SNPs and CPO might be due to the limited sample size of CPO subgroup.
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Affiliation(s)
- M Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - L Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - S Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Y Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - X Yin
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - C Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - L Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - H Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Z Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - W Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - L Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Y Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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Wang N, Wang R, Wang R, Tian Y, Shao C, Jia X, Chen S. The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism. PLoS One 2017; 12:e0181761. [PMID: 28777813 PMCID: PMC5544202 DOI: 10.1371/journal.pone.0181761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/06/2017] [Indexed: 02/02/2023] Open
Abstract
Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish pigmentation are identified. And the miRNA-mRNA regulatory network also provides a solid starting point for further elucidation of fish pigmentation deficiency.
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Affiliation(s)
- Na Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail: (NW); (SLC)
| | - Ruoqing Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Renkai Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yongsheng Tian
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Changwei Shao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Beijing Institute of Genomics, Chinese Academy of Sciences & Liaocheng People’s Hospital, Liaocheng, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail: (NW); (SLC)
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Kara N, Wei C, Commanday AC, Patton JG. miR-27 regulates chondrogenesis by suppressing focal adhesion kinase during pharyngeal arch development. Dev Biol 2017. [PMID: 28625871 PMCID: PMC5582384 DOI: 10.1016/j.ydbio.2017.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cranial neural crest cells are a multipotent cell population that generate all the elements of the pharyngeal cartilage with differentiation into chondrocytes tightly regulated by temporal intracellular and extracellular cues. Here, we demonstrate a novel role for miR-27, a highly enriched microRNA in the pharyngeal arches, as a positive regulator of chondrogenesis. Knock down of miR-27 led to nearly complete loss of pharyngeal cartilage by attenuating proliferation and blocking differentiation of pre-chondrogenic cells. Focal adhesion kinase (FAK) is a key regulator in integrin-mediated extracellular matrix (ECM) adhesion and has been proposed to function as a negative regulator of chondrogenesis. We show that FAK is downregulated in the pharyngeal arches during chondrogenesis and is a direct target of miR-27. Suppressing the accumulation of FAK in miR-27 morphants partially rescued the severe pharyngeal cartilage defects observed upon knock down of miR-27. These data support a crucial role for miR-27 in promoting chondrogenic differentiation in the pharyngeal arches through regulation of FAK.
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Affiliation(s)
- Nergis Kara
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Chunyao Wei
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Alexander C Commanday
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States.
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44
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Atsawasuwan P, Ouibaidin M, Dalal B, Khan H, Mohammed A. Calvarial bone development and suture closure in Dicer
-deficient mice. Orthod Craniofac Res 2017. [DOI: 10.1111/ocr.12169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- P. Atsawasuwan
- Department of Orthodontics; University of Illinois at Chicago; Chicago Illinois USA
| | - M. Ouibaidin
- Department of Orthodontics; University of Illinois at Chicago; Chicago Illinois USA
| | - B. Dalal
- Department of Orthodontics; University of Illinois at Chicago; Chicago Illinois USA
| | - H. Khan
- Department of Orthodontics; University of Illinois at Chicago; Chicago Illinois USA
| | - A. Mohammed
- Department of Orthodontics; University of Illinois at Chicago; Chicago Illinois USA
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45
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Schoen C, Aschrafi A, Thonissen M, Poelmans G, Von den Hoff JW, Carels CEL. MicroRNAs in Palatogenesis and Cleft Palate. Front Physiol 2017; 8:165. [PMID: 28420997 PMCID: PMC5378724 DOI: 10.3389/fphys.2017.00165] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/06/2017] [Indexed: 01/01/2023] Open
Abstract
Palatogenesis requires a precise spatiotemporal regulation of gene expression, which is controlled by an intricate network of transcription factors and their corresponding DNA motifs. Even minor perturbations of this network may cause cleft palate, the most common congenital craniofacial defect in humans. MicroRNAs (miRNAs), a class of small regulatory non-coding RNAs, have elicited strong interest as key regulators of embryological development, and as etiological factors in disease. MiRNAs function as post-transcriptional repressors of gene expression and are therefore able to fine-tune gene regulatory networks. Several miRNAs are already identified to be involved in congenital diseases. Recent evidence from research in zebrafish and mice indicates that miRNAs are key factors in both normal palatogenesis and cleft palate formation. Here, we provide an overview of recently identified molecular mechanisms underlying palatogenesis involving specific miRNAs, and discuss how dysregulation of these miRNAs may result in cleft palate.
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Affiliation(s)
- Christian Schoen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of HealthBethesda, MD, USA
| | - Michelle Thonissen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegen, Netherlands.,Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences, Radboud UniversityNijmegen, Netherlands
| | - Johannes W Von den Hoff
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Carine E L Carels
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Oral Health Sciences, University Hospitals-KU LeuvenLeuven, Belgium
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46
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O'Toole SM, Ferrer MM, Mekonnen J, Zhang H, Shima Y, Ladle DR, Nelson SB. Dicer maintains the identity and function of proprioceptive sensory neurons. J Neurophysiol 2016; 117:1057-1069. [PMID: 28003412 DOI: 10.1152/jn.00763.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022] Open
Abstract
Neuronal cell identity is established during development and must be maintained throughout an animal's life (Fishell G, Heintz N. Neuron 80: 602-612, 2013). Transcription factors critical for establishing neuronal identity can be required for maintaining it (Deneris ES, Hobert O. Nat Neurosci 17: 899-907, 2014). Posttranscriptional regulation also plays an important role in neuronal differentiation (Bian S, Sun T. Mol Neurobiol 44: 359-373, 2011), but its role in maintaining cell identity is less established. To better understand how posttranscriptional regulation might contribute to cell identity, we examined the proprioceptive neurons in the dorsal root ganglion (DRG), a highly specialized sensory neuron class, with well-established properties that distinguish them from other neurons in the ganglion. By conditionally ablating Dicer in mice, using parvalbumin (Pvalb)-driven Cre recombinase, we impaired posttranscriptional regulation in the proprioceptive sensory neuron population. Knockout (KO) animals display a progressive form of ataxia at the beginning of the fourth postnatal week that is accompanied by a cell death within the DRG. Before cell loss, expression profiling shows a reduction of proprioceptor specific genes and an increased expression of nonproprioceptive genes normally enriched in other ganglion neurons. Furthermore, although central connections of these neurons are intact, the peripheral connections to the muscle are functionally impaired. Posttranscriptional regulation is therefore necessary to retain the transcriptional identity and support functional specialization of the proprioceptive sensory neurons.NEW & NOTEWORTHY We have demonstrated that selectively impairing Dicer in parvalbumin-positive neurons, which include the proprioceptors, triggers behavioral changes, a lack of muscle connectivity, and a loss of transcriptional identity as observed through RNA sequencing. These results suggest that Dicer and, most likely by extension, microRNAs are crucially important for maintaining proprioception. Additionally, this study hints at the larger question of how neurons maintain their functional and molecular specificity.
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Affiliation(s)
- Sean M O'Toole
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Monica M Ferrer
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Jennifer Mekonnen
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Haihan Zhang
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Yasuyuki Shima
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - David R Ladle
- Department of Neuroscience, Cell Biology, and Physiology, Wright State University, Dayton, Ohio
| | - Sacha B Nelson
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
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Constantin L. The Role of MicroRNAs in Cerebellar Development and Autism Spectrum Disorder During Embryogenesis. Mol Neurobiol 2016; 54:6944-6959. [PMID: 27774573 DOI: 10.1007/s12035-016-0220-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/12/2016] [Indexed: 02/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNA molecules with wide-ranging and subtle effects on protein production. Their activity during the development of the cerebellum provides a valuable exemplar of how non-coding molecules may assist the development and function of the central nervous system and drive neurodevelopmental disorders. Three distinct aspects of miRNA contribution to early cerebellar development will here be reviewed. Aspects are the establishment of the cerebellar anlage, the generation and maturation of at least two principal cell types of the developing cerebellar microcircuit, and the etiology and early progression of autism spectrum disorder. It will be argued here that the autism spectrum is an adept model to explore miRNA impact on the cognitive and affective processes that descend from the developing cerebellum.
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Affiliation(s)
- Lena Constantin
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia. .,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
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48
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Regulatory non-coding RNA: new instruments in the orchestration of cell death. Cell Death Dis 2016; 7:e2333. [PMID: 27512954 PMCID: PMC5108314 DOI: 10.1038/cddis.2016.210] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/10/2016] [Accepted: 06/20/2016] [Indexed: 01/17/2023]
Abstract
Non-coding RNA (ncRNA) comprises a substantial portion of primary transcripts that are generated by genomic transcription, but are not translated into protein. The possible functions of these once considered ‘junk' molecules have incited considerable interest and new insights have emerged. The two major members of ncRNAs, namely micro RNA (miRNA) and long non-coding RNA (lncRNA), have important regulatory roles in gene expression and many important physiological processes, which has recently been extended to programmed cell death. The previous paradigm of programmed cell death only by apoptosis has recently expanded to include modalities of regulated necrosis (RN), and particularly necroptosis. However, most research efforts in this field have been on protein regulators, leaving the role of ncRNAs largely unexplored. In this review, we discuss important findings concerning miRNAs and lncRNAs that modulate apoptosis and RN pathways, as well as the miRNA–lncRNA interactions that affect cell death regulation.
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Ding HL, Hooper JE, Batzel P, Eames BF, Postlethwait JH, Artinger KB, Clouthier DE. MicroRNA Profiling during Craniofacial Development: Potential Roles for Mir23b and Mir133b. Front Physiol 2016; 7:281. [PMID: 27471470 PMCID: PMC4943961 DOI: 10.3389/fphys.2016.00281] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/21/2016] [Indexed: 01/01/2023] Open
Abstract
Defects in mid-facial development, including cleft lip/palate, account for a large number of human birth defects annually. In many cases, aberrant gene expression results in either a reduction in the number of neural crest cells (NCCs) that reach the frontonasal region and form much of the facial skeleton or subsequent failure of NCC patterning and differentiation into bone and cartilage. While loss of gene expression is often associated with developmental defects, aberrant upregulation of expression can also be detrimental. microRNAs (miRNAs) are a class of non-coding RNAs that normally repress gene expression by binding to recognition sequences located in the 3′ UTR of target mRNAs. miRNAs play important roles in many developmental systems, including midfacial development. Here, we take advantage of high throughput RNA sequencing (RNA-seq) from different tissues of the developing mouse midface to interrogate the miRs that are expressed in the midface and select a subset for further expression analysis. Among those examined, we focused on four that showed the highest expression level in in situ hybridization analysis. Mir23b and Mir24.1 are specifically expressed in the developing mouse frontonasal region, in addition to areas in the perichondrium, tongue musculature and cranial ganglia. Mir23b is also expressed in the palatal shelves and in anterior epithelium of the palate. In contrast, Mir133b and Mir128.2 are mainly expressed in head and trunk musculature. Expression analysis of mir23b and mir133b in zebrafish suggests that mir23b is expressed in the pharyngeal arch, otic vesicle, and trunk muscle while mir133b is similarly expressed in head and trunk muscle. Functional analysis by overexpression of mir23b in zebrafish leads to broadening of the ethmoid plate and aberrant cartilage structures in the viscerocranium, while overexpression of mir133b causes a reduction in ethmoid plate size and a significant midfacial cleft. These data illustrate that miRs are expressed in the developing midface and that Mir23b and Mir133b may have roles in this developmental process.
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Affiliation(s)
- Hai-Lei Ding
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus Aurora, CO, USA
| | - Joan E Hooper
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus Aurora, CO, USA
| | - Peter Batzel
- Department of Neuroscience, University of Oregon Eugene, OR, USA
| | - B Frank Eames
- Department of Neuroscience, University of OregonEugene, OR, USA; Department of Anatomy and Cell Biology, University of SaskatchewanSaskatoon, SK, Canada
| | | | - Kristin B Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus Aurora, CO, USA
| | - David E Clouthier
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus Aurora, CO, USA
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50
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Mohanty V, Shah A, Allender E, Siddiqui MR, Monick S, Ichi S, Mania-Farnell B, G McLone D, Tomita T, Mayanil CS. Folate Receptor Alpha Upregulates Oct4, Sox2 and Klf4 and Downregulates miR-138 and miR-let-7 in Cranial Neural Crest Cells. Stem Cells 2016; 34:2721-2732. [PMID: 27300003 DOI: 10.1002/stem.2421] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/09/2016] [Accepted: 05/28/2016] [Indexed: 12/20/2022]
Abstract
Prenatal folic acid (FA) supplementation prevents neural tube defects. Folate receptor alpha (FRα) is critical for embryonic development, including neural crest (NC) development. Previously we showed that FRα translocates to the nucleus in response to FA, where it acts as a transcription factor. In this study, we examined if FA through interaction with FRα regulates stem cell characteristics of cranial neural crest cells (CNCCs)-critical for normal development. We hypothesized that FRα upregulates coding genes and simultaneously downregulates non-coding miRNA which targets coding genes in CNCCs. Quantitative RT-PCR and chromatin immunoprecipitation showed that FRα upregulates Oct4, Sox2, and Klf4 by binding to their cis-regulator elements-5' enhancer/promoters defined by H3K27Ac and p300 occupancy. FA via FRα downregulates miRNAs, miR-138 and miR-let-7, which target Oct4 and Trim71 (an Oct4 downstream effector), respectively. Co-immunoprecipitation data suggests that FRα interacts with the Drosha-DGCR8 complex to affect pre-miRNA processing. Transfecting anti-miR-138 or anti-miR-let-7 into non-proliferating neural crest cells (NCCs) derived from Splotch (Sp-/- ), restored their proliferation potential. In summary, these results suggest a novel pleiotropic role of FRα: (a) direct activation of Oct4, Sox2, and Klf4 genes; and (b) repression of biogenesis of miRNAs that target these genes or their effector molecules. Stem Cells 2016;34:2721-2732.
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Affiliation(s)
- Vineet Mohanty
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amar Shah
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elise Allender
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - M Rizwan Siddiqui
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sarah Monick
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shunsuke Ichi
- Department of Neurosurgery, Japanese Red Cross Medical Center, Shibuya-Ku, Tokyo, Japan
| | | | - David G McLone
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tadanori Tomita
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chandra Shekhar Mayanil
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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