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Upreti A, Hoang TV, Li M, Tangeman JA, Dierker DS, Wagner BD, Tsonis PA, Liang C, Lachke SA, Robinson ML. miR-26 Deficiency Causes Alterations in Lens Transcriptome and Results in Adult-Onset Cataract. Invest Ophthalmol Vis Sci 2024; 65:42. [PMID: 38683565 PMCID: PMC11059818 DOI: 10.1167/iovs.65.4.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Despite strong evidence demonstrating that normal lens development requires regulation governed by microRNAs (miRNAs), the functional role of specific miRNAs in mammalian lens development remains largely unexplored. Methods A comprehensive analysis of miRNA transcripts in the newborn mouse lens, exploring both differential expression between lens epithelial cells and lens fiber cells and overall miRNA abundance, was conducted by miRNA sequencing. Mouse lenses lacking each of three abundantly expressed lens miRNAs (miR-184, miR-26, and miR-1) were analyzed to explore the role of these miRNAs in lens development. Results Mice lacking all three copies of miR-26 (miR-26TKO) developed postnatal cataracts as early as 4 to 6 weeks of age. RNA sequencing analysis of neonatal lenses from miR-26TKO mice exhibited abnormal reduced expression of a cohort of genes found to be lens enriched and linked to cataract (e.g., Foxe3, Hsf4, Mip, Tdrd7, and numerous crystallin genes) and abnormal elevated expression of genes related to neural development (Lhx3, Neurod4, Shisa7, Elavl3), inflammation (Ccr1, Tnfrsf12a, Csf2ra), the complement pathway, and epithelial to mesenchymal transition (Tnfrsf1a, Ccl7, Stat3, Cntfr). Conclusions miR-1, miR-184, and miR-26 are each dispensable for normal embryonic lens development. However, loss of miR-26 causes lens transcriptome changes and drives cataract formation.
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Affiliation(s)
- Anil Upreti
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, Ohio, United States
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
| | - Thanh V. Hoang
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, Ohio, United States
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
| | - Minghua Li
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
| | - Jared A. Tangeman
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, Ohio, United States
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
| | - David S. Dierker
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
| | - Brad D. Wagner
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
| | | | - Chun Liang
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States
| | - Michael L. Robinson
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, Ohio, United States
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, Ohio, United States
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Upreti A, Hoang TV, Li M, Tangeman JA, Dierker DS, Wagner BD, Tsonis PA, Liang C, Lachke SA, Robinson ML. miR-26 deficiency causes alterations in lens transcriptome and results in adult-onset cataract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577818. [PMID: 38352453 PMCID: PMC10862774 DOI: 10.1101/2024.01.29.577818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Purpose Despite strong evidence demonstrating that normal lens development requires regulation governed by miRNAs, the functional role of specific miRNAs in mammalian lens development remains largely unexplored. Methods A comprehensive analysis of miRNA transcripts in the newborn mouse lens, exploring both differential expression between lens epithelial cells and lens fiber cells and overall miRNA abundance was conducted by miRNA-seq. Mouse lenses lacking each of three abundantly expressed lens miRNAs: miR-184, miR-26 and miR-1 were analyzed to explore the role of these miRNAs in lens development. Results Mice lacking all three copies of miR-26 (miR-26TKO) developed postnatal cataracts as early as 4-6 weeks of age. RNA-seq analysis of neonatal lenses from miR-26TKO mice exhibited abnormal reduced expression of a cohort of genes found to be lens-enriched and linked to cataract (e.g. Foxe3, Hsf4, Mip, Tdrd7, and numerous crystallin genes), and abnormal elevated expression of genes related to neural development (Lhx3, Neurod4, Shisa7, Elavl3 ), inflammation (Ccr1, Tnfrsf12a, Csf2ra), the complement pathway, and epithelial to mesenchymal transition (Tnfrsf1a, Ccl7, Stat3, Cntfr). Conclusion miR-1, miR-184 and miR-26 are each dispensable for normal embryonic lens development. However, loss of miR-26 causes lens transcriptome changes and drives cataract formation.
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Affiliation(s)
- Anil Upreti
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Thanh V Hoang
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Minghua Li
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jared A Tangeman
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - David S Dierker
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Brad D Wagner
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | | | - Chun Liang
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Michael L Robinson
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
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Chen S, Zhang C, Shen L, Hu J, Chen X, Yu Y. Noncoding RNAs in cataract formation: star molecules emerge in an endless stream. Pharmacol Res 2022; 184:106417. [PMID: 36038044 DOI: 10.1016/j.phrs.2022.106417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
For decades, research on the pathological mechanism of cataracts has usually focused on the abnormal protein changes caused by a series of risk factors. However, an entire class of molecules, termed non-coding RNA (ncRNA), was discovered in recent years and proven to be heavily involved in cataract formation. Recent studies have recognized the key regulatory roles of ncRNAs in cataracts by shaping cellular activities such as proliferation, apoptosis, migration and epithelial-mesenchymal transition (EMT). This review summarizes our current insight into the biogenesis, properties and functions of ncRNAs and then discusses the development of research on ncRNAs in cataracts. Considering the significant role of ncRNA in cataract formation, research on novel associated regulatory mechanisms is urgently needed, and the development of therapeutic alternatives for the treatment of cataracts seems promising.
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Affiliation(s)
- Silong Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Chengshou Zhang
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Lifang Shen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Jianghua Hu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Department of Ophthalmology, Jiande Branch, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, China.
| | - Yibo Yu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China.
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4
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Stunf Pukl S. Are miRNAs Dynamic Biomarkers in Keratoconus? A Review of the Literature. Genes (Basel) 2022; 13:genes13040588. [PMID: 35456395 PMCID: PMC9025197 DOI: 10.3390/genes13040588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
Aim: A review of miRNA (microRNA) profiling studies in keratoconus. Methods: Literature search strategy—PubMed central database, using miRNA or microRNA and keratoconus as keywords. Results: Eleven experimental or clinical studies on humans regarding miRNA and keratoconus, published in English between 2009 and 2020 were retrieved. Conclusion: The publications regarding the role of miRNAs in keratoconus are scarce and diverse but provide some valuable information about potential new mechanisms of keratoconus development and progression. The cornea expresses almost 300 different miRNAs, 18 of which are specific, and miR-184 is by far the most abundant, with expression restricted to central basal and suprabasal epithelial cells. Mutations in the seed region of MIR184 were proved to be rare and nonspecific in patients with isolated keratoconus. Overall, in keratoconus, a total of 29 miRNAs were upregulated, and 11 were downregulated. It appeared that miR-143-3p, miR-182-5p, and miR-92a-3p were highly expressed, while the miRNAs connected to cell–cell junction, cell division, and motor activity were downregulated. In less advanced forms, altered expression of four miRNAs—miR-151a-3p, miR-194-5p, miR-195-5p, miR-185-5p—was proved in the cone epithelium; in contrast, in advanced keratoconus, the expression of miR-151a-3p and miR-194-5p remained altered, changes in the expression of miR-195 and miR-185 were not reported, and the expression of miR-138-5p, miR-146b-5p, miR-28-5p, and miR-181a-2-3p was also altered in the corneal epithelium. Keratoconus is a dynamic process of corneal stromal thinning that might result from a dynamic miRNA expression in the corneal epithelium exposed to environmental and behavioral factors causing repetitive traumas. Further experimental studies are needed to prove this hypothesis.
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Affiliation(s)
- Spela Stunf Pukl
- Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; ; Tel.: +386-41-382-487
- Eye Hospital, University Clinical Center Ljubljana, 1000 Ljubljana, Slovenia
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5
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Barnum CE, Al Saai S, Patel SD, Cheng C, Anand D, Xu X, Dash S, Siddam AD, Glazewski L, Paglione E, Polson SW, Chuma S, Mason RW, Wei S, Batish M, Fowler VM, Lachke SA. The Tudor-domain protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 (HSP27) and lens fiber cell morphology. Hum Mol Genet 2020; 29:2076-2097. [PMID: 32420594 PMCID: PMC7390939 DOI: 10.1093/hmg/ddaa096] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/10/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations of the RNA granule component TDRD7 (OMIM: 611258) cause pediatric cataract. We applied an integrated approach to uncover the molecular pathology of cataract in Tdrd7-/- mice. Early postnatal Tdrd7-/- animals precipitously develop cataract suggesting a global-level breakdown/misregulation of key cellular processes. High-throughput RNA sequencing integrated with iSyTE-bioinformatics analysis identified the molecular chaperone and cytoskeletal modulator, HSPB1, among high-priority downregulated candidates in Tdrd7-/- lens. A protein fluorescence two-dimensional difference in-gel electrophoresis (2D-DIGE)-coupled mass spectrometry screen also identified HSPB1 downregulation, offering independent support for its importance to Tdrd7-/- cataractogenesis. Lens fiber cells normally undergo nuclear degradation for transparency, posing a challenge: how is their cell morphology, also critical for transparency, controlled post-nuclear degradation? HSPB1 functions in cytoskeletal maintenance, and its reduction in Tdrd7-/- lens precedes cataract, suggesting cytoskeletal defects may contribute to Tdrd7-/- cataract. In agreement, scanning electron microscopy (SEM) revealed abnormal fiber cell morphology in Tdrd7-/- lenses. Further, abnormal phalloidin and wheat germ agglutinin (WGA) staining of Tdrd7-/- fiber cells, particularly those exhibiting nuclear degradation, reveals distinct regulatory mechanisms control F-actin cytoskeletal and/or membrane maintenance in post-organelle degradation maturation stage fiber cells. Indeed, RNA immunoprecipitation identified Hspb1 mRNA in wild-type lens lysate TDRD7-pulldowns, and single-molecule RNA imaging showed co-localization of TDRD7 protein with cytoplasmic Hspb1 mRNA in differentiating fiber cells, suggesting that TDRD7-ribonucleoprotein complexes may be involved in optimal buildup of key factors. Finally, Hspb1 knockdown in Xenopus causes eye/lens defects. Together, these data uncover TDRD7's novel upstream role in elevation of stress-responsive chaperones for cytoskeletal maintenance in post-nuclear degradation lens fiber cells, perturbation of which causes early-onset cataracts.
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Affiliation(s)
- Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salma Al Saai
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shaili D Patel
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Catherine Cheng
- School of Optometry, Indiana University, Bloomington, IN 47405, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Lisa Glazewski
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Emily Paglione
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shawn W Polson
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Shinichiro Chuma
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Robert W Mason
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Velia M Fowler
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
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6
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Amini-Farsani Z, Asgharzade S. The impact of miR-183/182/96 gene regulation on the maturation, survival, and function of photoreceptor cells in the retina. J Comp Neurol 2019; 528:1616-1625. [PMID: 31785157 DOI: 10.1002/cne.24833] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
MicroRNAs (MiRNAs) play important roles in posttranscriptional processes to regulate gene expression. MiRNAs control various biological processes, such as growth, development, and differentiation. The continuous physiological function of photoreceptors and retinal pigment epithelium requires precise regulation to maintain their homeostasis and function; hence, these cells are highly susceptible to premature death in retinal degenerative disorders. MiRNAs are essential for the retinal cell maturation and function; the miR-183 cluster represents one of the most important regulatory factors for the photoreceptor cells. Various studies together with bioinformatics analyses have shown that many genes contributing to the differentiation pathway of photoreceptors are targets of the miR-183 cluster, and the miR-183 cluster dysregulation causes certain defects in the differentiation of the photoreceptors and other retinal neurons by influencing the expression of target genes. Misexpression of miR-183 cluster in the human retinal epithelial cells leads to the reprogramming and transformation of these cells to neuron- and photoreceptor-like cells, which are associated with the expression of neuron- and photoreceptor-specific markers in human retinal pigment epitheliums cells. The knockout of this cluster causes the destruction of the outer segment of the photoreceptors, which subsequently causes the cells to exhibit severe susceptibility to light and eventually degenerate. Hundreds of target genes in this family are likely to affect the development and maintenance of the retina. Identifying the genes that are regulated by the miRNA-183 cluster provides researchers with important insights into the complex development and regeneration mechanism of the retina and may offer a new way for maintaining and regenerating photoreceptor cells in neurodegenerative diseases.
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Affiliation(s)
- Zeinab Amini-Farsani
- Young Researchers and Elites Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Samira Asgharzade
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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7
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MicroRNA-34a suppresses human lens epithelial cell proliferation and migration via downregulation of c-Met. Clin Chim Acta 2019; 495:326-330. [PMID: 30980790 DOI: 10.1016/j.cca.2019.04.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/09/2019] [Indexed: 01/07/2023]
Abstract
MicroRNAs (miRNAs) are endogenously expressed, non-coding, small RNAs which inhibit protein translation through binding to target mRNAs. Recent studies have demonstrated that miRNAs participate in the regulation of a variety of cell structures and functions including those for cell proliferation and migration. MicroRNA-34a (miR-34a), a potential effector of the p53 tumor suppressor gene, is extensively studied for its suppression of cell growth. In the present study, we investigated the function of miR-34a in human lens epithelial cells. Following confirming that miR-34a expression was increased in a P53 dependent manner in human lens epithelial cells after treatment with doxorubicin, we demonstrated that overexpression of miR-34a in the human lens epithelial cell line HLE B3 led to a significant decrease in cell proliferation and migration, with the use of MTS and transwell migration assays. Moreover, HGF enhanced the proliferation and migration of human lens epithelial cells. miR-34a was found to downregulate the expression of c-Met protein by Western blotting. Furthermore, overexpression of miR-34a downregulated the levels of phosphorylated Akt, phosphorylated ERK1/2 and other cell cycle regulators. miR-34a expression was significantly reduced in posterior capsule opacification (PCO) clinical samples. These results demonstrate that miR-34a may act as a suppressor in PCO by regulating human lens epithelial cell proliferation and migration through downregulation of c-Met.
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8
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Vechetti IJ, Wen Y, Chaillou T, Murach KA, Alimov AP, Figueiredo VC, Dal-Pai-Silva M, McCarthy JJ. Life-long reduction in myomiR expression does not adversely affect skeletal muscle morphology. Sci Rep 2019; 9:5483. [PMID: 30940834 PMCID: PMC6445125 DOI: 10.1038/s41598-019-41476-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
We generated an inducible, skeletal muscle-specific Dicer knockout mouse to deplete microRNAs in adult skeletal muscle. Following tamoxifen treatment, Dicer mRNA expression was significantly decreased by 87%. Wild-type (WT) and Dicer knockout (KO) mice were subjected to either synergist ablation or hind limb suspension for two weeks. There was no difference in muscle weight with hypertrophy or atrophy between WT and KO groups; however, even with the significant loss of Dicer expression, myomiR (miR-1, -133a and -206) expression was only reduced by 38% on average. We next aged WT and KO mice for ~22 months following Dicer inactivation to determine if myomiR expression would be further reduced over a prolonged timeframe and assess the effects of myomiR depletion on skeletal muscle phenotype. Skeletal muscle Dicer mRNA expression remained significantly decreased by 80% in old KO mice and sequencing of cloned Dicer mRNA revealed the complete absence of the floxed exons in KO skeletal muscle. Despite a further reduction of myomiR expression to ~50% of WT, no change was observed in muscle morphology between WT and KO groups. These results indicate the life-long reduction in myomiR levels did not adversely affect skeletal muscle phenotype and suggest the possibility that microRNA expression is uniquely regulated in skeletal muscle.
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Affiliation(s)
- Ivan J Vechetti
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
- Department of Morphology, São Paulo State University, Institute of Biosciences, Botucatu, Brazil
| | - Yuan Wen
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Thomas Chaillou
- Örebro University, School of Health Sciences, Örebro, Sweden
| | - Kevin A Murach
- Department of Rehabilitation Sciences, College of Health Sciences, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Alexander P Alimov
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Vandre C Figueiredo
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Department of Rehabilitation Sciences, College of Health Sciences, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Maeli Dal-Pai-Silva
- Department of Morphology, São Paulo State University, Institute of Biosciences, Botucatu, Brazil
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA.
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA.
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9
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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: 7] [Impact Index Per Article: 1.4] [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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10
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Non-coding RNAs in retinal development and function. Hum Genet 2018; 138:957-971. [DOI: 10.1007/s00439-018-1931-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/24/2018] [Indexed: 12/12/2022]
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11
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Drewry M, Helwa I, Allingham RR, Hauser MA, Liu Y. miRNA Profile in Three Different Normal Human Ocular Tissues by miRNA-Seq. Invest Ophthalmol Vis Sci 2017; 57:3731-9. [PMID: 27415791 PMCID: PMC4961003 DOI: 10.1167/iovs.16-19155] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Purpose Because microRNAs (miRNAs) have been associated with eye diseases, our study aims to profile ocular miRNA expression in normal human ciliary body (CB), cornea, and trabecular meshwork (TM) using miRNA-Seq to provide a foundation for better understanding of miRNA function and disease involvement in these tissues. Methods Total RNAs were extracted from seven normal human CB, seven cornea, and seven TM samples using mirVana total RNA isolation kit. miRNA-Seq was done with Illumina MiSeq. Bowtie software was used to trim and align generated sequence reads, and only exact matches to mature miRNAs from miRBase were included. The miRTarBase database was used to analyze miRNA target interactions, and the expression of five selected miRNAs was validated using droplet digital PCR (ddPCR). Results Using the miRNA extracted from 21 human samples, we found 378 miRNAs collectively expressed, of which the 11 most abundant miRNAs represented 80% of the total normalized reads. We also identified uniquely expressed miRNAs, of which five share 18 highly validated gene targets, and created a profile of miRNAs known to target genes associated with keratoconus and glaucoma. Using ddPCR, we validated the expression profile of five miRNAs from miRNA-Seq. Conclusions For the first time, we profiled miRNA expression in three human ocular tissues using miRNA-Seq, identifying many miRNAs that had not been previously reported in ocular tissue. Defining the relative expression of miRNAs in nondiseased eye tissues could help uncover changes in miRNA expression that accompany diseases such as glaucoma and keratoconus.
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Affiliation(s)
- Michelle Drewry
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Inas Helwa
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael A Hauser
- Department of Medicine and Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, United States 4Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, United States 5Ja
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Guo Y, Lu X, Wang H. Downregulation of miR-18a induces CTGF and promotes proliferation and migration of sodium hyaluronate treated human corneal epithelial cells. Gene 2016; 591:129-136. [PMID: 27390086 DOI: 10.1016/j.gene.2016.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 05/12/2016] [Accepted: 07/03/2016] [Indexed: 01/18/2023]
Abstract
Properly controlled corneal epithelial wound healing is critical for health of cornea, which involves cell proliferation, migration, anchoring and differentiation. Sodium hyaluronate (SH) has been proven to exert beneficial pharmacological effect on corneal wound healing, though the underlying mechanism remained open to investigation. MicroRNAs (miRNAs) are small single-stranded RNAs that could bind to 3'UTR of mRNAs of target genes. The multi-target regulation of miRNAs may favor treatment of corneal wound given the complicated processes implicated in the healing process, which has inspired initiatives to develop miRNA therapy in corneal wound healing. In this light, we used miRNAs profiling to detect whether miRNAs are also implicated in the mechanism underlying the stimulatory effect of SH on corneal epithelial wound healing. We found miR-18a was most susceptible to SH treatment, the target prediction of which were enriched in a bunch of pathways implicated in corneal wound healing. Connective tissue growth factor (CTGF) was found to be overrepresented in most significant enriched pathways and was experimentally confirmed as a bona fide target of miR-18a, which modulated cell migration and proliferation of human corneal epithelial cells.
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Affiliation(s)
- Yingzhuo Guo
- Department of Ophthalmology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, Guangdong Province, China; Department of Ophthalmology& Optometry, Hunan Provincial People's Hospital, Changsha 410005, Hunan Province,China
| | - Xiaohe Lu
- Department of Ophthalmology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, Guangdong Province, China.
| | - Hua Wang
- Department of Ophthalmology& Optometry, Hunan Provincial People's Hospital, Changsha 410005, Hunan Province,China
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13
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Dash S, Siddam AD, Barnum CE, Janga SC, Lachke SA. RNA-binding proteins in eye development and disease: implication of conserved RNA granule components. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:527-57. [PMID: 27133484 DOI: 10.1002/wrna.1355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/21/2016] [Indexed: 01/16/2023]
Abstract
The molecular biology of metazoan eye development is an area of intense investigation. These efforts have led to the surprising recognition that although insect and vertebrate eyes have dramatically different structures, the orthologs or family members of several conserved transcription and signaling regulators such as Pax6, Six3, Prox1, and Bmp4 are commonly required for their development. In contrast, our understanding of posttranscriptional regulation in eye development and disease, particularly regarding the function of RNA-binding proteins (RBPs), is limited. We examine the present knowledge of RBPs in eye development in the insect model Drosophila as well as several vertebrate models such as fish, frog, chicken, and mouse. Interestingly, of the 42 RBPs that have been investigated for their expression or function in vertebrate eye development, 24 (~60%) are recognized in eukaryotic cells as components of RNA granules such as processing bodies, stress granules, or other specialized ribonucleoprotein (RNP) complexes. We discuss the distinct developmental and cellular events that may necessitate potential RBP/RNA granule-associated RNA regulon models to facilitate posttranscriptional control of gene expression in eye morphogenesis. In support of these hypotheses, three RBPs and RNP/RNA granule components Tdrd7, Caprin2, and Stau2 are linked to ocular developmental defects such as congenital cataract, Peters anomaly, and microphthalmia in human patients or animal models. We conclude by discussing the utility of interdisciplinary approaches such as the bioinformatics tool iSyTE (integrated Systems Tool for Eye gene discovery) to prioritize RBPs for deriving posttranscriptional regulatory networks in eye development and disease. WIREs RNA 2016, 7:527-557. doi: 10.1002/wrna.1355 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University & Purdue University Indianapolis, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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14
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Anand D, Lachke SA. Systems biology of lens development: A paradigm for disease gene discovery in the eye. Exp Eye Res 2016; 156:22-33. [PMID: 26992779 DOI: 10.1016/j.exer.2016.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/19/2022]
Abstract
Over the past several decades, the biology of the developing lens has been investigated using molecular genetics-based approaches in various vertebrate model systems. These efforts, involving target gene knockouts or knockdowns, have led to major advances in our understanding of lens morphogenesis and the pathological basis of cataracts, as well as of other lens related eye defects. In particular, we now have a functional understanding of regulators such as Pax6, Six3, Sox2, Oct1 (Pou2f1), Meis1, Pnox1, Zeb2 (Sip1), Mab21l1, Foxe3, Tfap2a (Ap2-alpha), Pitx3, Sox11, Prox1, Sox1, c-Maf, Mafg, Mafk, Hsf4, Fgfrs, Bmp7, and Tdrd7 in this tissue. However, whether these individual regulators interact or their targets overlap, and the significance of such interactions during lens morphogenesis, is not well defined. The arrival of high-throughput approaches for gene expression profiling (microarrays, RNA-sequencing (RNA-seq), etc.), which can be coupled with chromatin immunoprecipitation (ChIP) or RNA immunoprecipitation (RIP) assays, along with improved computational resources and publically available datasets (e.g. those containing comprehensive protein-protein, protein-DNA information), presents new opportunities to advance our understanding of the lens tissue on a global systems level. Such systems-level knowledge will lead to the derivation of the underlying lens gene regulatory network (GRN), defined as a circuit map of the regulator-target interactions functional in lens development, which can be applied to expedite cataract gene discovery. In this review, we cover the various systems-level approaches such as microarrays, RNA-seq, and ChIP that are already being applied to lens studies and discuss strategies for assembling and interpreting these vast amounts of high-throughput information for effective dispersion to the scientific community. In particular, we discuss strategies for effective interpretation of this new information in the context of the rich knowledge obtained through the application of traditional single-gene focused experiments on the lens. Finally, we discuss our vision for integrating these diverse high-throughput datasets in a single web-based user-friendly tool iSyTE (integrated Systems Tool for Eye gene discovery) - a resource that is already proving effective in the identification and characterization of genes linked to lens development and cataract. We anticipate that application of a similar approach to other ocular tissues such as the retina and the cornea, and even other organ systems, will significantly impact disease gene discovery.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
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15
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Khan SY, Hackett SF, Lee MCW, Pourmand N, Talbot CC, Riazuddin SA. Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing. Invest Ophthalmol Vis Sci 2015. [PMID: 26225632 DOI: 10.1167/iovs.14-16253] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Transcriptome is the entire repertoire of transcripts present in a cell at any particular time. We undertook a next-generation whole transcriptome sequencing approach to gain insight into the transcriptional landscape of the developing mouse lens. METHODS We ascertained mouse lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The ocular tissue at each time point was maintained as two distinct pools serving as biological replicates for each developmental stage. The mRNA and small RNA libraries were paired-end sequenced on Illumina HiSeq 2000 and subsequently analyzed using bioinformatics tools. RESULTS Mapping of mRNA and small RNA libraries generated 187.56 and 154.22 million paired-end reads, respectively. We detected a total of 14,465 genes in the mouse ocular lens at the above-mentioned six developmental stages. Of these, 46 genes exhibited a 40-fold differential (higher or lower) expression at one the five developmental stages (E18, P0, P3, P6, and P9) compared with their expression level at E15. Likewise, small RNA profiling identified 379 microRNAs (miRNAs) expressed in mouse lens at six developmental time points. Of these, 49 miRNAs manifested an 8-fold differential (higher or lower) expression at one the five developmental stages, as mentioned above compared with their expression level at E15. CONCLUSIONS We report a comprehensive profile of developing murine lens transcriptome including both mRNA and miRNA through next-generation RNA sequencing. A complete repository of the lens transcriptome of six developmental time points will be monumental in elucidating processes essential for the development of the ocular lens and maintenance of its transparency.
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Affiliation(s)
- Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Sean F Hackett
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Mei-Chong W Lee
- Departpart of Biomolecular Engineering, University of California, Santa Cruz, California, United States
| | - Nader Pourmand
- Departpart of Biomolecular Engineering, University of California, Santa Cruz, California, United States
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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Abstract
Corneal wound healing is a complex process involving cell death, migration, proliferation, differentiation, and extracellular matrix remodeling. Many similarities are observed in the healing processes of corneal epithelial, stromal and endothelial cells, as well as cell-specific differences. Corneal epithelial healing largely depends on limbal stem cells and remodeling of the basement membrane. During stromal healing, keratocytes get transformed to motile and contractile myofibroblasts largely due to activation of transforming growth factor-β (TGF-β) system. Endothelial cells heal mostly by migration and spreading, with cell proliferation playing a secondary role. In the last decade, many aspects of wound healing process in different parts of the cornea have been elucidated, and some new therapeutic approaches have emerged. The concept of limbal stem cells received rigorous experimental corroboration, with new markers uncovered and new treatment options including gene and microRNA therapy tested in experimental systems. Transplantation of limbal stem cell-enriched cultures for efficient re-epithelialization in stem cell deficiency and corneal injuries has become reality in clinical setting. Mediators and course of events during stromal healing have been detailed, and new treatment regimens including gene (decorin) and stem cell therapy for excessive healing have been designed. This is a very important advance given the popularity of various refractive surgeries entailing stromal wound healing. Successful surgical ways of replacing the diseased endothelium have been clinically tested, and new approaches to accelerate endothelial healing and suppress endothelial-mesenchymal transformation have been proposed including Rho kinase (ROCK) inhibitor eye drops and gene therapy to activate TGF-β inhibitor SMAD7. Promising new technologies with potential for corneal wound healing manipulation including microRNA, induced pluripotent stem cells to generate corneal epithelium, and nanocarriers for corneal drug delivery are discussed. Attention is also paid to problems in wound healing understanding and treatment, such as lack of specific epithelial stem cell markers, reliable identification of stem cells, efficient prevention of haze and stromal scar formation, lack of data on wound regulating microRNAs in keratocytes and endothelial cells, as well as virtual lack of targeted systems for drug and gene delivery to select corneal cells.
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Affiliation(s)
- Alexander V Ljubimov
- Eye Program, Board of Governors Regenerative Medicine Institute, Departments of Biomedical Sciences and Neurosurgery, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
| | - Mehrnoosh Saghizadeh
- Eye Program, Board of Governors Regenerative Medicine Institute, Departments of Biomedical Sciences and Neurosurgery, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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Eghrari AO, Riazuddin SA, Gottsch JD. Overview of the Cornea: Structure, Function, and Development. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 134:7-23. [PMID: 26310146 DOI: 10.1016/bs.pmbts.2015.04.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The cornea is a transparent tissue with significant refractive and barrier functions. The epithelium serves as the principal barrier to fluid and pathogens, a function performed through production of tight junctions, and constant repopulation through differentiation and maturation of dividing cells in its basal cell layer. It is supported posteriorly by basement membrane and Bowman's layer and assists in maintenance of stromal dehydration. The stroma composes the majority of corneal volume, provides support and clarity, and assists in ocular immunity. The posterior cornea, composed of Descemet membrane and endothelium, is essential for stromal dehydration, maintained through tight junctions and endothelial pumps. Corneal development begins with primitive formation of epithelium and lens, followed by waves of migration from cells of neural crest origin between these two structures to produce the stroma and endothelium. Descemet membrane is secreted by the latter and gradually thickens.
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Affiliation(s)
- Allen O Eghrari
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - S Amer Riazuddin
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John D Gottsch
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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Cushing L, Costinean S, Xu W, Jiang Z, Madden L, Kuang P, Huang J, Weisman A, Hata A, Croce CM, Lü J. Disruption of miR-29 Leads to Aberrant Differentiation of Smooth Muscle Cells Selectively Associated with Distal Lung Vasculature. PLoS Genet 2015; 11:e1005238. [PMID: 26020233 PMCID: PMC4447351 DOI: 10.1371/journal.pgen.1005238] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/26/2015] [Indexed: 12/11/2022] Open
Abstract
Differentiation of lung vascular smooth muscle cells (vSMCs) is tightly regulated during development or in response to challenges in a vessel specific manner. Aberrant vSMCs specifically associated with distal pulmonary arteries have been implicated in the pathogenesis of respiratory diseases, such as pulmonary arterial hypertension (PAH), a progressive and fatal disease, with no effective treatment. Therefore, it is highly relevant to understand the underlying mechanisms of lung vSMC differentiation. miRNAs are known to play critical roles in vSMC maturation and function of systemic vessels; however, little is known regarding the role of miRNAs in lung vSMCs. Here, we report that miR-29 family members are the most abundant miRNAs in adult mouse lungs. Moreover, high levels of miR-29 expression are selectively associated with vSMCs of distal vessels in both mouse and human lungs. Furthermore, we have shown that disruption of miR-29 in vivo leads to immature/synthetic vSMC phenotype specifically associated with distal lung vasculature, at least partially due to the derepression of KLF4, components of the PDGF pathway and ECM-related genes associated with synthetic phenotype. Moreover, we found that expression of FBXO32 in vSMCs is significantly upregulated in the distal vasculature of miR-29 null lungs. This indicates a potential important role of miR-29 in smooth muscle cell function by regulating FBXO32 and SMC protein degradation. These results are strongly supported by findings of a cell autonomous role of endogenous miR-29 in promoting SMC differentiation in vitro. Together, our findings suggested a vessel specific role of miR-29 in vSMC differentiation and function by targeting several key negative regulators. The pathogenesis of some vascular diseases, such as PAH is selectively associated with aberrant differentiation and proliferation of vSMCs of distal arteries. While significant progresses have been made in understanding the core mechanism of differentiation and proliferation of vSMCs, little is known regarding vessel specific regulations. By investigating the expression and function of miR-29 in vivo, we found a vessel selective enriched expression and function of miR-29 during mouse lung development. Interestingly, disruption of miR-29 results in defects in vSMCs differentiation of distal vessels, reminiscent of vSMC phenotype observed in the early stage of PAH in which immature/synthetic vSMCs of distal arteries failed to differentiate and were unable to tune down the expression of collagens and other extracellular-related genes. This is the first evidence that miR-29 selectively regulates vSMCs differentiation and vessel wall formation. Future implications are to study the expression and function of miR-29 in human pulmonary vascular diseases, which might lead to establishing miR-29 as a therapeutic target for disease intervention.
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Affiliation(s)
- Leah Cushing
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Stefan Costinean
- Department of Pathology, Ohio State Wexner Medical Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Wei Xu
- Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University, College of Physicians & Surgeons, New York, New York, United States of America
| | - Zhihua Jiang
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Lindsey Madden
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Pingping Kuang
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Jingshu Huang
- Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University, College of Physicians & Surgeons, New York, New York, United States of America
| | - Alexandra Weisman
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Akiko Hata
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, Massachusetts, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Carlo M. Croce
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Jining Lü
- Columbia Center for Human Development, Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University, College of Physicians & Surgeons, New York, New York, United States of America
- * E-mail:
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Cvekl A, Ashery-Padan R. The cellular and molecular mechanisms of vertebrate lens development. Development 2014; 141:4432-47. [PMID: 25406393 PMCID: PMC4302924 DOI: 10.1242/dev.107953] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ocular lens is a model system for understanding important aspects of embryonic development, such as cell specification and the spatiotemporally controlled formation of a three-dimensional structure. The lens, which is characterized by transparency, refraction and elasticity, is composed of a bulk mass of fiber cells attached to a sheet of lens epithelium. Although lens induction has been studied for over 100 years, recent findings have revealed a myriad of extracellular signaling pathways and gene regulatory networks, integrated and executed by the transcription factor Pax6, that are required for lens formation in vertebrates. This Review summarizes recent progress in the field, emphasizing the interplay between the diverse regulatory mechanisms employed to form lens progenitor and precursor cells and highlighting novel opportunities to fill gaps in our understanding of lens tissue morphogenesis.
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Affiliation(s)
- Aleš Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine and Sagol School of Neuroscience, Tel-Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
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Herwig MC, Loeffler KU, Gembruch U, Kuchelmeister K, Müller AM. Anterior segment developmental anomalies in a 33-week-old fetus with MIDAS syndrome. Pediatr Dev Pathol 2014; 17:491-5. [PMID: 25291437 DOI: 10.2350/13-11-1408-cr.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report anterior segment abnormalities in both eyes of a 33-week-old fetus endorsing the diagnosis of MIDAS (microphthalmia, dermal aplasia, and sclerocornea) syndrome. After abortion, the fetus was examined by a standard pediatric autopsy that included macroscopic and microscopic examination of both eyes. Postmortem findings included craniofacial stigmata (such as hypertelorism, a flat nose and low-set ears) and an agenesis of the corpus callosum. Array comparative genomic hybridization revealed a deletion of the short arm of the X chromosome (region Xp22.2 to p22.32). Ophthalmopathologic examination of the eyes revealed microphthalmia with anterior segment developmental anomalies, in particular sclerocornea and Peters' anomaly, respectively. General pathology findings plus the ocular findings allowed the diagnosis of MIDAS syndrome. A discussion of differential diagnoses is provided. This case report indicates that ophthalmopathologic investigation of fetal eyes can be of great value for the further classification of syndromes.
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Affiliation(s)
- Martina C Herwig
- 1 Department of Ophthalmology, Division of Ophthalmic Pathology, University of Bonn, Ernst-Abbe-Str. 2, 53127 Bonn, Germany
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MicroRNA and diseases: therapeutic potential as new generation of drugs. Biochimie 2014; 104:12-26. [PMID: 24859535 DOI: 10.1016/j.biochi.2014.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 05/08/2014] [Indexed: 01/01/2023]
Abstract
MicroRNA (miRNA) is a small non-coding regulatory RNA of 21-25 nucleotides (nts) in length. miRNA works as a post-transcriptional regulator of a specific mRNA by inducing degradation or translation repression resulting in gene silencing. A large number of miRNA have been reported and many more are yet to be discovered. Aberrant expression of miRNA has been linked to numerous diseases. Attempts have been made to attenuate miRNA misregulation under pathophysiological conditions. Additionally, the potential use of miRNA in the diagnosis and treatment of diseases has been studied. Several preclinical and clinical results have been obtained, and miRNA-based therapeutics are still under investigations. In this review, the role of miRNA in a variety of pathological conditions has been summarized. Recent findings from preclinical and clinical investigations examining the role of miRNA as diagnostic markers, and their potential as drug candidates, are also highlighted. The current results summarized in this review may elucidate new dimensions of miRNA therapeutic and diagnostic techniques for biomedical academic and industry research.
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Differentially expressed wound healing-related microRNAs in the human diabetic cornea. PLoS One 2013; 8:e84425. [PMID: 24376808 PMCID: PMC3869828 DOI: 10.1371/journal.pone.0084425] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/14/2013] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are powerful gene expression regulators, but their corneal repertoire and potential changes in corneal diseases remain unknown. Our purpose was to identify miRNAs altered in the human diabetic cornea by microarray analysis, and to examine their effects on wound healing in cultured telomerase-immortalized human corneal epithelial cells (HCEC) in vitro. Total RNA was extracted from age-matched human autopsy normal (n=6) and diabetic (n=6) central corneas, Flash Tag end-labeled, and hybridized to Affymetrix® GeneChip® miRNA Arrays. Select miRNAs associated with diabetic cornea were validated by quantitative RT-PCR (Q-PCR) and by in situ hybridization (ISH) in independent samples. HCEC were transfected with human pre-miR™miRNA precursors (h-miR) or their inhibitors (antagomirs) using Lipofectamine 2000. Confluent transfected cultures were scratch-wounded with P200 pipette tip. Wound closure was monitored by digital photography. Expression of signaling proteins was detected by immunostaining and Western blot. Using microarrays, 29 miRNAs were identified as differentially expressed in diabetic samples. Two miRNA candidates showing the highest fold increased in expression in the diabetic cornea were confirmed by Q-PCR and further characterized. HCEC transfection with h-miR-146a or h-miR-424 significantly retarded wound closure, but their respective antagomirs significantly enhanced wound healing vs. controls. Cells treated with h-miR-146a or h-miR-424 had decreased p-p38 and p-EGFR staining, but these increased over control levels close to the wound edge upon antagomir treatment. In conclusion, several miRNAs with increased expression in human diabetic central corneas were found. Two such miRNAs inhibited cultured corneal epithelial cell wound healing. Dysregulation of miRNA expression in human diabetic cornea may be an important mediator of abnormal wound healing.
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Identification and characterization of FGF2-dependent mRNA: microRNA networks during lens fiber cell differentiation. G3-GENES GENOMES GENETICS 2013; 3:2239-55. [PMID: 24142921 PMCID: PMC3852386 DOI: 10.1534/g3.113.008698] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) and fibroblast growth factor (FGF) signaling regulate a wide range of cellular functions, including cell specification, proliferation, migration, differentiation, and survival. In lens, both these systems control lens fiber cell differentiation; however, a possible link between these processes remains to be examined. Herein, the functional requirement for miRNAs in differentiating lens fiber cells was demonstrated via conditional inactivation of Dicer1 in mouse (Mus musculus) lens. To dissect the miRNA-dependent pathways during lens differentiation, we used a rat (Rattus norvegicus) lens epithelial explant system, induced by FGF2 to differentiate, followed by mRNA and miRNA expression profiling. Transcriptome and miRNome analysis identified extensive FGF2-regulated cellular responses that were both independent and dependent on miRNAs. We identified 131 FGF2-regulated miRNAs. Seventy-six of these miRNAs had at least two in silico predicted and inversely regulated target mRNAs. Genes modulated by the greatest number of FGF-regulated miRNAs include DNA-binding transcription factors Nfib, Nfat5/OREBP, c-Maf, Ets1, and N-Myc. Activated FGF signaling influenced bone morphogenetic factor/transforming growth factor-β, Notch, and Wnt signaling cascades implicated earlier in lens differentiation. Specific miRNA:mRNA interaction networks were predicted for c-Maf, N-Myc, and Nfib (DNA-binding transcription factors); Cnot6, Cpsf6, Dicer1, and Tnrc6b (RNA to miRNA processing); and Ash1l, Med1/PBP, and Kdm5b/Jarid1b/Plu1 (chromatin remodeling). Three miRNAs, including miR-143, miR-155, and miR-301a, down-regulated expression of c-Maf in the 3′-UTR luciferase reporter assays. These present studies demonstrate for the first time global impact of activated FGF signaling in lens cell culture system and predicted novel gene regulatory networks connected by multiple miRNAs that regulate lens differentiation.
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Conte I, Banfi S, Bovolenta P. Non-coding RNAs in the development of sensory organs and related diseases. Cell Mol Life Sci 2013; 70:4141-55. [PMID: 23588489 PMCID: PMC11113508 DOI: 10.1007/s00018-013-1335-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/25/2013] [Accepted: 03/27/2013] [Indexed: 12/21/2022]
Abstract
Genomes are transcribed well beyond the conventionally annotated protein-encoding genes and produce many thousands of regulatory non-coding RNAs (ncRNAs). In the last few years, ncRNAs, especially microRNAs and long non-coding RNA, have received increasing attention because of their implication in the function of chromatin-modifying complexes and in the regulation of transcriptional and post-transcriptional events. The morphological events and the genetic networks responsible for the development of sensory organs have been well delineated and therefore sensory organs have provided a useful scenario to address the role of ncRNAs. In this review, we summarize the current information on the importance of microRNAs and long non-coding RNAs during the development of the eye, inner ear, and olfactory system in vertebrates. We will also discuss those cases in which alteration of ncRNA expression has been linked to pathological conditions affecting these organs.
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Affiliation(s)
- Ivan Conte
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | - Paola Bovolenta
- Centro de Biología Molecular ‘Severo Ochoa’, CSIC–UAM, c/Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
- CIBER de Enfermedades Raras, ISCIII, Madrid, Spain
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Ma W, Hu S, Yao G, Xie S, Ni M, Liu Q, Gao X, Zhang J, Huang X, Zhang Y. An androgen receptor-microrna-29a regulatory circuitry in mouse epididymis. J Biol Chem 2013; 288:29369-81. [PMID: 23960076 DOI: 10.1074/jbc.m113.454066] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs are involved in a number of cellular processes; thus, their deregulation is usually apt to the occurrence of diverse diseases. Previous studies indicate that abnormally up-regulated miR-29a is associated with several diseases, such as human acute myeloid leukemia and diabetes; therefore, the proper level of miR-29a is critical for homeostasis. Herein, we observed that miR-29a was repressed by androgen/androgen receptor signaling in mouse epididymis by targeting a conserved androgen response element located 8 kb upstream of miR-29b1a loci. It is well known that multiple regulatory programs often form a complicated network. Here, we found that miR-29a reversibly suppressed androgen receptor and its target genes by targeting IGF1 and p53 pathways. miR-29b1a-overexpressing transgenic mice displayed epididymis hypoplasia partially similar to the phenotype of those mice with an impaired androgen-androgen receptor signal system. Taken together, the results demonstrated that there is a regulatory circuitry between the androgen signaling pathway and miR-29a in mouse epididymis that may be vital for epididymal development and functions.
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Affiliation(s)
- Wubin Ma
- From the Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
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Shaham O, Gueta K, Mor E, Oren-Giladi P, Grinberg D, Xie Q, Cvekl A, Shomron N, Davis N, Keydar-Prizant M, Raviv S, Pasmanik-Chor M, Bell RE, Levy C, Avellino R, Banfi S, Conte I, Ashery-Padan R. Pax6 regulates gene expression in the vertebrate lens through miR-204. PLoS Genet 2013; 9:e1003357. [PMID: 23516376 PMCID: PMC3597499 DOI: 10.1371/journal.pgen.1003357] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 01/17/2013] [Indexed: 12/22/2022] Open
Abstract
During development, tissue-specific transcription factors regulate both protein-coding and non-coding genes to control differentiation. Recent studies have established a dual role for the transcription factor Pax6 as both an activator and repressor of gene expression in the eye, central nervous system, and pancreas. However, the molecular mechanism underlying the inhibitory activity of Pax6 is not fully understood. Here, we reveal that Trpm3 and the intronic microRNA gene miR-204 are co-regulated by Pax6 during eye development. miR-204 is probably the best known microRNA to function as a negative modulator of gene expression during eye development in vertebrates. Analysis of genes altered in mouse Pax6 mutants during lens development revealed significant over-representation of miR-204 targets among the genes up-regulated in the Pax6 mutant lens. A number of new targets of miR-204 were revealed, among them Sox11, a member of the SoxC family of pro-neuronal transcription factors, and an important regulator of eye development. Expression of Trpm/miR-204 and a few of its targets are also Pax6-dependent in medaka fish eyes. Collectively, this study identifies a novel evolutionarily conserved mechanism by which Pax6 controls the down-regulation of multiple genes through direct up-regulation of miR-204. The transcription factor Pax6 is reiteratively employed in space and time for the establishment of progenitor pools and the differentiation of neuronal and non-neuronal lineages of the CNS, pancreas, and eye. Execution of these diverse developmental programs depends on simultaneous activation and repression of gene networks functioning downstream of Pax6. MicroRNAs function as inhibitors of gene expression. Many microRNA genes are transcribed through common promoters of host genes. In this study, using wide-scale analysis of changes in gene expression following Pax6 deletion in the lens, we discover that Pax6 regulates the gene Trpm3 and its hosted microRNA, miR-204. We then show that miR-204 suppresses several target genes in the lens, notably the neuronal gene Sox11. Lastly, by conducting parallel experiments in the medaka fish, we show that Pax6 control of miR-204 and its target genes is evolutionarily conserved between mammals and fish, stressing the biological importance of this pathway. Pax6 regulation of miR-204 explains part of the complex, divergent inhibitory activity of Pax6 in ocular progenitor cells, which is required to establish and maintain the identity and function of ocular tissues.
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Affiliation(s)
- Ohad Shaham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karen Gueta
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eyal Mor
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pazit Oren-Giladi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dina Grinberg
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Qing Xie
- Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ales Cvekl
- Department of Genetics and Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Noa Davis
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Maya Keydar-Prizant
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shaul Raviv
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rachel E. Bell
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Carmit Levy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine, Naples, Italy
- * E-mail: (IC); (RA-P)
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (IC); (RA-P)
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The eye as a model of ageing in translational research--molecular, epigenetic and clinical aspects. Ageing Res Rev 2013; 12:490-508. [PMID: 23274270 DOI: 10.1016/j.arr.2012.11.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 11/16/2012] [Accepted: 11/19/2012] [Indexed: 12/13/2022]
Abstract
The eye and visual system are valuable in many areas of translational research such as stem cell therapy, transplantation research and gene therapy. Changes in many ocular tissues can be measured directly, easily and objectively in vivo (e.g. lens transparency; retinal blood vessel calibre; corneal endothelial cell counts) and so the eye may also be a uniquely useful site as a model of ageing. This review details cellular, molecular and epigenetic mechanisms related to ageing within the eye, and describes ocular parameters that can be directly measured clinically and which might be of value in ageing research as the translational "window to the rest of the body". The eye is likely to provide a valuable model for validating biomarkers of ageing at molecular, epigenetic, cellular and clinical levels. A research agenda to definitively establish the relationship between biomarkers of ageing and ocular parameters is proposed.
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Ocular surface development and gene expression. J Ophthalmol 2013; 2013:103947. [PMID: 23533700 PMCID: PMC3595720 DOI: 10.1155/2013/103947] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/16/2013] [Indexed: 01/10/2023] Open
Abstract
The ocular surface-a continuous epithelial surface with regional specializations including the surface and glandular epithelia of the cornea, conjunctiva, and lacrimal and meibomian glands connected by the overlying tear film-plays a central role in vision. Molecular and cellular events involved in embryonic development, postnatal maturation, and maintenance of the ocular surface are precisely regulated at the level of gene expression by a well-coordinated network of transcription factors. A thorough appreciation of the biological characteristics of the ocular surface in terms of its gene expression profiles and their regulation provides us with a valuable insight into the pathophysiology of various blinding disorders that disrupt the normal development, maturation, and/or maintenance of the ocular surface. This paper summarizes the current status of our knowledge related to the ocular surface development and gene expression and the contribution of different transcription factors to this process.
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Shalom-Feuerstein R, Serror L, De La Forest Divonne S, Petit I, Aberdam E, Camargo L, Damour O, Vigouroux C, Solomon A, Gaggioli C, Itskovitz-Eldor J, Ahmad S, Aberdam D. Pluripotent stem cell model reveals essential roles for miR-450b-5p and miR-184 in embryonic corneal lineage specification. Stem Cells 2012; 30:898-909. [PMID: 22367714 DOI: 10.1002/stem.1068] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Approximately 6 million people worldwide are suffering from severe visual impairments or blindness due to corneal diseases. Corneal allogeneic transplantation is often required to restore vision; however, shortage in corneal grafts and immunorejections remain major challenges. The molecular basis of corneal diseases is poorly understood largely due to lack of appropriate cellular models. Here, we described a robust differentiation of human-induced pluripotent stem cells (hiPSCs) derived from hair follicles or skin fibroblasts into corneal epithelial-like cells. We found that BMP4, coupled with corneal fibroblast-derived conditioned medium and collagen IV allowed efficient corneal epithelial commitment of hiPSCs in a manner that recapitulated corneal epithelial lineage development with high purity. Organotypic reconstitution assays suggested the ability of these cells to stratify into a corneal-like epithelium. This model allowed us identifying miR-450b-5p as a molecular switch of Pax6, a major regulator of eye development. miR-450b-5p and Pax6 were reciprocally distributed at the presumptive epidermis and ocular surface, respectively. miR-450b-5p inhibited Pax6 expression and corneal epithelial fate in vitro, altogether, suggesting that by repressing Pax6, miR-450b-5p triggers epidermal specification of the ectoderm, while its absence allows ocular epithelial development. Additionally, miR-184 was detectable in early eye development and corneal epithelial differentiation of hiPSCs. The knockdown of miR-184 resulted in a decrease in Pax6 and K3, in line with recent findings showing that a point mutation in miR-184 leads to corneal dystrophy. Altogether, these data indicate that hiPSCs are valuable for modeling corneal development and may pave the way for future cell-based therapy.
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Effect of high sugar levels on miRNA expression. Studies with galactosemic mice lenses. Mol Vis 2012; 18:1609-18. [PMID: 22736950 PMCID: PMC3380916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/11/2012] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Development of cataract is associated with apoptotic death of the lens epithelial cells. The purpose of this investigation was to examine whether this could be explained by enhancement in the expression of certain pro-apoptotic microRNAs (miRs), known to induce apoptosis by hybridizing with target mRNAs, with the consequence of gene silencing. In addition, it was intended to investigate if such expression could be antagonized by reactive oxygen species (ROS) scavengers. METHODS CD-1 mice weighing about 20 g were divided into three groups and fed diets, respectively, as follows: Control diet, 25% galactose diet, and 25% galactose diet containing 1% sodium pyruvate. After eight days of such a regimen, the mice were euthanized, their lenses promptly isolated and frozen in liquid nitrogen, and RNAs isolated by extraction with standard methods and converted to cDNAs. The miR-specific cDNAs were then quantified by polymerase chain reaction (PCR) using a 96-well microRNA array cassette using an ABI 7900 HT PCR machine. The results were then analyzed using Bioscience software. RESULTS The lens samples were positive for all of the 84 miRs expected, on the basis of the specific sequences used for amplification. However, as would be apparent from the microarray plot for the normal and galactosemic lenses, expression of at least 24 apoptotic miRs was upregulated. Six apoptotic miRs were downregulated. In the lenses of animals where the galactose diet was fortified with sodium pyruvate, the expression of 12 miRs was completely prevented. The upregulation observed in the other 14 miRs was also significantly downregulated. A comparison of the galactose and galactose plus pyruvate group clearly indicated that pyruvate inhibits the transcription of apoptotic miRS. CONCLUSIONS The prevention of galactose-induced enhancement in the expression of apoptotic miRs by pyruvate, a compound well known to scavenge reactive oxygen species as well as to inhibit their formation, strongly suggests that the upregulation of miRs in galactosemic animals is due to generation of reactive oxygen species. This is in conformity with our previous studies showing that pyruvate and other ROS scavengers inhibit apoptosis as well as cataract formation.
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Iliff BW, Riazuddin SA, Gottsch JD. A single-base substitution in the seed region of miR-184 causes EDICT syndrome. Invest Ophthalmol Vis Sci 2012; 53:348-53. [PMID: 22131394 PMCID: PMC3292370 DOI: 10.1167/iovs.11-8783] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/15/2011] [Accepted: 11/15/2011] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To investigate the cause of the syndrome characterized by endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning (EDICT). METHODS Previously a multigenerational family was reported that comprised 10 individuals affected by syndromal anterior segment dysgenesis. Blood samples were re-collected from eight affected and two unaffected individuals, and genomic DNA was extracted. A total of 24 candidate genes and 4 microRNAs residing within the critical interval were sequenced bidirectionally. In silico analyses were performed to examine the effect of the causal variant on the stability of the pre-microRNA structure. RESULTS Bidirectional sequencing identified the single-base substitution +57C>T in miR-184. This variation segregated with the disease phenotype and was absent in the 1000 Genomes project, 1130 control chromosomes, and 28 nonhuman vertebrates. CONCLUSIONS The single-base-pair substitution in the seed region of miR-184 is responsible for the disease phenotype observed in EDICT syndrome.
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Affiliation(s)
- Benjamin W. Iliff
- From the Center for Corneal Genetics, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - S. Amer Riazuddin
- From the Center for Corneal Genetics, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John D. Gottsch
- From the Center for Corneal Genetics, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Ma W, Xie S, Ni M, Huang X, Hu S, Liu Q, Liu A, Zhang J, Zhang Y. MicroRNA-29a inhibited epididymal epithelial cell proliferation by targeting nuclear autoantigenic sperm protein (NASP). J Biol Chem 2011; 287:10189-10199. [PMID: 22194605 DOI: 10.1074/jbc.m111.303636] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cell proliferation often decreases gradually during postnatal development of some organs. However, the underlying molecular mechanisms remain unclear. Epididymis, playing important roles in sperm maturation, is a typical organ of this type, which displays a decreased proliferation during postnatal development and even ceased at the adult stage. Here, epididymis was employed as a model to explore the underlying mechanisms. We profiled the microRNA and mRNA expression of newborn (1 day) and adult (90 day) rat epididymis by microarray analysis, and found that the level of miR-29a was dramatically up-regulated during postnatal development of rat epididymis. Subsequent investigations demonstrated that overexpression of miR-29a inhibited the proliferation of epididymal epithelial cells in vitro. The nuclear autoantigenic sperm protein (NASP), a novel target of miR-29a, was significantly down-regulated during postnatal development of rat epididymis. Further analysis showed that silence of NASP mimicked the anti-proliferation effect of miR-29a, whereas overexpression of this protein attenuated the effect of miR-29a. As in rat epididymis, miR-29a was up-regulated and Nasp was down-regulated during postnatal development of mouse epididymis, heart, liver, and lung. Moreover, miR-29a can also inhibit the proliferation of cancer cells by targeting Nasp. Thus, an increase of miR-29a, and hence decrease of Nasp, may contribute to inhibit cell proliferation during postnatal organ development.
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Affiliation(s)
- Wubin Ma
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031,; Graduate School, Chinese Academy of Sciences, Shanghai 200031
| | - Shengsong Xie
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031,; Graduate School, Chinese Academy of Sciences, Shanghai 200031
| | - Minjie Ni
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031
| | - Xingxu Huang
- Model Animal Research Center, Nanjing University, Nanjing 210061, and
| | - Shuanggang Hu
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031,; Graduate School, Chinese Academy of Sciences, Shanghai 200031
| | - Qiang Liu
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031
| | - Aihua Liu
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031
| | - Jinsong Zhang
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031
| | - Yonglian Zhang
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031,; Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China.
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Fowler JC, Zecchini VR, Jones PH. Intestinal activation of Notch signaling induces rapid onset hepatic steatosis and insulin resistance. PLoS One 2011; 6:e20767. [PMID: 21698231 PMCID: PMC3116826 DOI: 10.1371/journal.pone.0020767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/09/2011] [Indexed: 02/07/2023] Open
Abstract
Here we investigate the effects of expressing an activated mutant of Notch (ICD-E) in an inducible transgenic mouse model. Hepatic expression of ICD-E in adult animals has no detectable phenotype, but simultaneous induction of ICD-E in both the liver and small intestine results in hepatic steatosis, lipogranuloma formation and mild insulin resistance within 96 hours. This supports work that suggests that fatty liver disease may result from disruption of the gut-liver axis. In the intestine, ICD-E expression is known to produce a transient change in the proportion of goblet cells followed by shedding of the recombinant epithelium. We report additional intestinal transcriptional changes following ICD-E expression, finding significant transcriptional down-regulation of rpL29 (ribosomal protein L29), which is implicated in the regulation of intestinal flora. These results provide further evidence of a gut-liver axis in the development of fatty liver disease and insulin resistance and validate a new model for future studies of hepatic steatosis.
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Affiliation(s)
- Joanna C. Fowler
- Medical Research Council Cancer Cell Unit, Cambridge, United Kingdom
| | | | - Philip H. Jones
- Medical Research Council Cancer Cell Unit, Cambridge, United Kingdom
- * E-mail:
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Nie X, Wang Q, Jiao K. Dicer activity in neural crest cells is essential for craniofacial organogenesis and pharyngeal arch artery morphogenesis. Mech Dev 2011; 128:200-7. [PMID: 21256960 DOI: 10.1016/j.mod.2010.12.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 11/30/2010] [Accepted: 12/15/2010] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) play important roles in regulating gene expression during numerous biological/pathological processes. Dicer encodes an RNase III endonuclease that is essential for generating most, if not all, functional miRNAs. In this work, we applied a conditional gene inactivation approach to examine the function of Dicer during neural crest cell (NCC) development. Mice with NCC-specific inactivation of Dicer died perinatally. Cranial and cardiac NCC migration into target tissues was not affected by Dicer disruption, but their subsequent development was disturbed. NCC derivatives and their associated mesoderm-derived cells displayed massive apoptosis, leading to severe abnormalities during craniofacial morphogenesis and organogenesis. In addition, the 4th pharyngeal arch artery (PAA) remodeling was affected, resulting in interrupted aortic arch artery type B (IAA-B) in mutant animals. Taken together, our results show that Dicer activity in NCCs is essential for craniofacial development and pharyngeal arch artery morphogenesis.
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Affiliation(s)
- Xuguang Nie
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Davis N, Mor E, Ashery-Padan R. Roles for Dicer1 in the patterning and differentiation of the optic cup neuroepithelium. Development 2011; 138:127-38. [DOI: 10.1242/dev.053637] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The embryonic ocular neuroepithilium generates a myriad of cell types, including the neuroretina, the pigmented epithelium, the ciliary and iris epithelia, and the iris smooth muscles. As in other regions of the developing nervous system, the generation of these various cell types requires a coordinated sequence of patterning, specification and differentiation events. We investigated the roles of microRNAs (miRNAs) in the development of optic cup (OC)-derived structures. We inactivated Dicer1, a key mediator of miRNA biosynthesis, within the OC in overlapping yet distinct spatiotemporal patterns. Ablation of Dicer1 in the inner layer of the OC resulted in patterning alteration, particularly at the most distal margins. Following loss of Dicer1, this region generated a cryptic population of cells with a mixed phenotype of neuronal and ciliary body (CB) progenitors. Notably, inactivation of Dicer1 in the retinal progenitors further resulted in abrogated neurogenesis, with prolongation of ganglion cell birth and arrested differentiation of other neuronal subtypes, including amacrine and photoreceptor cells. These alterations were accompanied by changes in the expression of Notch and Hedgehog signaling components, indicating the sensitivity of the pathways to miRNA activity. Moreover, this study revealed the requirement of miRNAs for morphogenesis of the iris and for the regulation of CB cell type proliferation and differentiation. Together, analysis of the three genetic models revealed novel, stage-dependent roles for miRNAs in the development of the ocular sub-organs, which are all essential for normal vision.
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Affiliation(s)
- Noa Davis
- Sackler Faculty of Medicine, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Eyal Mor
- Sackler Faculty of Medicine, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Ashery-Padan
- Sackler Faculty of Medicine, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
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Karali M, Peluso I, Gennarino VA, Bilio M, Verde R, Lago G, Dollé P, Banfi S. miRNeye: a microRNA expression atlas of the mouse eye. BMC Genomics 2010; 11:715. [PMID: 21171988 PMCID: PMC3018480 DOI: 10.1186/1471-2164-11-715] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 12/20/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution. RESULTS In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina. CONCLUSIONS This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures.
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Affiliation(s)
- Marianthi Karali
- Telethon Institute for Genetics and Medicine, Via P. Castellino 111, Naples, Italy
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Epigenetic regulatory mechanisms in vertebrate eye development and disease. Heredity (Edinb) 2010; 105:135-51. [PMID: 20179734 DOI: 10.1038/hdy.2010.16] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic DNA is organized as a nucleoprotein polymer termed chromatin with nucleosomes serving as its repetitive architectural units. Cellular differentiation is a dynamic process driven by activation and repression of specific sets of genes, partitioning the genome into transcriptionally active and inactive chromatin domains. Chromatin architecture at individual genes/loci may remain stable through cell divisions, from a single mother cell to its progeny during mitosis, and represents an example of epigenetic phenomena. Epigenetics refers to heritable changes caused by mechanisms distinct from the primary DNA sequence. Recent studies have shown a number of links between chromatin structure, gene expression, extracellular signaling, and cellular differentiation during eye development. This review summarizes recent advances in this field, and the relationship between sequence-specific DNA-binding transcription factors and their roles in recruitment of chromatin remodeling enzymes. In addition, lens and retinal differentiation is accompanied by specific changes in the nucleolar organization, expression of non-coding RNAs, and DNA methylation. Epigenetic regulatory mechanisms in ocular tissues represent exciting areas of research that have opened new avenues for understanding normal eye development, inherited eye diseases and eye diseases related to aging and the environment.
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Tang Y, Crowley TE, Kumar NM. Global gene expression analysis of lenses from different mouse strains and in the alpha3Cx46 knockout mouse. Mol Vis 2010; 16:113-21. [PMID: 20104256 PMCID: PMC2810875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 01/21/2010] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Disruption of the mouse gene encoding the gap junction subunit alpha3 connexin 46 (alpha3Cx46) results in the formation of lens cataracts that have a severity affected by the genetic background of the mouse strain. To identify the genes that influence the severity of the nuclear opacity, global gene expression was analyzed in lenses from the 129SvJae strain and compared to the C57BL/6J strain. METHODS Lens transcripts were subjected to cDNA microarray analysis. Results on selected genes were confirmed by real-time PCR. RESULTS GENES THAT WERE DETERMINED TO BE ALTERED IN EXPRESSION LEVELS AS A RESULT OF STRAIN DIFFERENCES COULD BE CLUSTERED INTO THREE GROUPS: energy metabolism, stress response, and cell growth. CONCLUSIONS There were no observed changes in gene expression as a result of the lack of alpha3Cx46 in the different mouse strains, suggesting that the pathways mediated by this connexin do not influence gene transcription in the lens. Analysis of the transcript changes due to strain differences provides new insights into potential genetic modifiers of cataractogenesis. More detailed experimentation will be needed to determine if these observed changes do indeed affect cataractogenesis.
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Affiliation(s)
- Yajun Tang
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
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40
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Joo JH, Kim YH, Dunn NW, Sugrue SP. Disruption of mouse corneal epithelial differentiation by conditional inactivation of pnn. Invest Ophthalmol Vis Sci 2009; 51:1927-34. [PMID: 19892877 DOI: 10.1167/iovs.09-4591] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose. To investigate the specific role of Pinin (Pnn) in the development of anterior eye segment in mice. Methods. Conditional inactivation of Pnn in the developing surface eye ectoderm and lens was achieved by creating mice carrying a Pnn null and a floxed Pnn allele as well as a Pax6-Cre-GFP (Le-Cre) transgene. The resultant Pnn conditional knockout mice were examined by histologic and immunohistologic approaches. Results. Pax6-Cre-mediated deletion of Pnn resulted in severe malformation of lens placode-derived tissues including cornea and lens. Pnn mutant corneal epithelium displayed the loss of corneal epithelial identity and appeared epidermis-like, downregulating corneal keratins (K12) and ectopically expressing epidermal keratins (K10 and K14). This squamous metaplasia of Pnn mutant corneal epithelium closely correlated with significantly elevated beta-catenin activity and Tcf4 level. In addition, Pnn inactivation also led to misregulated level of p68 RNA helicase in mutant corneal epithelium. Conclusions. These data indicate that Pnn plays an essential role in modulating and/or orchestrating the activities of major developmental factors of anterior eye segments.
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Affiliation(s)
- Jeong-Hoon Joo
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
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