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Gupta S, Lytvynchuk L, Ardan T, Studenovska H, Faura G, Eide L, Znaor L, Erceg S, Stieger K, Motlik J, Bharti K, Petrovski G. Retinal Pigment Epithelium Cell Development: Extrapolating Basic Biology to Stem Cell Research. Biomedicines 2023; 11:310. [PMID: 36830851 PMCID: PMC9952929 DOI: 10.3390/biomedicines11020310] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
The retinal pigment epithelium (RPE) forms an important cellular monolayer, which contributes to the normal physiology of the eye. Damage to the RPE leads to the development of degenerative diseases, such as age-related macular degeneration (AMD). Apart from acting as a physical barrier between the retina and choroidal blood vessels, the RPE is crucial in maintaining photoreceptor (PR) and visual functions. Current clinical intervention to treat early stages of AMD includes stem cell-derived RPE transplantation, which is still in its early stages of evolution. Therefore, it becomes essential to derive RPEs which are functional and exhibit features as observed in native human RPE cells. The conventional strategy is to use the knowledge obtained from developmental studies using various animal models and stem cell-based exploratory studies to understand RPE biogenies and developmental trajectory. This article emphasises such studies and aims to present a comprehensive understanding of the basic biology, including the genetics and molecular pathways of RPE development. It encompasses basic developmental biology and stem cell-based developmental studies to uncover RPE differentiation. Knowledge of the in utero developmental cues provides an inclusive methodology required for deriving RPEs using stem cells.
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Affiliation(s)
- Santosh Gupta
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | - Lyubomyr Lytvynchuk
- Department of Ophthalmology, Justus Liebig University Giessen, University Hospital Giessen and Marburg GmbH, 35392 Giessen, Germany
- Karl Landsteiner Institute for Retinal Research and Imaging, 1030 Vienna, Austria
| | - Taras Ardan
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 27721 Libechov, Czech Republic
| | - Hana Studenovska
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, 16206 Prague, Czech Republic
| | - Georgina Faura
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ljubo Znaor
- Department of Ophthalmology, University of Split School of Medicine and University Hospital Centre, 21000 Split, Croatia
| | - Slaven Erceg
- Research Center “Principe Felipe”, Stem Cell Therapies in Neurodegenerative Diseases Laboratory, 46012 Valencia, Spain
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 11720 Prague, Czech Republic
| | - Knut Stieger
- Department of Ophthalmology, Justus Liebig University Giessen, University Hospital Giessen and Marburg GmbH, 35392 Giessen, Germany
| | - Jan Motlik
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 27721 Libechov, Czech Republic
| | - Kapil Bharti
- Ocular and Stem Cell Translational Research Section, NEI, NIH, Bethesda, MD 20892, USA
| | - Goran Petrovski
- Center for Eye Research and Innovative Diagnostics, Department of Ophthalmology, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
- Department of Ophthalmology, University of Split School of Medicine and University Hospital Centre, 21000 Split, Croatia
- Department of Ophthalmology, Oslo University Hospital, 0450 Oslo, Norway
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2
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Rajool Dezfuly A, Safaee A, Salehi H. Therapeutic effects of mesenchymal stem cells-derived extracellular vesicles' miRNAs on retinal regeneration: a review. Stem Cell Res Ther 2021; 12:530. [PMID: 34620234 PMCID: PMC8499475 DOI: 10.1186/s13287-021-02588-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs), which consist of microvesicles and exosomes, are secreted from all cells to transform vital information in the form of lipids, proteins, mRNAs and small RNAs such as microRNAs (miRNAs). Many studies demonstrated that EVs' miRNAs have effects on target cells. Numerous people suffer from the blindness caused by retinal degenerations. The death of retinal neurons is irreversible and creates permanent damage to the retina. In the absence of acceptable cures for retinal degenerative diseases, stem cells and their paracrine agents including EVs have become a promising therapeutic approach. Several studies showed that the therapeutic effects of stem cells are due to the miRNAs of their EVs. Considering the effects of microRNAs in retinal cells development and function and studies which provide the possible roles of mesenchymal stem cells-derived EVs miRNA content on retinal diseases, we focused on the similarities between these two groups of miRNAs that could be helpful for promoting new therapeutic techniques for retinal degenerative diseases.
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Affiliation(s)
- Ali Rajool Dezfuly
- Department of Anatomical and Molecular Biology Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azadeh Safaee
- Department of Anatomical and Molecular Biology Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Salehi
- Department of Anatomical and Molecular Biology Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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3
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Kuznetsova AV, Rzhanova LA, Aleksandrova MA. Small Noncoding RNA in Regulation of Differentiation of Retinal Pigment Epithelium. Russ J Dev Biol 2021. [DOI: 10.1134/s106236042103005x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Swamy V, McGaughey D. Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0. Invest Ophthalmol Vis Sci 2019; 60:3236-3246. [PMID: 31343654 PMCID: PMC6660187 DOI: 10.1167/iovs.19-27106] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Purpose We develop an accessible and reliable RNA sequencing (RNA-seq) transcriptome database of healthy human eye tissues and a matching reactive web application to query gene expression in eye and body tissues. Methods We downloaded the raw sequence data for 1375 RNA-seq samples across 54 tissues in the Genotype-Tissue Expression (GTEx) project as a noneye reference set. We then queried several public repositories to find all healthy, nonperturbed, human eye-related tissue RNA-seq samples. The 916 eye and 1375 GTEx samples were sent into a Snakemake-based reproducible pipeline we wrote to quantify all known transcripts and genes, removes samples with poor sequence quality and mislabels, normalizes expression values across each tissue, perform 882 differential expression tests, calculate GO term enrichment, and output all as a single SQLite database file: the Eye in a Disk (EiaD) dataset. Furthermore, we rewrote the web application eyeIntegration (available in the public domain at https://eyeIntegration.nei.nih.gov) to display EiaD. Results The new eyeIntegration portal provides quick visualization of human eye-related transcriptomes published to date by database version, gene/transcript, 19 eye tissues, and 54 body tissues. As a test of the value of this unified pan-eye dataset, we showed that fetal and organoid retina are highly similar at a pan-transcriptome level, but display distinct differences in certain pathways and gene families, such as protocadherin and HOXB family members. Conclusions The eyeIntegration v1.0 web app serves the pan-human eye and body transcriptome dataset, EiaD. This offers the eye community a powerful and quick means to test hypotheses on human gene and transcript expression across 54 body and 19 eye tissues.
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Affiliation(s)
- Vinay Swamy
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - David McGaughey
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
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5
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Overexpression of MiR-183/96/182 Triggers Retina-Like Fate in Human Bone Marrow-Derived Mesenchymal Stem Cells (hBMSCs) in Culture. J Ophthalmol 2019; 2019:2454362. [PMID: 31885884 PMCID: PMC6927023 DOI: 10.1155/2019/2454362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/30/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022] Open
Abstract
Retinal degeneration is considered as a condition ensued by different blinding disorders such as retinitis pigmentosa, age-related macular degeneration, and diabetic retinopathy, which can cause loss of photoreceptor cells and also lead to significant vision deficiencies. Although there is no efficient treatment in this domain, transplantation of stem cells has been regarded as a therapeutic approach for retinal degeneration. Thus, the purpose of this study was to analyze the potential of human bone marrow-derived mesenchymal stem cells (hBMSCs) to differentiate into photoreceptor cells via transfection of microRNA (miRNA) in vitro for regenerative medicine purposes. To this end, miR-183/96/182 cluster was transfected into hBMSCs; then, qRT-PCR was performed to measure the expression levels of miR-183/96/182 cluster and some retina-specific neuronal genes such as OTX2, NRL, PKCα, and recoverin. CRX and rhodopsin (RHO) levels were also measured through qRT-PCR and immunocytochemistry, and subsequently, cellular change morphology was detected. The findings showed no changes in the morphology of the given cells, and the expression of the neuroretinal genes such as OTX2, NRL, and PKCα. Moreover, recoverin was upregulated upon miR-183/-96/-182 overexpression in cultured hBMSCs. Ectopic overexpression of the miR-183 cluster could further increase the expression of CRX and RHO at the messenger RNA (mRNA) and protein levels. Furthermore, the data indicated that the miR-183 cluster could serve as a crucial function in photoreceptor cell differentiation. In fact, miRNAs could be assumed as potential targets to exploit silent neuronal differentiation. Ultimately, it was suggested that in vitro overexpression of miR-183 cluster could trigger reprogramming of the hBMSCs to retinal neuron fate, especially photoreceptor cells.
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Louer EMM, Lorés-Motta L, Ion AM, Den Hollander AI, Deen PMT. Single nucleotide polymorphism rs13079080 is associated with differential regulation of the succinate receptor 1 (SUCNR1) gene by miRNA-4470. RNA Biol 2019; 16:1547-1554. [PMID: 31304868 PMCID: PMC6779389 DOI: 10.1080/15476286.2019.1643100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Oxidative stress is a feature of many common diseases. It leads to excessive formation and subsequent release of the mitochondrial metabolite succinate, which acts as a signalling molecule through binding the succinate receptor (SUCNR1). Recently, a potential role for SUCNR1 was proposed in age-related macular degeneration (AMD), a common cause of vision loss in the elderly associated with increased oxidative stress. Here, we evaluated the potential effect of genetic variants in SUCNR1 on its expression through differential micro-RNA (miRNA) binding to target mRNA, and investigated the relevance of altered SUCNR1 expression in AMD pathogenesis. We analysed common SUCNR1 SNPs for potential miRNA binding sites and identified rs13079080, located in the 3'-UTR and binding site for miRNA-4470. Both miRNA-4470 and SUCNR1 were found to be expressed in human retina. Moreover, using a luciferase reporter assay, a 60% decrease in activity was observed when miRNA-4470 was co-expressed with the C allele compared to the T allele of rs13079080. Finally, genotyping rs13079080 in an AMD case-control cohort revealed a protective effect of the TT genotype on AMD compared to the CC genotype (p = 0.007, odds ratio = 0.66). However, the association was not confirmed in the case-control study of the International AMD Genomics Consortium. Our study demonstrates that the T allele of rs13079080 in SUCNR1 disrupts a binding site for miRNA-4470, potentially increasing SUCNR1 expression and consequently increasing the capacity of sensing and dealing with oxidative stress. Therefore, it would be worthwhile assessing the relevance of rs13079080 in other oxidative stress-associated diseases in future studies.
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Affiliation(s)
- Elja M M Louer
- Dept of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands.,Dept of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center , Nijmegen , The Netherlands
| | - Laura Lorés-Motta
- Dept of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center , Nijmegen , The Netherlands
| | - Ana Mãdãlina Ion
- Dept of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands.,Dept of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center , Nijmegen , The Netherlands
| | - Anneke I Den Hollander
- Dept of Ophthalmology, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center , Nijmegen , The Netherlands.,Dept of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center , Nijmegen , The Netherlands
| | - Peter M T Deen
- Dept of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands
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7
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Bryan JM, Fufa TD, Bharti K, Brooks BP, Hufnagel RB, McGaughey DM. Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks. Hum Mol Genet 2019; 27:3325-3339. [PMID: 30239781 DOI: 10.1093/hmg/ddy239] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
The human eye is built from several specialized tissues which direct, capture and pre-process information to provide vision. The gene expression of the different eye tissues has been extensively profiled with RNA-seq across numerous studies. Large consortium projects have also used RNA-seq to study gene expression patterning across many different human tissues, minus the eye. There has not been an integrated study of expression patterns from multiple eye tissues compared with other human body tissues. We have collated all publicly available healthy human eye RNA-seq datasets as well as dozens of other tissues. We use this fully integrated dataset to probe the biological processes and pan expression relationships between the cornea, retina, retinal pigment epithelium (RPE)-choroid complex, and the rest of the human tissues with differential expression, clustering and gene ontology term enrichment tools. We also leverage our large collection of retina and RPE-choroid tissues to build the first human weighted gene correlation networks and use them to highlight known biological pathways and eye gene disease enrichment. We also have integrated publicly available single-cell RNA-seq data from mouse retina into our framework for validation and discovery. Finally, we make all these data, analyses and visualizations available via a powerful interactive web application (https://eyeintegration.nei.nih.gov/).
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Affiliation(s)
- John M Bryan
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Temesgen D Fufa
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kapil Bharti
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - David M McGaughey
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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8
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Tasharrofi N, Kouhkan F, Soleimani M, Soheili ZS, Kabiri M, Mahmoudi Saber M, Dorkoosh FA. Survival Improvement in Human Retinal Pigment Epithelial Cells via Fas Receptor Targeting by miR-374a. J Cell Biochem 2017; 118:4854-4861. [PMID: 28543858 DOI: 10.1002/jcb.26160] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/22/2017] [Indexed: 01/09/2023]
Abstract
Oxidative conditions of the eye could contribute to retinal cells loss through activating the Fas-L/Fas pathway. This phenomenon is one of the leading causes of some ocular diseases like age-related macular degeneration (AMD). By targeting proteins at their mRNA level, microRNAs (miRNAs) can regulate gene expression and cell function. The aim of the present study is to investigate Fas targeting by miR-374a and find whether it can inhibit Fas-mediated apoptosis in primary human retinal pigment epithelial (RPE) cells under oxidative stress. So, the primary human RPE cells were transfected with pre-miR-374a pLEX construct using polymeric carrier and were exposed to H2 O2 (200 μM) as an oxidant agent for induction of Fas expression. Fas expression at mRNA and protein level was evaluated by quantitative real-time PCR and Western blot analysis, respectively. These results revealed that miR-374a could prevent Fas upregulation under oxidative conditions. Moreover, Luciferase activity assay confirmed that Fas could be a direct target of miR-374a. The cell viability studies demonstrated that caspase-3 activity was negligible in miR-374a treated cells compared to the controls. Our data suggest miR-374a is a negative regulator of Fas death receptor which is able to enhance the cell survival and protect RPE cells against oxidative conditions. J. Cell. Biochem. 118: 4854-4861, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Nooshin Tasharrofi
- Faculty of Pharmacy, Department of Pharmaceutical Nanotechnology, Tehran University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy, Department of Pharmaceutics, Tehran University of Medical Science, Tehran, Iran
- Stem Cell Technology Research Center, Tehran, Iran
| | | | - Masoud Soleimani
- Faculty of Medical Science, Department of Hematology, Tarbiat Modares University, Tehran, Iran
| | - Zahra-Sheila Soheili
- Faculty of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mahboubeh Kabiri
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Mohaddeseh Mahmoudi Saber
- Faculty of Pharmacy, Department of Pharmaceutical Nanotechnology, Tehran University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy, Department of Pharmaceutics, Tehran University of Medical Science, Tehran, Iran
- Faculty of Pharmacy, Nanotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farid Abedin Dorkoosh
- Faculty of Pharmacy, Department of Pharmaceutics, Tehran University of Medical Science, Tehran, Iran
- Faculty of Pharmacy, Medical Biomaterial Research Center (MBRC), Tehran University of Medical Science, No. 1462, Kargar Ave, Tehran, Iran
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9
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Appropriately differentiated ARPE-19 cells regain phenotype and gene expression profiles similar to those of native RPE cells. Mol Vis 2017; 23:60-89. [PMID: 28356702 PMCID: PMC5360456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 03/03/2017] [Indexed: 11/30/2022] Open
Abstract
PURPOSE The RPE cell line ARPE-19 provides a dependable and widely used alternative to native RPE. However, replication of the native RPE phenotype becomes more difficult because these cells lose their specialized phenotype after multiple passages. Compounding this problem is the widespread use of ARPE-19 cells in an undifferentiated state to attempt to model RPE functions. We wished to determine whether suitable culture conditions and differentiation could restore the RPE-appropriate expression of genes and proteins to ARPE-19, along with a functional and morphological phenotype resembling native RPE. We compared the transcriptome of ARPE-19 cells kept in long-term culture with those of primary and other human RPE cells to assess the former's inherent plasticity relative to the latter. METHODS ARPE-19 cells at passages 9 to 12 grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum were differentiated for up to 4 months. Immunocytochemistry was performed on ARPE-19 cells grown on filters. Total RNA extracted from ARPE-19 cells cultured for either 4 days or 4 months was used for RNA sequencing (RNA-Seq) analysis using a 2 × 50 bp paired end protocol. The RNA-Seq data were analyzed to identify the affected pathways and recognize shared ontological classification among differentially expressed genes. RPE-specific mRNAs and miRNAs were assessed with quantitative real-time (RT)-PCR, and proteins with western blotting. RESULTS ARPE-19 cells grown for 4 months developed the classic native RPE phenotype with heavy pigmentation. RPE-expressed genes, including RPE65, RDH5, and RDH10, as well as miR-204/211, were greatly increased in the ARPE-19 cells maintained at confluence for 4 months. The RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of the genes in the differentiated ARPE-19 cells. Of the 16,757 genes with detectable signals, nearly 1,681 genes were upregulated, and 1,629 genes were downregulated with a fold change of 2.5 or more differences between 4 months and 4 days of culture. Gene Ontology analysis showed that the upregulated genes were associated with visual cycle, phagocytosis, pigment synthesis, cell differentiation, and RPE-related transcription factors. The majority of the downregulated genes play a role in cell cycle and proliferation. CONCLUSIONS The ARPE-19 cells cultured for 4 months developed a phenotype characteristic of native RPE and expressed proteins, mRNAs, and miRNAs characteristic of the RPE. Comparison of the ARPE-19 RNA-Seq data set with that of primary human fetal RPE, embryonic stem cell-derived RPE, and native RPE revealed an important overall similar expression ratio among all the models and native tissue. However, none of the cultured models reached the absolute values in the native tissue. The results of this study demonstrate that low-passage ARPE-19 cells can express genes specific to native human RPE cells when appropriately cultured and differentiated.
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10
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Yao S. MicroRNA biogenesis and their functions in regulating stem cell potency and differentiation. Biol Proced Online 2016; 18:8. [PMID: 26966421 PMCID: PMC4785656 DOI: 10.1186/s12575-016-0037-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/22/2016] [Indexed: 01/07/2023] Open
Abstract
Stem cells are unspecialized/undifferentiated cells that exist in embryos and adult tissues or can be converted from somatic differentiated cells. Use of stem cells for tissue regeneration and tissue engineering has been a cornerstone of the regenerative medicine. Stem cells are also believed to exist in cancer tissues, namely cancer stem cells (CSCs). Growing evidence suggests that CSCs are the culprit of cancer dormancy, progression and recurrence, and thus have recently received great attention. MicroRNAs (miRNAs) are a group of short, non-coding RNAs that regulate expression of a wide range of genes at a post-transcriptional manner. They are emerging as key regulators of stem cell behaviors. This mini review summarizes the basic biogenesis and mode of actions of miRNAs, recent progress and discoveries of miRNAs in cellular reprogramming, stem cell differentiation and cellular communication, as well as miRNAs in CSCs. Some potential of miRNAs in future biomedical applications and research pertaining to stem cells are briefly discussed.
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Affiliation(s)
- Shaomian Yao
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803 USA
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11
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Baras AS, Mitchell CJ, Myers JR, Gupta S, Weng LC, Ashton JM, Cornish TC, Pandey A, Halushka MK. miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy. PLoS One 2015; 10:e0143066. [PMID: 26571139 PMCID: PMC4646525 DOI: 10.1371/journal.pone.0143066] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/30/2015] [Indexed: 02/02/2023] Open
Abstract
Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM). Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA) are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench), miRge was faster (4 to 32-fold) and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.html.
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Affiliation(s)
- Alexander S. Baras
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christopher J. Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jason R. Myers
- Genomics Research Center, University of Rochester, Rochester, New York, United States of America
| | - Simone Gupta
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Lien-Chun Weng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John M. Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, United States of America
| | - Toby C. Cornish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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12
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Ng TK, Yung JSY, Choy KW, Cao D, Leung CKS, Cheung HS, Pang CP. Transdifferentiation of periodontal ligament-derived stem cells into retinal ganglion-like cells and its microRNA signature. Sci Rep 2015; 5:16429. [PMID: 26549845 PMCID: PMC4637909 DOI: 10.1038/srep16429] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/13/2015] [Indexed: 12/21/2022] Open
Abstract
Retinal diseases are the leading causes of irreversible visual impairment and blindness in the developed countries. Human retina has limited regenerative power to replace cell loss. Stem cell replacement therapy has been proposed as a viable option. Previously, we have induced human adult periodontal ligament stem cells (PDLSCs) to the retinal lineage. In this study, we modified our induction protocol to direct human adult PDLSCs into retinal ganglion-like cells and determined the microRNA (miRNA) signature of this transdifferentiation process. The differentiated PDLSCs demonstrated the characteristics of functional neurons as they expressed neuronal and retinal ganglion cell markers (ATOH7, POU4F2, β-III tubulin, MAP2, TAU, NEUROD1 and SIX3), formed synapses and showed glutamate-induced calcium responses as well as spontaneous electrical activities. The global miRNA expression profiling identified 44 upregulated and 27 downregulated human miRNAs after retinal induction. Gene ontology analysis of the predicted miRNA target genes confirmed the transdifferentiation is closely related to neuronal differentiation processes. Furthermore, the expressions of 2 miRNA-targeted candidates, VEGF and PTEN, were significantly upregulated during the induction process. This study identified the transdifferentiation process of human adult stem cells into retinal ganglion-like cells and revealed the involvement of both genetic and miRNA regulatory mechanisms.
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Affiliation(s)
- Tsz Kin Ng
- Department of Ophthalmology &Visual Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Jasmine S Y Yung
- Department of Ophthalmology &Visual Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Kwong Wai Choy
- Department of Obstetrics &Gynaecology, The Chinese University of Hong Kong, Hong Kong
| | - Di Cao
- Department of Ophthalmology &Visual Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Christopher K S Leung
- Department of Ophthalmology &Visual Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Herman S Cheung
- Geriatric Research, Education and Clinical Center, Miami Veterans Affairs Medical Center, Miami, FL, United States.,Department of Biomedical Engineering, College of Engineering, University of Miami, Coral Gables, FL, United States
| | - Chi Pui Pang
- Department of Ophthalmology &Visual Sciences, The Chinese University of Hong Kong, Hong Kong
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13
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Liu F, Weng X, Lin P, Zheng C, Xu H, Liu X, Ye H, Li X. Duhuo Jisheng decoction inhibits endoplasmic reticulum stress in chondrocytes induced by tunicamycin through the downregulation of miR-34a. Int J Mol Med 2015; 36:1311-8. [PMID: 26329269 DOI: 10.3892/ijmm.2015.2331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/13/2015] [Indexed: 11/05/2022] Open
Abstract
Our previous study showed that Duhuo Jisheng decoction (DHJSD) inhibited chondrocyte apoptosis by the mitochondria-dependent signaling pathway. Endoplasmic reticulum (ER) stress is upstream of the mitochondria-dependent signaling pathway and has been shown to promote chondrocyte apoptosis that occurs in osteoarthritis (OA). The present study aimed to evaluate whether DHJSD inhibits the chondrocyte apoptosis by regulating ER stress. DHJSD enhanced the viability of tunicamycin (TM)‑exposed chondrocytes, a model of ER stress-induced apoptosis, in a dose‑ and time‑dependent manner, as shown by MTT assay. The present results showed that DHJSD and sodium 4-phenylbutyrate (PBA), an ER stress inhibitor, reduced TM‑induced chondrocyte apoptosis by 4',6-diamidino‑2-phenylindole staining. To gain insight into the mechanisms of DHJSD that are responsible for enhancing the viability and inhibiting TM‑induced chondrocyte apoptosis, the associated mRNA expressions and protein levels were detected by reverse transcription‑polymerase chain reaction (RT‑PCR) and western blot analysis, respectively. The results showed that the expression levels of Xbp1, Xbp1s and Bcl‑2 were increased, and the expression levels of Bip, Atf4, Chop, Bax, caspase‑9 and ‑3 were decreased in the TM‑exposed chondrocytes treated with DHJSD or PBA compared with that in the TM‑exposed chondrocytes. To identify the possible mechanisms, the expression of miR‑34a was examined by the TaqMan microRNA assay, and was downregulated in the TM‑exposed chondrocytes treated with DHJSD or PBA compared with that in the TM-exposed chondrocytes. DHJSD inhibits ER stress in chondrocytes induced by exposure to TM by downregulating miR‑34a, suggesting that DHJSD may be a potential therapeutic agent for OA.
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Affiliation(s)
- Fayuan Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Xiaping Weng
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Pingdong Lin
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Chunsong Zheng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Huifeng Xu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Xianxiang Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Hongzhi Ye
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Xihai Li
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
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14
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Yuan Z, Ding S, Yan M, Zhu X, Liu L, Tan S, Jin Y, Sun Y, Li Y, Huang T. Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells. Gene 2015; 569:239-49. [PMID: 26028588 DOI: 10.1016/j.gene.2015.05.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs. Moreover, we found marked major-to-minor arm-switching events in 14 pre-miRNAs during the hESC to RPE cell differentiation phases. Our study for the first time reports exploring the variability of miRNA expression during the differentiation of hESCs into RPE cells and the results show that miRNA variability is a ubiquitous phenomenon in the ESC differentiation.
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Affiliation(s)
- Zhidong Yuan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China.
| | - Suping Ding
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Xiao Zhu
- Guangdong Province Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, China
| | - Lili Liu
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Shuhua Tan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yuanchang Jin
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yufeng Li
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Ting Huang
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
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15
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Choi SW, Kim JJ, Seo MS, Park SB, Kang TW, Lee JY, Lee BC, Kang I, Shin TH, Kim HS, Yu KR, Kang KS. miR-410 Inhibition Induces RPE Differentiation of Amniotic Epithelial Stem Cells via Overexpression of OTX2 and RPE65. Stem Cell Rev Rep 2014; 11:376-86. [DOI: 10.1007/s12015-014-9568-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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16
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Wang HC, Greene WA, Kaini RR, Shen-Gunther J, Chen HIH, Cai H, Wang Y. Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium. Cancer Inform 2014; 13:25-35. [PMID: 25392691 PMCID: PMC4218680 DOI: 10.4137/cin.s14074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/26/2014] [Accepted: 08/27/2014] [Indexed: 12/11/2022] Open
Abstract
The purpose of this study is to characterize the microRNA (miRNA) expression profiles of induced pluripotent stem (iPS) cells and retinal pigment epithelium (RPE) derived from induced pluripotent stem cells (iPS-RPE). MiRNAs have been demonstrated to play critical roles in both maintaining pluripotency and facilitating differentiation. Gene expression networks accountable for maintenance and induction of pluripotency are linked and share components with those networks implicated in oncogenesis. Therefore, we hypothesize that miRNA expression profiling will distinguish iPS cells from their iPS-RPE progeny. To identify and analyze differentially expressed miRNAs, RPE was derived from iPS using a spontaneous differentiation method. MiRNA microarray analysis identified 155 probes that were statistically differentially expressed between iPS and iPS-RPE cells. Up-regulated miRNAs including miR-181c and miR-129–5p may play a role in promoting differentiation, while down-regulated miRNAs such as miR-367, miR-18b, and miR-20b are implicated in cell proliferation. Subsequent miRNA–target and network analysis revealed that these miRNAs are involved in cellular development, cell cycle progression, cell death, and survival. A systematic interrogation of temporal and spatial expression of iPS-RPE miRNAs and their associated target mRNAs will provide new insights into the molecular mechanisms of carcinogenesis, eye differentiation and development.
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Affiliation(s)
- Heuy-Ching Wang
- Ocular Trauma, US Army Institute of Surgical Research, JBSA Fort Sam Houston, TX, USA
| | - Whitney A Greene
- Ocular Trauma, US Army Institute of Surgical Research, JBSA Fort Sam Houston, TX, USA
| | - Ramesh R Kaini
- Ocular Trauma, US Army Institute of Surgical Research, JBSA Fort Sam Houston, TX, USA
| | - Jane Shen-Gunther
- Gynecologic Oncology, Department of Clinical Investigation, Brooke Army Medical Center, JBSA Fort Sam Houston, TX, USA
| | - Hung-I H Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA. ; South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
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17
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Greene WA, Muñiz A, Plamper ML, Kaini RR, Wang HC. MicroRNA expression profiles of human iPS cells, retinal pigment epithelium derived from iPS, and fetal retinal pigment epithelium. J Vis Exp 2014:e51589. [PMID: 24999033 DOI: 10.3791/51589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The objective of this report is to describe the protocols for comparing the microRNA (miRNA) profiles of human induced-pluripotent stem (iPS) cells, retinal pigment epithelium (RPE) derived from human iPS cells (iPS-RPE), and fetal RPE. The protocols include collection of RNA for analysis by microarray, and the analysis of microarray data to identify miRNAs that are differentially expressed among three cell types. The methods for culture of iPS cells and fetal RPE are explained. The protocol used for differentiation of RPE from human iPS is also described. The RNA extraction technique we describe was selected to allow maximal recovery of very small RNA for use in a miRNA microarray. Finally, cellular pathway and network analysis of microarray data is explained. These techniques will facilitate the comparison of the miRNA profiles of three different cell types.
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Affiliation(s)
- Whitney A Greene
- Ocular Trauma, U.S. Army Institute of Surgical Research, JBSA Fort Sam Houston
| | - Alberto Muñiz
- Ocular Trauma, U.S. Army Institute of Surgical Research, JBSA Fort Sam Houston
| | - Mark L Plamper
- Ocular Trauma, U.S. Army Institute of Surgical Research, JBSA Fort Sam Houston
| | - Ramesh R Kaini
- Ocular Trauma, U.S. Army Institute of Surgical Research, JBSA Fort Sam Houston
| | - Heuy-Ching Wang
- Ocular Trauma, U.S. Army Institute of Surgical Research, JBSA Fort Sam Houston;
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18
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Human Pluripotent Stem Cell-Derived Retinal Pigmented Epithelium in Retinal Treatment: from Bench to Bedside. Mol Neurobiol 2014; 50:597-612. [DOI: 10.1007/s12035-014-8684-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/17/2014] [Indexed: 01/23/2023]
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19
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Liu Z, Jiang R, Yuan S, Wang N, Feng Y, Hu G, Zhu X, Huang K, Ma J, Xu G, Liu Q, Xue Z, Fan G. Integrated analysis of DNA methylation and RNA transcriptome during in vitro differentiation of human pluripotent stem cells into retinal pigment epithelial cells. PLoS One 2014; 9:e91416. [PMID: 24638073 PMCID: PMC3956675 DOI: 10.1371/journal.pone.0091416] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/12/2014] [Indexed: 12/22/2022] Open
Abstract
Using the paradigm of in vitro differentiation of hESCs/iPSCs into retinal pigment epithelial (RPE) cells, we have recently profiled mRNA and miRNA transcriptomes to define a set of RPE mRNA and miRNA signature genes implicated in directed RPE differentiation. In this study, in order to understand the role of DNA methylation in RPE differentiation, we profiled genome-scale DNA methylation patterns using the method of reduced representation bisulfite sequencing (RRBS). We found dynamic waves of de novo methylation and demethylation in four stages of RPE differentiation. Integrated analysis of DNA methylation and RPE transcriptomes revealed a reverse-correlation between levels of DNA methylation and expression of a subset of miRNA and mRNA genes that are important for RPE differentiation and function. Gene Ontology (GO) analysis suggested that genes undergoing dynamic methylation changes were related to RPE differentiation and maturation. We further compared methylation patterns among human ESC- and iPSC-derived RPE as well as primary fetal RPE (fRPE) cells, and discovered that specific DNA methylation pattern is useful to classify each of the three types of RPE cells. Our results demonstrate that DNA methylation may serve as biomarkers to characterize the cell differentiation process during the conversion of human pluripotent stem cells into functional RPE cells.
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Affiliation(s)
- Zhenshan Liu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Suzhou Institute of Tongji University, Suzhou, Jiangsu, China
| | - Rongfeng Jiang
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Songtao Yuan
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Na Wang
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yun Feng
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ganlu Hu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xianmin Zhu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Kevin Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jieliang Ma
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guotong Xu
- Tongji Eye Institute and Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Qinghuai Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- * E-mail: (QL); (ZX); (GF)
| | - Zhigang Xue
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Suzhou Institute of Tongji University, Suzhou, Jiangsu, China
- * E-mail: (QL); (ZX); (GF)
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Advanced Institute of Translational Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail: (QL); (ZX); (GF)
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20
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Masuda T, Wahlin K, Wan J, Hu J, Maruotti J, Yang X, Iacovelli J, Wolkow N, Kist R, Dunaief JL, Qian J, Zack DJ, Esumi N. Transcription factor SOX9 plays a key role in the regulation of visual cycle gene expression in the retinal pigment epithelium. J Biol Chem 2014; 289:12908-21. [PMID: 24634209 DOI: 10.1074/jbc.m114.556738] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The retinal pigment epithelium (RPE) performs specialized functions to support retinal photoreceptors, including regeneration of the visual chromophore. Enzymes and carrier proteins in the visual cycle function sequentially to regenerate and continuously supply 11-cis-retinal to retinal photoreceptor cells. However, it is unknown how the expression of the visual cycle genes is coordinated at the transcriptional level. Here, we show that the proximal upstream regions of six visual cycle genes contain chromatin-accessible sex-determining region Y box (SOX) binding sites, that SOX9 and LIM homeobox 2 (LHX2) are coexpressed in the nuclei of mature RPE cells, and that SOX9 acts synergistically with orthodenticle homeobox 2 (OTX2) to activate the RPE65 and retinaldehyde binding protein 1 (RLBP1) promoters and acts synergistically with LHX2 to activate the retinal G protein-coupled receptor (RGR) promoter. ChIP reveals that SOX9 and OTX2 bind to the promoter regions of RPE65, RLBP1, and RGR and that LHX2 binds to those of RPE65 and RGR in bovine RPE. ChIP with human fetal RPE cells shows that SOX9 and OTX2 also bind to the human RPE65, RLBP1, and RGR promoters. Conditional inactivation of Sox9 in mouse RPE results in reduced expression of several visual cycle genes, most dramatically Rpe65 and Rgr. Furthermore, bioinformatic analysis predicts that multiple common microRNAs (miRNAs) regulate visual cycle genes, and cotransfection of miRNA mimics with luciferase reporter constructs validated some of the predicted miRNAs. These results implicate SOX9 as a key regulator of visual cycle genes, reveal for the first time the functional role of LHX2 in the RPE, and suggest the possible regulation of visual cycle genes by common miRNAs.
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Affiliation(s)
- Tomohiro Masuda
- From the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
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21
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MicroRNAs in the Neural Retina. Int J Genomics 2014; 2014:165897. [PMID: 24745005 PMCID: PMC3972879 DOI: 10.1155/2014/165897] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 12/11/2022] Open
Abstract
The health and function of the visual system rely on a collaborative interaction between diverse classes of molecular regulators. One of these classes consists of transcription factors, which are known to bind to DNA and control the transcription activities of their target genes. For a long time, it was thought that the transcription factors were the only regulators of gene expression. More recently, however, a novel class of regulators emerged. This class consists of a large number of small noncoding endogenous RNAs, namely, miRNAs. The miRNAs compose an essential component of posttranscriptional gene regulation, since they ultimately control the fate of gene transcripts. The retina, as a part of the central nervous system, is a well-established model for unraveling the molecular mechanisms underlying neuronal and glial functions. Numerous recent efforts have been made towards identification of miRNAs and their inferred roles in the visual pathway. In this review, we summarize the current state of our knowledge regarding the expression and function of miRNA in the neural retina and we discuss their potential uses as biomarkers for some retinal disorders.
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22
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Rungsiwiwut R, Manolertthewan C, Numchaisrika P, Ahnonkitpanit V, Virutamasen P, Techakumphu M, Pruksananonda K. The ROCK inhibitor Y-26732 enhances the survival and proliferation of human embryonic stem cell-derived neural progenitor cells upon dissociation. Cells Tissues Organs 2013; 198:127-38. [PMID: 24158103 DOI: 10.1159/000354031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2013] [Indexed: 11/19/2022] Open
Abstract
Human neural progenitor cells (hNPCs) are the starting material required for neuronal subtype differentiation. Proliferation of hNPCs allows researchers to study the mechanistic complexities and microenvironments present during neural differentiation and to explore potential applications for hNPCs in cell therapies. The use of enzymatic dissociation during hNPC proliferation causes dissociation-induced apoptosis; therefore, in the present study, we examined the effect of the p-160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-26732 on dissociation-induced apoptosis of hNPCs. We generated hNPCs via embryoid body formation using serum-free culture medium supplemented with noggin. The established hNPCs were characterized and the effect of the ROCK inhibitor on hNPC dissociation was studied. We demonstrated that supplementation of the culture media with 10 μM Y-26732 efficiently reduced apoptosis of dissociated hNPCs; this supplementation was effective when the inhibitor was applied either at (i) 24 h before dissociation of the cells and at 24 h after plating the cells or (ii) at 24 h after plating of the cells only. In addition to reducing apoptosis, both supplementation conditions with Y-26732 enhanced the proliferation of dissociated hNPCs. Our findings provide the optimal time window for ROCK treatment of hNPC dissociation in respect to apoptosis and cell proliferation.
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Affiliation(s)
- Ruttachuk Rungsiwiwut
- Human Embryonic Stem Cell Research Center, Reproductive Medicine Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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23
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Fuhrmann S, Zou C, Levine EM. Retinal pigment epithelium development, plasticity, and tissue homeostasis. Exp Eye Res 2013; 123:141-50. [PMID: 24060344 DOI: 10.1016/j.exer.2013.09.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/05/2013] [Accepted: 09/07/2013] [Indexed: 12/13/2022]
Abstract
The retinal pigment epithelium (RPE) is a simple epithelium interposed between the neural retina and the choroid. Although only 1 cell-layer in thickness, the RPE is a virtual workhorse, acting in several capacities that are essential for visual function and preserving the structural and physiological integrities of neighboring tissues. Defects in RPE function, whether through chronic dysfunction or age-related decline, are associated with retinal degenerative diseases including age-related macular degeneration. As such, investigations are focused on developing techniques to replace RPE through stem cell-based methods, motivated primarily because of the seemingly limited regeneration or self-repair properties of mature RPE. Despite this, RPE cells have an unusual capacity to transdifferentiate into various cell types, with the particular fate choices being highly context-dependent. In this review, we describe recent findings elucidating the mechanisms and steps of RPE development and propose a developmental framework for understanding the apparent contradiction in the capacity for low self-repair versus high transdifferentiation.
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Affiliation(s)
- Sabine Fuhrmann
- Department of Ophthalmology & Visual Sciences, John A. Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA.
| | - ChangJiang Zou
- Department of Ophthalmology & Visual Sciences, John A. Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA.
| | - Edward M Levine
- Department of Ophthalmology & Visual Sciences, John A. Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA.
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