101
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Baba Y, Watabe Y, Sagara H, Watanabe S. Sall1 plays pivotal roles for lens fiber cell differentiation in mouse. Biochem Biophys Res Commun 2019; 512:927-933. [PMID: 30929925 DOI: 10.1016/j.bbrc.2019.03.098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/16/2019] [Indexed: 10/27/2022]
Abstract
Mammals possess four Sall transcription factors that play various roles in organogenesis. Previously, we found that Sall1 is expressed in microglia in the central nervous system, and it plays pivotal roles in microglia maturation. In the eye, Sall1 was also expressed in the developing lens, and we examined its role in lens development. A knock-in mouse harboring the EGFP gene in the Sall1 locus (Sall1-gfp) was used to analyze the Sall1 expression pattern. In Sall1-gfp/wild, EGFP was expressed throughout the presumptive lens at E11.5, and subsequently the expression in the lens epithelium became weaker. After birth, signals were observed in the equator region. The effects of Sall1 knockout on lens development were examined in Sall1-gfp/gfp. Lens sections revealed small vacuole-like holes and gaps in the center of the lens fibers at E14.5. Subsequently, the vacuoles appeared in most regions of the fiber cells. Electron microscopic analysis indicated that the vacuoles were between the fiber cells, leading to huge gaps. In addition, contact between the lens epithelium and apical end of the fiber cell was disrupted, and there were gaps between the adjoining lens epithelial cells. However, gap junction structure was observed by electron microscopic analysis, and immunostaining of Zo1 showed rather appropriate expression pattern. Immunohistochemistry indicated that the major lens transcription factors Prox1 and Pax6 were expressed in relatively normal patterns. However, although the expression of Prox1 and Pax6 decreased in nuclei in the control lens, it remained in Sall1-gfp/gfp. In addition, lower expression level of c-Maf protein was observed. Therefore, Sall1 is strongly expressed in the lens from the early developmental stage and plays an essential role in the maintenance of fiber cell and lens epithelium adhesion.
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Affiliation(s)
- Yukihiro Baba
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yui Watabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroshi Sagara
- Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
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102
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Bountali A, Tonge DP, Mourtada-Maarabouni M. RNA sequencing reveals a key role for the long non-coding RNA MIAT in regulating neuroblastoma and glioblastoma cell fate. Int J Biol Macromol 2019; 130:878-891. [PMID: 30836187 DOI: 10.1016/j.ijbiomac.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/29/2022]
Abstract
Myocardial Infarction Associated Transcript (MIAT) is a subnuclear lncRNA that interferes with alternative splicing and is associated with increased risk of various heart conditions and nervous system tumours. The current study aims to elucidate the role of MIAT in cell survival, apoptosis and migration in neuroblastoma and glioblastoma multiforme. To this end, MIAT was silenced by MIAT-specific siRNAs in neuroblastoma and glioblastoma cell lines, and RNA sequencing together with a series of functional assays were performed. The RNA sequencing has revealed that the expression of an outstanding number of genes is altered, including genes involved in cancer-related processes, such as cell growth and survival, apoptosis, reactive oxygen species (ROS) production and migration. Furthermore, the functional studies have confirmed the RNA sequencing leads, with our key findings suggesting that MIAT knockdown eliminates long-term survival and migration and increases basal apoptosis in neuroblastoma and glioblastoma cell lines. Taken together with the recent demonstration of the involvement of MIAT in glioblastoma, our observations suggest that MIAT could possess tumour-promoting properties, thereby acting as an oncogene, and has the potential to be used as a reliable biomarker for neuroblastoma and glioblastoma and be employed for prognostic, predictive and, potentially, therapeutic purposes for these cancers.
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Affiliation(s)
- Aikaterini Bountali
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Daniel P Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Mirna Mourtada-Maarabouni
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK.
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103
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Nakamoto C, Durward E, Horie M, Nakamoto M. Nell2 regulates the contralateral-versus-ipsilateral visual projection as a domain-specific positional cue. Development 2019; 146:dev.170704. [PMID: 30745429 DOI: 10.1242/dev.170704] [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: 08/15/2018] [Accepted: 01/29/2019] [Indexed: 01/15/2023]
Abstract
In mammals with binocular vision, retinal ganglion cell (RGC) axons from each eye project to eye-specific domains in the contralateral and ipsilateral dorsal lateral geniculate nucleus (dLGN), underpinning disparity-based stereopsis. Although domain-specific axon guidance cues that discriminate contralateral and ipsilateral RGC axons have long been postulated as a key mechanism for development of the eye-specific retinogeniculate projection, the molecular nature of such cues has remained elusive. Here, we show that the extracellular glycoprotein Nell2 (neural epidermal growth factor-like-like 2) is expressed in the dorsomedial region of the dLGN, which ipsilateral RGC axons terminate in and contralateral axons avoid. In Nell2 mutant mice, contralateral RGC axons abnormally invaded the ipsilateral domain of the dLGN, and ipsilateral axons terminated in partially fragmented patches, forming a mosaic pattern of contralateral and ipsilateral axon-termination zones. In vitro, Nell2 exerted inhibitory effects on contralateral, but not ipsilateral, RGC axons. These results provide evidence that Nell2 acts as a domain-specific positional label in the dLGN that discriminates contralateral and ipsilateral RGC axons, and that it plays essential roles in the establishment of the eye-specific retinogeniculate projection.
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Affiliation(s)
- Chizu Nakamoto
- Aberdeen Developmental Biology Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Elaine Durward
- Aberdeen Developmental Biology Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Masato Horie
- Department of CNS Research, Otsuka Pharmaceutical, 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Masaru Nakamoto
- Aberdeen Developmental Biology Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
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104
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Stem cell-based retina models. Adv Drug Deliv Rev 2019; 140:33-50. [PMID: 29777757 DOI: 10.1016/j.addr.2018.05.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/16/2018] [Accepted: 05/12/2018] [Indexed: 12/23/2022]
Abstract
From the early days of cell biological research, the eye-especially the retina-has evoked broad interest among scientists. The retina has since been thoroughly investigated and numerous models have been exploited to shed light on its development, morphology, and function. Apart from various animal models and human clinical and anatomical research, stem cell-based models of animal and human cells of origin have entered the field, especially during the last decade. Despite the observation that the retina of different species comprises endogenous stem cells, most stem cell-related research in the human retina is now based on pluripotent stem cell models. Herein, systems of two-dimensional (2D) cultures and co-cultures of distinctly differentiated retinal subtypes revealed a variety of cellular aspects but have in many aspects been replaced by three-dimensional (3D) structures-the so-called retinal organoids. These organoids not only contain all major retinal cell subtypes compared to the physiological situation, but also show a distinct layering in close proximity to the in vivo morphology. Nevertheless, all these models have inherent advantages and disadvantages, which are expounded and summarized in this review. Finally, we discuss current application aspects of stem cell-based retina models and the specific promises they hold for the future.
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105
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Abstract
This chapter provides an overview of the early developmental origins of six ocular tissues: the cornea, lens, ciliary body, iris, neural retina, and retina pigment epithelium. Many of these tissue types are concurrently specified and undergo a complex set of morphogenetic movements that facilitate their structural interconnection. Within the context of vertebrate eye organogenesis, we also discuss the genetic hierarchies of transcription factors and signaling pathways that regulate growth, patterning, cell type specification and differentiation.
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Affiliation(s)
- Joel B Miesfeld
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, Davis, CA, United States
| | - Nadean L Brown
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, Davis, CA, United States.
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106
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Kautzman AG, Keeley PW, Ackley CR, Leong S, Whitney IE, Reese BE. Xkr8 Modulates Bipolar Cell Number in the Mouse Retina. Front Neurosci 2018; 12:876. [PMID: 30559640 PMCID: PMC6286994 DOI: 10.3389/fnins.2018.00876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/09/2018] [Indexed: 12/25/2022] Open
Abstract
The present study interrogated a quantitative trait locus (QTL) on Chr 4 associated with the population sizes of two types of bipolar cell in the mouse retina. This locus was identified by quantifying the number of rod bipolar cells and Type 2 cone bipolar cells across a panel of recombinant inbred (RI) strains of mice derived from two inbred laboratory strains, C57BL/6J (B6/J) and A/J, and mapping a proportion of that variation in cell number, for each cell type, to this shared locus. There, we identified the candidate gene X Kell blood group precursor related family member 8 homolog (Xkr8). While Xkr8 has no documented role in the retina, we localize robust expression in the mature retina via in situ hybridization, confirm its developmental presence via immunolabeling, and show that it is differentially regulated during the postnatal period between the B6/J and A/J strains using qPCR. Microarray analysis, derived from whole eye mRNA from the entire RI strain set, demonstrates significant negative correlation of Xkr8 expression with the number of each of these two types of bipolar cells, and the variation in Xkr8 expression across the strains maps a cis-eQTL, implicating a regulatory variant discriminating the parental genomes. Xkr8 plasmid electroporation during development yielded a reduction in the number of bipolar cells in the retina, while sequence analysis of Xkr8 in the two parental strain genomes identified a structural variant in the 3′ UTR that may disrupt mRNA stability, and two SNPs in the promoter that create transcription factor binding sites. We propose that Xkr8, via its participation in mediating cell death, plays a role in the specification of bipolar cell number in the retina.
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Affiliation(s)
- Amanda G Kautzman
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Patrick W Keeley
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Caroline R Ackley
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephanie Leong
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Irene E Whitney
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Benjamin E Reese
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
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107
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Hao S, Wang L, Zhao K, Zhu X, Ye F. Rs1894720 polymorphism in MIAT increased susceptibility to age-related hearing loss by modulating the activation of miR-29b/SIRT1/PGC-1α signaling. J Cell Biochem 2018; 120:4975-4986. [PMID: 30556210 DOI: 10.1002/jcb.27773] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 09/06/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND MIAT may be implicated in the pathogenesis of age-related hearing loss (AHL). This study aimed to clarify the effect of a MIAT signaling pathway on the risk of AHL. METHODS Terminal deoxynucleotidyl transferase dUTP nick-end labeling assay, auditory brainstem response (ABR) and quantitative hair cell counts were used to compare the hearing functions in different groups of mice. 5,5,6,6-Tetrachloro-1,1,3,3-tetraethylbenzimidazolylcarbocyanine iodide (JC-1) dye method was used to establish the potential association between mitochondrial dysfunction and aging. Real-time polymerase chain reaction, Western blot analysis, computational analysis, and luciferase assay were conducted to establish a myocardial infarction associated transcript (MIAT) signaling pathway, whose role in the pathogenesis of AHL was further validated by 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay and flow cytometry. RESULTS Aged C57BL/6 mice were associated with a more severe level of hair cell loss, while exhibiting a higher ABR threshold at various frequencies as well as a lower percentage of inner/outer hair cells. A reduced mitochondrial membrane potential in the cochleae of aged C57BL/6 mice indicated the presence of mitochondrial dysfunction in these mice. Relative expression of MIAT, Sirtuin1 (SIRT1), and peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) was downregulated in aged mice, with microRNA-29b (miR-29b) being highly expressed. Also, MIAT binds to miR-29b, an inhibitor of SIRT1 expression. The regulatory relationship among MIAT, miR-29b, and SIRT1 was further validated by comparing the differentiated expression of these factors in cells treated with phosphate-buffered saline + H2 O2, a negative control + H2 O2, MIAT + H2 O2 , or H2 O2 + anti-miR-29b. CONCLUSION MIAT could elevate the expression of SIRT1/PGC-1α via downregulating miR-29b. And the downregulated SIRT/PGC-1α increased the incidence of AHL via promoting the apoptosis of cochlear hair cells.
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Affiliation(s)
- Shaojuan Hao
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Le Wang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kun Zhao
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaodan Zhu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fanglei Ye
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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108
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Guimarães RPDM, Landeira BS, Coelho DM, Golbert DCF, Silveira MS, Linden R, de Melo Reis RA, Costa MR. Evidence of Müller Glia Conversion Into Retina Ganglion Cells Using Neurogenin2. Front Cell Neurosci 2018; 12:410. [PMID: 30483060 PMCID: PMC6240664 DOI: 10.3389/fncel.2018.00410] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/22/2018] [Indexed: 01/09/2023] Open
Abstract
Degenerative retinopathies are the leading causes of irreversible visual impairment in the elderly, affecting hundreds of millions of patients. Müller glia cells (MGC), the main type of glia found in the vertebrate retina, can resume proliferation in the rodent adult injured retina but contribute weakly to tissue repair when compared to zebrafish retina. However, postnatal and adult mouse MGC can be genetically reprogrammed through the expression of the transcription factor (TF) Achaete-scute homolog 1 (ASCL1) into induced neurons (iNs), displaying key hallmarks of photoreceptors, bipolar and amacrine cells, which may contribute to regenerate the damaged retina. Here, we show that the TF neurogenin 2 (NEUROG2) is also sufficient to lineage-reprogram postnatal mouse MGC into iNs. The efficiency of MGC lineage conversion by NEUROG2 is similar to that observed after expression of ASCL1 and both TFs induce the generation of functionally active iNs. Treatment of MGC cultures with EGF and FGF2 prior to Neurog2 or Ascl1 expression enhances reprogramming efficiencies, what can be at least partially explained by an increase in the frequency of MGCs expressing sex determining region Y (SRY)-box 2 (SOX2). Transduction of either Neurog2 or Ascl1 led to the upregulation of key retina neuronal genes in MGC-derived iNs, but only NEUROG2 induced a consistent increase in the expression of putative retinal ganglion cell (RGC) genes. Moreover, in vivo electroporation of Neurog2 in late progenitors from the neonatal rat retina, which are transcriptionally similar to MGCs, also induced a shift in the generation of retinal cell subtypes, favoring neuronal differentiation at the expense of MGCs and resuming the generation of RGCs. Altogether, our data indicate that NEUROG2 induces lineage conversion of postnatal rodent MGCs into RGC-like iNs in vitro and resumes the generation of this neuronal type from late progenitors of the retina in vivo.
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Affiliation(s)
- Roberta Pereira de Melo Guimarães
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil.,Lab Neurogenesis, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Lab Neurochemistry, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Diego Marques Coelho
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment, IMD, Federal University of Rio Grande do Norte, Rio de Janeiro, Brazil
| | | | - Mariana S Silveira
- Lab Neurogenesis, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Linden
- Lab Neurogenesis, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo A de Melo Reis
- Lab Neurochemistry, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos R Costa
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
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109
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Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proc Natl Acad Sci U S A 2018; 115:E11061-E11070. [PMID: 30401736 DOI: 10.1073/pnas.1809609115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNA (miRNA)-124 is expressed in neurons, where it represses genes inhibitory for neuronal differentiation, including the RNA binding protein PTBP1. PTBP1 maintains nonneuronal splicing patterns of mRNAs that switch to neuronal isoforms upon neuronal differentiation. We find that primary (pri)-miR-124-1 is expressed in mouse embryonic stem cells where mature miR-124 is absent. PTBP1 binds to this precursor RNA upstream of the miRNA stem-loop to inhibit mature miR-124 expression in vivo and DROSHA cleavage of pri-miR-124-1 in vitro. This function for PTBP1 in repressing miR-124 biogenesis defines an additional regulatory loop in the already intricate interplay between these two molecules. Applying mathematical modeling to examine the dynamics of this regulation, we find that the pool of pri-miR-124 whose maturation is blocked by PTBP1 creates a robust and self-reinforcing transition in gene expression as PTBP1 is depleted during early neuronal differentiation. While interlocking regulatory loops are often found between miRNAs and transcriptional regulators, our results indicate that miRNA targeting of posttranscriptional regulators also reinforces developmental decisions. Notably, induction of neuronal differentiation observed upon PTBP1 knockdown likely results from direct derepression of miR-124, in addition to indirect effects previously described.
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110
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Indolfi C, Iaconetti C, Gareri C, Polimeni A, De Rosa S. Non-coding RNAs in vascular remodeling and restenosis. Vascul Pharmacol 2018; 114:49-63. [PMID: 30368024 DOI: 10.1016/j.vph.2018.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 10/08/2018] [Accepted: 10/18/2018] [Indexed: 02/06/2023]
Abstract
Vascular smooth muscle cells (VSMCs) and endothelial cells (ECs) are crucial in vascular remodeling. They exert pivotal roles in the development and progression of atherosclerosis, vascular response to injury, and restenosis after transcatheter angioplasty. As a witness of their importance in the cardiovascular system, a large body of evidence has accumulated about the role played by micro RNAs (miRNA) in modulating both VSMCs and ECs. More recently, a growing number of long noncoding RNA (lncRNAs) came beneath the spotlights in this research field. Several mechanisms have been revealed by which lncRNAs are able to exert a relevant biological impact on vascular remodeling. The aim of this review is to provide an integrated summary of ncRNAs that exert a relevant biological function in VSMCs and ECs of the vascular wall, with emphasis on the available clinical evidence of the potential usefulness of these molecules as circulating biomarkers of in-stent restenosis.
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Affiliation(s)
- Ciro Indolfi
- Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, Italy; URT CNR of IFC, University Magna Graecia, Italy.
| | - Claudio Iaconetti
- Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, Italy
| | - Clarice Gareri
- Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, Italy
| | - Alberto Polimeni
- Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, Italy
| | - Salvatore De Rosa
- Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, Italy
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111
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Zhang X, Li DY, Reilly MP. Long intergenic noncoding RNAs in cardiovascular diseases: Challenges and strategies for physiological studies and translation. Atherosclerosis 2018; 281:180-188. [PMID: 30316538 DOI: 10.1016/j.atherosclerosis.2018.09.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/05/2018] [Accepted: 09/27/2018] [Indexed: 12/25/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as important mediators of many biological processes relevant to human pathophysiologies, including cardiovascular diseases. In vitro studies have provided important knowledge of cellular functions and mechanisms for an increasing number of lincRNAs. Dysregulated lncRNAs have been associated with cell fate programming and development, vascular diseases, atherosclerosis, dyslipidemia and metabolic syndrome, and cardiac pathological hypertrophy. However, functional interrogation of individual lincRNAs in physiological and disease states is largely limited. The complex nature of lincRNA actions and poor species conservation of human lincRNAs pose substantial challenges to physiological studies in animal model systems and in clinical translation. This review summarizes recent findings of specific lincRNA physiological studies, including MALAT1, MeXis, Lnc-DC and others, in the context of cardiovascular diseases, examines complex mechanisms of lincRNA actions, reviews in vivo research strategies to delineate lincRNA functions and highlights challenges and approaches for physiological studies of primate-specific lincRNAs.
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Affiliation(s)
- Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Daniel Y Li
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA.
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112
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Yang C, Kelaini S, Caines R, Margariti A. RBPs Play Important Roles in Vascular Endothelial Dysfunction Under Diabetic Conditions. Front Physiol 2018; 9:1310. [PMID: 30294283 PMCID: PMC6158626 DOI: 10.3389/fphys.2018.01310] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/30/2018] [Indexed: 12/17/2022] Open
Abstract
Diabetes is one of the major health care problems worldwide leading to huge suffering and burden to patients and society. Diabetes is also considered as a cardiovascular disorder because of the correlation between diabetes and an increased incidence of cardiovascular disease. Vascular endothelial cell dysfunction is a major mediator of diabetic vascular complications. It has been established that diabetes contributes to significant alteration of the gene expression profile of vascular endothelial cells. Post-transcriptional regulation by RNA binding proteins (RBPs) plays an important role in the alteration of gene expression profile under diabetic conditions. The review focuses on the roles and mechanisms of critical RBPs toward diabetic vascular endothelial dysfunction. Deeper understanding of the post- transcriptional regulation by RBPs could lead to new therapeutic strategies against diabetic manifestation in the future.
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Affiliation(s)
- Chunbo Yang
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
| | - Sophia Kelaini
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
| | - Rachel Caines
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
| | - Andriana Margariti
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
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113
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Abstract
SIGNIFICANCE To maintain homeostasis, gene expression has to be tightly regulated by complex and multiple mechanisms occurring at the epigenetic, transcriptional, and post-transcriptional levels. One crucial regulatory component is represented by long noncoding RNAs (lncRNAs), nonprotein-coding RNA species implicated in all of these levels. Thus, lncRNAs have been associated with any given process or pathway of interest in a variety of systems, including the heart. Recent Advances: Mounting evidence implicates lncRNAs in cardiovascular diseases (CVD) and progression and their presence in the blood of heart disease patients indicates that they are attractive potential biomarkers. CRITICAL ISSUES Our understanding of the regulation and molecular mechanisms of action of most lncRNAs remains rudimentary. A challenge is represented by their often low evolutionary sequence conservation that limits the use of animal models for preclinical studies. Nevertheless, a growing number of lncRNAs with an impact on heart function is rapidly accumulating. In this study, we will discuss (i) lncRNAs that control heart homeostasis and disease; (ii) concepts, approaches, and methodologies necessary to study lncRNAs in the heart; and (iii) challenges posed and opportunities presented by lncRNAs as potential therapeutic targets and biomarkers. FUTURE DIRECTIONS A deeper knowledge of the molecular mechanisms underpinning CVDs is necessary to develop more effective treatments. Further studies are needed to clarify the regulation and function of lncRNAs in the heart before they can be considered as therapeutic targets and disease biomarkers. Antioxid. Redox Signal. 29, 880-901.
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Affiliation(s)
- Simona Greco
- 1 Molecular Cardiology Laboratory, IRCCS Policlinico San Donato , Milan, Italy
| | - Antonio Salgado Somoza
- 2 Cardiovascular Research Unit, Luxembourg Institute of Health (LIH) , Luxembourg, Luxembourg
| | - Yvan Devaux
- 2 Cardiovascular Research Unit, Luxembourg Institute of Health (LIH) , Luxembourg, Luxembourg
| | - Fabio Martelli
- 1 Molecular Cardiology Laboratory, IRCCS Policlinico San Donato , Milan, Italy
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114
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Chowdhury R, Laboissonniere LA, Wester AK, Muller M, Trimarchi JM. The Trim family of genes and the retina: Expression and functional characterization. PLoS One 2018; 13:e0202867. [PMID: 30208054 PMCID: PMC6135365 DOI: 10.1371/journal.pone.0202867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/10/2018] [Indexed: 11/19/2022] Open
Abstract
To better understand the mechanisms that govern the development of retinal neurons, it is critical to gain additional insight into the specific intrinsic factors that control cell fate decisions and neuronal maturation. In the developing mouse retina, Atoh7, a highly conserved transcription factor, is essential for retinal ganglion cell development. Moreover, Atoh7 expression in the developing retina occurs during a critical time period when progenitor cells are in the process of making cell fate decisions. We performed transcriptome profiling of Atoh7+ individual cells isolated from mouse retina. One of the genes that we found significantly correlated with Atoh7 in our transcriptomic data was the E3 ubiquitin ligase, Trim9. The correlation between Trim9 and Atoh7 coupled with the expression of Trim9 in the early mouse retina led us to hypothesize that this gene may play a role in the process of cell fate determination. To address the role of Trim9 in retinal development, we performed a functional analysis of Trim9 in the mouse and did not detect any morphological changes in the retina in the absence of Trim9. Thus, Trim9 alone does not appear to be involved in cell fate determination or early ganglion cell development in the mouse retina. We further hypothesize that the reason for this lack of phenotype may be compensation by one of the many additional TRIM family members we find expressed in the developing retina.
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Affiliation(s)
- Rebecca Chowdhury
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Lauren A. Laboissonniere
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Andrea K. Wester
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Madison Muller
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Jeffrey M. Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
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115
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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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116
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Albrecht NE, Alevy J, Jiang D, Burger CA, Liu BI, Li F, Wang J, Kim SY, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gaspero A, Justice MJ, Westenskow PD, Yamamoto S, Seavitt JR, Beaudet AL, Dickinson ME, Samuel MA. Rapid and Integrative Discovery of Retina Regulatory Molecules. Cell Rep 2018; 24:2506-2519. [PMID: 30157441 PMCID: PMC6170014 DOI: 10.1016/j.celrep.2018.07.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/15/2018] [Accepted: 07/27/2018] [Indexed: 12/26/2022] Open
Abstract
Retinal function relies on precisely organized neurons and synapses and a properly patterned vasculature to support them. Alterations in these features can result in vision loss. However, our understanding of retinal organization pathways remains incomplete because of a lack of methods to rapidly identify neuron and vasculature regulators in mammals. Here we developed a pipeline for the identification of neural and synaptic integrity genes by high-throughput retinal screening (INSiGHT) that analyzes candidate expression, vascular patterning, cellular organization, and synaptic arrangement. Using this system, we examined 102 mutant mouse lines and identified 16 unique retinal regulatory genes. Fifteen of these candidates are identified as novel retina regulators, and many (9 of 16) are associated with human neural diseases. These results expand the genetic landscape involved in retinal circuit organization and provide a road map for continued discovery of mammalian retinal regulators and disease-causing alleles.
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Affiliation(s)
- Nicholas E Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan Alevy
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney A Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian I Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fenge Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julia Wang
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angelina Gaspero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica J Justice
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Peter D Westenskow
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary E Dickinson
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie A Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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117
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Léger H, Santana E, Leu NA, Smith ET, Beltran WA, Aguirre GD, Luca FC. Ndr kinases regulate retinal interneuron proliferation and homeostasis. Sci Rep 2018; 8:12544. [PMID: 30135513 PMCID: PMC6105603 DOI: 10.1038/s41598-018-30492-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022] Open
Abstract
Ndr2/Stk38l encodes a protein kinase associated with the Hippo tumor suppressor pathway and is mutated in a naturally-occurring canine early retinal degeneration (erd). To elucidate the retinal functions of Ndr2 and its paralog Ndr1/Stk38, we generated Ndr1 and Ndr2 single knockout mice. Although retinal lamination appeared normal in these mice, Ndr deletion caused a subset of Pax6-positive amacrine cells to proliferate in differentiated retinas, while concurrently decreasing the number of GABAergic, HuD and Pax6-positive amacrine cells. Retinal transcriptome analyses revealed that Ndr2 deletion increased expression of neuronal stress genes and decreased expression of synaptic organization genes. Consistent with the latter, Ndr deletion dramatically reduced levels of Aak1, an Ndr substrate that regulates vesicle trafficking. Our findings indicate that Ndr kinases are important regulators of amacrine and photoreceptor cells and suggest that Ndr kinases inhibit the proliferation of a subset of terminally differentiated cells and modulate interneuron synapse function via Aak1.
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Affiliation(s)
- Hélène Léger
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - Evelyn Santana
- Division of Experimental Retinal Therapies, Department of Clinical Sciences and Advanced Medicine, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - N Adrian Leu
- Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - Eliot T Smith
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - William A Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences and Advanced Medicine, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - Gustavo D Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences and Advanced Medicine, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - Francis C Luca
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States.
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118
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Abstract
Eukaryotic cells depend on precise genome organization within the nucleus to maintain an appropriate gene-expression profile. Critical to this process is the packaging of functional domains of open and closed chromatin to specific regions of the nucleus, but how this is regulated remains unclear. In this study, we show that the zinc finger protein Casz1 regulates higher-order nuclear organization of rod photoreceptors in the mouse retina by repressing nuclear lamina function, which leads to central localization of heterochromatin. Loss of Casz1 in rods leads to an abnormal transcriptional profile followed by degeneration. These results identify Casz1 as a regulator of higher-order genome organization. Genome organization plays a fundamental role in the gene-expression programs of numerous cell types, but determinants of higher-order genome organization are poorly understood. In the developing mouse retina, rod photoreceptors represent a good model to study this question. They undergo a process called “chromatin inversion” during differentiation, in which, as opposed to classic nuclear organization, heterochromatin becomes localized to the center of the nucleus and euchromatin is restricted to the periphery. While previous studies showed that the lamin B receptor participates in this process, the molecular mechanisms regulating lamina function during differentiation remain elusive. Here, using conditional genetics, we show that the zinc finger transcription factor Casz1 is required to establish and maintain the inverted chromatin organization of rod photoreceptors and to safeguard their gene-expression profile and long-term survival. At the mechanistic level, we show that Casz1 interacts with the polycomb repressor complex in a splice variant-specific manner and that both are required to suppress the expression of the nuclear envelope intermediate filament lamin A/C in rods. Lamin A is in turn sufficient to regulate heterochromatin organization and nuclear position. Furthermore, we show that Casz1 is sufficient to expand and centralize the heterochromatin of fibroblasts, suggesting a general role for Casz1 in nuclear organization. Together, these data support a model in which Casz1 cooperates with polycomb to control rod genome organization, in part by silencing lamin A/C.
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119
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Singh AJ, Chang CN, Ma HY, Ramsey SA, Filtz TM, Kioussi C. FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb. Sci Rep 2018; 8:7670. [PMID: 29769607 PMCID: PMC5956100 DOI: 10.1038/s41598-018-25998-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle in the forelimb develops during embryonic and fetal development and perinatally. While much is known regarding the molecules involved in forelimb myogenesis, little is known about the specific mechanisms and interactions. Migrating skeletal muscle precursor cells express Pax3 as they migrate into the forelimb from the dermomyotome. To compare gene expression profiles of the same cell population over time, we isolated lineage-traced Pax3+ cells (Pax3EGFP) from forelimbs at different embryonic days. We performed whole transcriptome profiling via RNA-Seq of Pax3+ cells to construct gene networks involved in different stages of embryonic and fetal development. With this, we identified genes involved in the skeletal, muscular, vascular, nervous and immune systems. Expression of genes related to the immune, skeletal and vascular systems showed prominent increases over time, suggesting a non-skeletal myogenic context of Pax3-derived cells. Using co-expression analysis, we observed an immune-related gene subnetwork active during fetal myogenesis, further implying that Pax3-derived cells are not a strictly myogenic lineage, and are involved in patterning and three-dimensional formation of the forelimb through multiple systems.
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Affiliation(s)
- Arun J Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Chih-Ning Chang
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA.,Molecular Cell Biology Graduate Program, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Hsiao-Yen Ma
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Stephen A Ramsey
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, 97331, USA.,School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Theresa M Filtz
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Chrissa Kioussi
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA.
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120
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Kautzman AG, Keeley PW, Borhanian S, Ackley CR, Reese BE. Genetic Control of Rod Bipolar Cell Number in the Mouse Retina. Front Neurosci 2018; 12:285. [PMID: 29867309 PMCID: PMC5954209 DOI: 10.3389/fnins.2018.00285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/11/2018] [Indexed: 12/31/2022] Open
Abstract
Genetic variants modulate the numbers of various retinal cell types in mice. For instance, there is minimal variation in the number of rod bipolar cells (RBCs) in two inbred strains of mice (A/J and C57BL/6J), yet their F1 offspring contain significantly more RBCs than either parental strain. To investigate the genetic source of this variation, we mapped the variation in the number of RBCs across 24 genetically distinct recombinant inbred (RI) strains (the AXB/BXA strain-set), seeking to identify quantitative trait loci (QTL). We then sought to identify candidate genes and potential casual variants at those genomic loci. Variation in RBC number mapped to three genomic loci, each modulating cell number in excess of one-third of the range observed across the RI strains. At each of these loci, we identified candidate genes containing variants that might alter gene function or expression. The latter genes were also analyzed using a transcriptome database, revealing a subset for which expression correlated with variation in RBC number. Using an electroporation strategy, we demonstrate that early postnatal expression of one of them, Ggct (gamma-glutamyl cyclotransferase), modulates bipolar cell number. We identify candidate regulatory variants for this gene, finding a large structural variant (SV) in the putative promoter that reduces expression using a luciferase assay. This SV reducing Ggct expression in vitro is likely the causal variant within the gene associated with the variation in Ggct expression in vivo, implicating it as a quantitative trait variant (QTV) participating in the control of RBC number.
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Affiliation(s)
- Amanda G Kautzman
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Patrick W Keeley
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Sarra Borhanian
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Caroline R Ackley
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Benjamin E Reese
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.,Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
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121
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Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs SL, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. Nat Commun 2018; 9:1364. [PMID: 29636475 PMCID: PMC5893535 DOI: 10.1038/s41467-018-03856-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Age-related macular degeneration (AMD) is a significant cause of vision loss in the elderly. The extent to which epigenetic changes regulate AMD progression is unclear. Here we globally profile chromatin accessibility using ATAC-Seq in the retina and retinal pigmented epithelium (RPE) from AMD and control patients. Global decreases in chromatin accessibility occur in the RPE with early AMD, and in the retina of advanced disease, suggesting that dysfunction in the RPE drives disease onset. Footprints of photoreceptor and RPE-specific transcription factors are enriched in differentially accessible regions (DARs). Genes associated with DARs show altered expression in AMD. Cigarette smoke treatment of RPE cells recapitulates chromatin accessibility changes seen in AMD, providing an epigenetic link between a known risk factor for AMD and AMD pathology. Finally, overexpression of HDAC11 is partially responsible for the observed reduction in chromatin accessibility, suggesting that HDAC11 may be a potential new therapeutic target for AMD.
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Affiliation(s)
- Jie Wang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Peng Shang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Srinivasa R Sripathi
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pingwu Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Marisol Cano
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuli Xia
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Hugo W Moser Research Institute at Kennedy Krieger, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Shannath L Merbs
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Donald J Zack
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James T Handa
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Debasish Sinha
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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122
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Sun C, Huang L, Li Z, Leng K, Xu Y, Jiang X, Cui Y. Long non-coding RNA MIAT in development and disease: a new player in an old game. J Biomed Sci 2018. [PMID: 29534728 PMCID: PMC5851271 DOI: 10.1186/s12929-018-0427-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs), which are a portion of non-protein-coding RNAs (ncRNAs), have manifested a paramount role in the pathophysiology of human diseases, particularly in pathogenesis and progression of disease. Main body of the abstract Myocardial infarction associated transcript (MIAT), which was recently found to demonstrate aberrant expression in various diseases, such as myocardial infarction, schizophrenia, ischemic stroke, diabetic complications, age-related cataract and cancers, is a novel disease-related lncRNA. This work summarize current evidence regarding the biological functions and underlying mechanisms of lncRNA MIAT during disease development. Short conclusion LncRNA MIAT likely represents a feasible cancer biomarker or therapeutic target.
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Affiliation(s)
- Cheng Sun
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 XueFu Avenue, Harbin, Heilongjiang Province, China
| | - Lining Huang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 XueFu Avenue, Harbin, Heilongjiang Province, China
| | - Zhenglong Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 XueFu Avenue, Harbin, Heilongjiang Province, China
| | - Kaiming Leng
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 XueFu Avenue, Harbin, Heilongjiang Province, China
| | - Yi Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 XueFu Avenue, Harbin, Heilongjiang Province, China
| | - Xingming Jiang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 XueFu Avenue, Harbin, Heilongjiang Province, China.
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 XueFu Avenue, Harbin, Heilongjiang Province, China.
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123
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Pesaresi M, Bonilla-Pons SA, Simonte G, Sanges D, Di Vicino U, Cosma MP. Endogenous Mobilization of Bone-Marrow Cells Into the Murine Retina Induces Fusion-Mediated Reprogramming of Müller Glia Cells. EBioMedicine 2018. [PMID: 29525572 PMCID: PMC5952225 DOI: 10.1016/j.ebiom.2018.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Müller glial cells (MGCs) represent the most plastic cell type found in the retina. Following injury, zebrafish and avian MGCs can efficiently re-enter the cell cycle, proliferate and generate new functional neurons. The regenerative potential of mammalian MGCs, however, is very limited. Here, we showed that N-methyl-d-aspartate (NMDA) damage stimulates murine MGCs to re-enter the cell cycle and de-differentiate back to a progenitor-like stage. These events are dependent on the recruitment of endogenous bone marrow cells (BMCs), which, in turn, is regulated by the stromal cell-derived factor 1 (SDF1)-C-X-C motif chemokine receptor type 4 (CXCR4) pathway. BMCs mobilized into the damaged retina can fuse with resident MGCs, and the resulting hybrids undergo reprogramming followed by re-differentiation into cells expressing markers of ganglion and amacrine neurons. Our findings constitute an important proof-of-principle that mammalian MGCs retain their regenerative potential, and that such potential can be activated via cell fusion with recruited BMCs. In this perspective, our study could contribute to the development of therapeutic strategies based on the enhancement of mammalian endogenous repair capabilities. Endogenous bone marrow cells migrate into NMDA-damaged murine retinae and fuse with retinal Müller glial cells (MGCs). MGCs can be reprogrammed to retinal progenitors to then differentiate into ganglion and amacrine neurons. Modulation of the SDF1/CXCR4 pathway regulates BMC migration, BMC-MGC fusion, and MGC reprogramming.
Retinal degeneration is present in a large and heterogeneous group of debilitating diseases, often not curable. Cell therapy represents an interesting approach to regenerate injured retinal tissue. However, it comes with some hurdles in terms of engraftment and differentiation of the transplanted cells. Here, we reported that murine Müller glia cells can be converted into retinal neurons after fusion with endogenous bone marrow cells. The efficiency of this mechanism can be enhanced by perturbation of the SDF1/CXCR4 signaling pathway. Our study provides an important proof-of-principle that the limited endogenous regeneration capability of mammals can be enhanced by modulation of specific signaling pathways.
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Affiliation(s)
- Martina Pesaresi
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sergi A Bonilla-Pons
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.; Universitat de Barcelona (UB), Barcelona, Spain
| | - Giacoma Simonte
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Daniela Sanges
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Umberto Di Vicino
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.; ICREA, Barcelona, Spain..
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124
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Age-Related Macular Degeneration: New Paradigms for Treatment and Management of AMD. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:8374647. [PMID: 29484106 PMCID: PMC5816845 DOI: 10.1155/2018/8374647] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 12/06/2017] [Indexed: 12/03/2022]
Abstract
Age-related macular degeneration (AMD) is a well-characterized and extensively studied disease. It is currently considered the leading cause of visual disability among patients over 60 years. The hallmark of early AMD is the formation of drusen, pigmentary changes at the macula, and mild to moderate vision loss. There are two forms of AMD: the “dry” and the “wet” form that is less frequent but is responsible for 90% of acute blindness due to AMD. Risk factors have been associated with AMD progression, and they are taking relevance to understand how AMD develops: (1) advanced age and the exposition to environmental factors inducing high levels of oxidative stress damaging the macula and (2) this damage, which causes inflammation inducing a vicious cycle, altogether causing central vision loss. There is neither a cure nor treatment to prevent AMD. However, there are some treatments available for the wet form of AMD. This article will review some molecular and cellular mechanisms associated with the onset of AMD focusing on feasible treatments for each related factor in the development of this pathology such as vascular endothelial growth factor, oxidative stress, failure of the clearance of proteins and organelles, and glial cell dysfunction in AMD.
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125
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Clark BS, Blackshaw S. Understanding the Role of lncRNAs in Nervous System Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:253-282. [PMID: 28815543 DOI: 10.1007/978-981-10-5203-3_9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of lncRNAs has expanded within mammals in tandem with the evolution of increased brain complexity, suggesting that lncRNAs play an integral role in this process. In this chapter, we will highlight the identification and characterization of lncRNAs in nervous system development. We discuss the potential role of lncRNAs in nervous system and brain evolution, along with efforts to create comprehensive catalogues that analyze spatial and temporal changes in lncRNA expression during nervous system development. Additionally, we focus on recent endeavors that attempt to assign function to lncRNAs during nervous system development. We highlight discrepancies that have been observed between in vitro and in vivo studies of lncRNA function and the challenges facing researchers in conducting mechanistic analyses of lncRNAs in the developing nervous system. Altogether, this chapter highlights the emerging role of lncRNAs in the developing brain and sheds light on novel, RNA-mediated mechanisms by which nervous system development is controlled.
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Affiliation(s)
- Brian S Clark
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seth Blackshaw
- Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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126
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Budak G, Dash S, Srivastava R, Lachke SA, Janga SC. Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues. Exp Eye Res 2018; 168:57-68. [PMID: 29337142 DOI: 10.1016/j.exer.2018.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 01/23/2023]
Abstract
Advances in sequencing have facilitated nucleotide-resolution genome-wide transcriptomic profiles across multiple mouse eye tissues. However, these RNA sequencing (RNA-seq) based eye developmental transcriptomes are not organized for easy public access, making any further analysis challenging. Here, we present a new database "Express" (http://www.iupui.edu/∼sysbio/express/) that unifies various mouse lens and retina RNA-seq data and provides user-friendly visualization of the transcriptome to facilitate gene discovery in the eye. We obtained RNA-seq data encompassing 7 developmental stages of lens in addition to that on isolated lens epithelial and fibers, as well as on 11 developmental stages of retina/isolated retinal rod photoreceptor cells from publicly available wild-type mouse datasets. These datasets were pre-processed, aligned, quantified and normalized for expression levels of known and novel transcripts using a unified expression quantification framework. Express provides heatmap and browser view allowing easy navigation of the genomic organization of transcripts or gene loci. Further, it allows users to search candidate genes and export both the visualizations and the embedded data to facilitate downstream analysis. We identified total of >81,000 transcripts in the lens and >178,000 transcripts in the retina across all the included developmental stages. This analysis revealed that a significant number of the retina-expressed transcripts are novel. Expression of several transcripts in the lens and retina across multiple developmental stages was independently validated by RT-qPCR for established genes such as Pax6 and Lhx2 as well as for new candidates such as Elavl4, Rbm5, Pabpc1, Tia1 and Tubb2b. Thus, Express serves as an effective portal for analyzing pruned RNA-seq expression datasets presently collected for the lens and retina. It will allow a wild-type context for the detailed analysis of targeted gene-knockout mouse ocular defect models and facilitate the prioritization of candidate genes from Exome-seq data of eye disease patients.
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Affiliation(s)
- Gungor Budak
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, United States
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, United States; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, United States
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, United States.
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127
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Yang L, Lyu L, Wu W, Lei D, Tu Y, Xu D, Feng J, He L. Genome-wide identification of long non-coding RNA and mRNA profiling using RNA sequencing in subjects with sensitive skin. Oncotarget 2017; 8:114894-114910. [PMID: 29383128 PMCID: PMC5777740 DOI: 10.18632/oncotarget.23147] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/14/2017] [Indexed: 12/15/2022] Open
Abstract
Sensitive skin (SS) is a condition of subjective cutaneous hyper-reactivity. The role of long non-coding RNAs (lncRNAs) in subjects with SS is unclear. Therefore, the aim of the present study was to provide a comprehensive profile of the mRNAs and lncRNAs in subjects with SS. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis presented the characteristics of associated protein-coding genes. In addition, a co-expression network of lncRNA and mRNA was constructed to identify potential underlying regulation targets; the results were verified by quantitative real-time PCR (qRT-PCR) and RNA-seq analyses in patients with SS and normal samples. Compared with the normal skin group, 266 novel lncRNAs and 6750 annotated lncRNAs were identified in the SS group. A total of 71 lncRNA transcripts and 2615 mRNA transcripts were differentially expressed (P < 0.05). The heat signature of the SS samples could be distinguished from the normal skin samples, whereas the majority of the genes that were present in enriched pathways were those that participated in focal adhesion, PI3K-Akt signaling, and cancer-related pathways. Five transcripts were selected for qRT-PCR analysis and the results were consistent with RNA-seq. The results suggested that LNC_000265 may play a role in the epidermal barrier structure of patient with SS. The data suggest novel genes and pathways that may be involved in the pathogenesis of SS and highlight potential targets that could be used for individualized treatment applications.
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Affiliation(s)
- Li Yang
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lechun Lyu
- Technology Transfer Center, Kunming Medical University, Department of Physiology, Kunming Medical University, Kunming, China
| | - Wenjuan Wu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dongyun Lei
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ying Tu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dan Xu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiaqi Feng
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li He
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
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128
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Shang W, Tang Z, Gao Y, Qi H, Su X, Zhang Y, Yang R. LncRNA RNCR3 promotes Chop expression by sponging miR-185-5p during MDSC differentiation. Oncotarget 2017; 8:111754-111769. [PMID: 29340089 PMCID: PMC5762357 DOI: 10.18632/oncotarget.22906] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) play a critical role in regulating immune responses in cancer and other pathological conditions. Mechanism(s) regulating MDSC differentiation and function is not completely clear, especially epigenetic regulation. In this study, we found that MDSCs express retinal non-coding RNA3 (RNCR3), and the expression in MDSCs is upregulated by inflammatory and tumor associated factors. RNCR3 may function as a competing endogenous RNA (ceRNA) to promote Chop expression by sponging miR-185-5p during MDSC differentiation. RNCR3 knockdown suppressed differentiation and function of MDSCs in vitro and in vivo. Quantitative RT-PCR showed that RNCR3 was negatively regulated by miR-185-5p in MDSCs. MiR-185-5p affected the expansion of MDSCs and reversed the effect of RNCR3 on MDSC differentiation and function through directly targeting Chop. Thus, our results suggest a RNCR3/miR-185-5p/Chop autologously strengthening network to promote MDSC differentiation and suppressive function in response to extracellular inflammatory and tumor-associated signals.
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Affiliation(s)
- Wencong Shang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, China.,Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Zhenzhen Tang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, China.,Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Yunhuan Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, China.,Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Houbao Qi
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, China.,Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Xiaomin Su
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, China.,Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Yuan Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, China.,Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Rongcun Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, China.,Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
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129
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Roles of miRNAs and long noncoding RNAs in the progression of diabetic retinopathy. Biosci Rep 2017; 37:BSR20171157. [PMID: 29074557 PMCID: PMC5705777 DOI: 10.1042/bsr20171157] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/22/2017] [Accepted: 10/25/2017] [Indexed: 02/07/2023] Open
Abstract
Diabetic retinopathy (DR) is the leading cause of blindness in working-age adults across the world. The pathogenesis of DR is multifactorial and the molecular mechanisms are still not fully understood. Accumulating evidence has demonstrated that noncoding RNAs (ncRNAs) may be aberrantly expressed and may play vital roles in the development of DR. Amongst ncRNAs, miRNAs and long ncRNAs (lncRNAs) are known for their regulatory functions. Here, we summarize the functions and mechanisms of known aberrantly expressed miRNAs and lncRNAs in DR. Additionally, a novel lncRNA–mRNA–miRNA network is included in this review. We highlight original studies that provide detailed data about the mechanisms of miRNAs and lncRNAs, their applications as diagnostic or prognostic biomarkers, and their potential therapeutic targets. In conclusion, this review will help us gain a better understanding of the molecular mechanisms by which miRNAs and lncRNAs perform their functions in DR, and provide general strategies and directions for future research.
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130
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Decoding resistant hypertension signalling pathways. Clin Sci (Lond) 2017; 131:2813-2834. [PMID: 29184046 DOI: 10.1042/cs20171398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
Abstract
Resistant hypertension (RH) is a clinical condition in which the hypertensive patient has become resistant to drug therapy and is often associated with increased cardiovascular morbidity and mortality. Several signalling pathways have been studied and related to the development and progression of RH: modulation of sympathetic activity by leptin and aldosterone, primary aldosteronism, arterial stiffness, endothelial dysfunction and variations in the renin-angiotensin-aldosterone system (RAAS). miRNAs comprise a family of small non-coding RNAs that participate in the regulation of gene expression at post-transcriptional level. miRNAs are involved in the development of both cardiovascular damage and hypertension. Little is known of the molecular mechanisms that lead to development and progression of this condition. This review aims to cover the potential roles of miRNAs in the mechanisms associated with the development and consequences of RH, and explore the current state of the art of diagnostic and therapeutic tools based on miRNA approaches.
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131
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Todd L, Suarez L, Quinn C, Fischer AJ. Retinoic Acid-Signaling Regulates the Proliferative and Neurogenic Capacity of Müller Glia-Derived Progenitor Cells in the Avian Retina. Stem Cells 2017; 36:392-405. [PMID: 29193451 DOI: 10.1002/stem.2742] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/16/2017] [Accepted: 11/03/2017] [Indexed: 12/26/2022]
Abstract
In the retina, Müller glia have the potential to become progenitor cells with the ability to proliferate and regenerate neurons. However, the ability of Müller glia-derived progenitor cells (MGPCs) to proliferate and produce neurons is limited in higher vertebrates. Using the chick model system, we investigate how retinoic acid (RA)-signaling influences the proliferation and the formation of MGPCs. We observed an upregulation of cellular RA binding proteins (CRABP) in the Müller glia of damaged retinas where the formation of MGPCs is known to occur. Activation of RA-signaling was stimulated, whereas inhibition suppressed the proliferation of MGPCs in damaged retinas and in fibroblast growth factor 2-treated undamaged retinas. Furthermore, inhibition of RA-degradation stimulated the proliferation of MGPCs. Levels of Pax6, Klf4, and cFos were upregulated in MGPCs by RA agonists and downregulated in MGPCs by RA antagonists. Activation of RA-signaling following MGPC proliferation increased the percentage of progeny that differentiated as neurons. Similarly, the combination of RA and insulin-like growth factor 1 (IGF1) significantly increased neurogenesis from retinal progenitors in the circumferential marginal zone (CMZ). In summary, RA-signaling stimulates the formation of proliferating MGPCs and enhances the neurogenic potential of MGPCs and stem cells in the CMZ. Stem Cells 2018;36:392-405.
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Affiliation(s)
- Levi Todd
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Lilianna Suarez
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Colin Quinn
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Andy J Fischer
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
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132
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Hartl D, Krebs AR, Jüttner J, Roska B, Schübeler D. Cis-regulatory landscapes of four cell types of the retina. Nucleic Acids Res 2017; 45:11607-11621. [PMID: 29059322 PMCID: PMC5714137 DOI: 10.1093/nar/gkx923] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/28/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022] Open
Abstract
The retina is composed of ∼50 cell-types with specific functions for the process of vision. Identification of the cis-regulatory elements active in retinal cell-types is key to elucidate the networks controlling this diversity. Here, we combined transcriptome and epigenome profiling to map the regulatory landscape of four cell-types isolated from mouse retinas including rod and cone photoreceptors as well as rare inter-neuron populations such as horizontal and starburst amacrine cells. Integration of this information reveals sequence determinants and candidate transcription factors for controlling cellular specialization. Additionally, we refined parallel reporter assays to enable studying the transcriptional activity of large collection of sequences in individual cell-types isolated from a tissue. We provide proof of concept for this approach and its scalability by characterizing the transcriptional capacity of several hundred putative regulatory sequences within individual retinal cell-types. This generates a catalogue of cis-regulatory regions active in retinal cell types and we further demonstrate their utility as potential resource for cellular tagging and manipulation.
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Affiliation(s)
- Dominik Hartl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
- University of Basel, Faculty of Sciences, Petersplatz 1, CH 4003 Basel, Switzerland
| | - Arnaud R. Krebs
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
| | - Josephine Jüttner
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
- University of Basel, Department of Ophthalmology, Mittlere Strasse 91, CH 4031 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
- University of Basel, Faculty of Sciences, Petersplatz 1, CH 4003 Basel, Switzerland
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133
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Daum JM, Keles Ö, Holwerda SJ, Kohler H, Rijli FM, Stadler M, Roska B. The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch. eLife 2017; 6:31437. [PMID: 29106373 PMCID: PMC5685475 DOI: 10.7554/elife.31437] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/03/2017] [Indexed: 11/16/2022] Open
Abstract
High-resolution daylight vision is mediated by cone photoreceptors. The molecular program responsible for the formation of their light sensor, the outer segment, is not well understood. We correlated daily changes in ultrastructure and gene expression in postmitotic mouse cones, between birth and eye opening, using serial block-face electron microscopy (EM) and RNA sequencing. Outer segments appeared rapidly at postnatal day six and their appearance coincided with a switch in gene expression. The switch affected over 14% of all expressed genes. Genes that switched off were rich in transcription factors and neurogenic genes. Those that switched on contained genes relevant for cone function. Chromatin rearrangements in enhancer regions occurred before the switch was completed, but not after. We provide a resource comprised of correlated EM, RNAseq, and ATACseq data, showing that the growth of a key compartment of a postmitotic cell involves an extensive switch in gene expression and chromatin accessibility.
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Affiliation(s)
- Janine M Daum
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Özkan Keles
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sjoerd Jb Holwerda
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Michael Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Insitute of Bioinformatics, Basel, Switzerland
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
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134
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Andersen RE, Lim DA. Forging our understanding of lncRNAs in the brain. Cell Tissue Res 2017; 371:55-71. [PMID: 29079882 DOI: 10.1007/s00441-017-2711-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
During both development and adulthood, the human brain expresses many thousands of long noncoding RNAs (lncRNAs), and aberrant lncRNA expression has been associated with a wide range of neurological diseases. Although the biological significance of most lncRNAs remains to be discovered, it is now clear that certain lncRNAs carry out important functions in neurodevelopment, neural cell function, and perhaps even diseases of the human brain. Given the relatively inclusive definition of lncRNAs-transcripts longer than 200 nucleotides with essentially no protein coding potential-this class of noncoding transcript is both large and very diverse. Furthermore, emerging data indicate that lncRNA genes can act via multiple, non-mutually exclusive molecular mechanisms, and specific functions are difficult to predict from lncRNA expression or sequence alone. Thus, the different experimental approaches used to explore the role of a lncRNA might each shed light upon distinct facets of its overall molecular mechanism, and combining multiple approaches may be necessary to fully illuminate the function of any particular lncRNA. To understand how lncRNAs affect brain development and neurological disease, in vivo studies of lncRNA function are required. Thus, in this review, we focus our discussion upon a small set of neural lncRNAs that have been experimentally manipulated in mice. Together, these examples illustrate how studies of individual lncRNAs using multiple experimental approaches can help reveal the richness and complexity of lncRNA function in both neurodevelopment and diseases of the brain.
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Affiliation(s)
- Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA.,Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA. .,San Francisco Veterans Affairs Medical Center, San Francisco, CA, 94121, USA.
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135
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Remez LA, Onishi A, Menuchin-Lasowski Y, Biran A, Blackshaw S, Wahlin KJ, Zack DJ, Ashery-Padan R. Pax6 is essential for the generation of late-born retinal neurons and for inhibition of photoreceptor-fate during late stages of retinogenesis. Dev Biol 2017; 432:140-150. [PMID: 28993200 DOI: 10.1016/j.ydbio.2017.09.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/08/2016] [Accepted: 09/23/2017] [Indexed: 12/16/2022]
Abstract
In the developing retina, as in other regions of the CNS, neural progenitors give rise to individual cell types during discrete temporal windows. Pax6 is expressed in retinal progenitor cells (RPCs) throughout the course of retinogenesis, and has been shown to be required during early retinogenesis for generation of most early-born cell types. In this study, we examined the function of Pax6 in postnatal mouse retinal development. We found that Pax6 is essential for the generation of late-born interneurons, while inhibiting photoreceptor differentiation. Generation of bipolar interneurons requires Pax6 expression in RPCs, while Pax6 is required for the generation of glycinergic, but not for GABAergic or non-GABAergic-non-glycinergic (nGnG) amacrine cell subtypes. In contrast, overexpression of either full-length Pax6 or its 5a isoform in RPCs induces formation of cells with nGnG amacrine features, and suppresses generation of other inner retinal cell types. Moreover, overexpression of both Pax6 variants prevents photoreceptor differentiation, most likely by inhibiting Crx expression. Taken together, these data show that Pax6 acts in RPCs to control differentiation of multiple late-born neuronal cell types.
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Affiliation(s)
- Liv Aleen Remez
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Akishi Onishi
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Yotam Menuchin-Lasowski
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Assaf Biran
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Karl J Wahlin
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, United States
| | - Donlad J Zack
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel.
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136
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Li Y, Xu F, Xiao H, Han F. Long noncoding RNA BDNF‐AS inversely regulated BDNF and modulated high‐glucose induced apoptosis in human retinal pigment epithelial cells. J Cell Biochem 2017; 119:817-823. [DOI: 10.1002/jcb.26245] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 06/26/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Yanyan Li
- Department of OphthalmologyThe Second Affiliated Hospital of Mudanjiang Medical UniversityMudanjiangChina
| | - Feng Xu
- Department of GerontologyThe Second Affiliated Hospital of Mudanjiang Medical UniversityMudanjiangChina
| | - Hanyan Xiao
- Second Department of NeurologyThe Second Affiliated Hospital of Mudanjiang Medical UniversityMudanjiangChina
| | - Feng Han
- Department of OphthalmologyThe Second Affiliated Hospital of Mudanjiang Medical UniversityMudanjiangChina
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137
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Groman-Lupa S, Adewumi J, Park KU, Brzezinski JA. The Transcription Factor Prdm16 Marks a Single Retinal Ganglion Cell Subtype in the Mouse Retina. Invest Ophthalmol Vis Sci 2017; 58:5421-5433. [PMID: 29053761 PMCID: PMC5656415 DOI: 10.1167/iovs.17-22442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/20/2017] [Indexed: 12/04/2022] Open
Abstract
Purpose Retinal ganglion cells (RGC) can be categorized into roughly 30 distinct subtypes. How these subtypes develop is poorly understood, in part because few unique subtype markers have been characterized. We tested whether the Prdm16 transcription factor is expressed by RGCs as a class or within particular ganglion cell subtypes. Methods Embryonic and mature retinal sections and flatmount preparations were examined by immunohistochemistry for Prdm16 and several other cell type-specific markers. To visualize the morphology of Prdm16+ cells, we utilized Thy1-YFP-H transgenic mice, where a small random population of RGCs expresses yellow fluorescent protein (YFP) throughout the cytoplasm. Results Prdm16 was expressed in the retina starting late in embryogenesis. Prdm16+ cells coexpressed the RGC marker Brn3a. These cells were arranged in an evenly spaced pattern and accounted for 2% of all ganglion cells. Prdm16+ cells coexpressed parvalbumin, but not calretinin, melanopsin, Smi32, or CART. This combination of marker expression and morphology data from Thy1-YFP-H mice suggested that the Prdm16+ cells represented a single ganglion cell subtype. Prdm16 also marked vascular endothelial cells and mural cells of retinal arterioles. Conclusions A single subtype of ganglion cell appears to be uniquely marked by Prdm16 expression. While the precise identity of these ganglion cells is unclear, they most resemble the G9 subtype described by Völgyi and colleagues in 2009. Future studies are needed to determine the function of these ganglion cells and whether Prdm16 regulates their development.
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Affiliation(s)
- Sergio Groman-Lupa
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Joseph Adewumi
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
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138
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Ito SI, Onishi A, Takahashi M. Chemically-induced photoreceptor degeneration and protection in mouse iPSC-derived three-dimensional retinal organoids. Stem Cell Res 2017; 24:94-101. [DOI: 10.1016/j.scr.2017.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/07/2017] [Accepted: 08/21/2017] [Indexed: 01/02/2023] Open
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139
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Berdasco M, Gómez A, Rubio MJ, Català-Mora J, Zanón-Moreno V, Lopez M, Hernández C, Yoshida S, Nakama T, Ishikawa K, Ishibashi T, Boubekeur AM, Louhibi L, Pujana MA, Sayols S, Setien F, Corella D, de Torres C, Parareda A, Mora J, Zhao L, Zhang K, Lleonart ME, Alonso J, Simó R, Caminal JM, Esteller M. DNA Methylomes Reveal Biological Networks Involved in Human Eye Development, Functions and Associated Disorders. Sci Rep 2017; 7:11762. [PMID: 28924151 PMCID: PMC5603607 DOI: 10.1038/s41598-017-12084-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/04/2017] [Indexed: 01/07/2023] Open
Abstract
This work provides a comprehensive CpG methylation landscape of the different layers of the human eye that unveils the gene networks associated with their biological functions and how these are disrupted in common visual disorders. Herein, we firstly determined the role of CpG methylation in the regulation of ocular tissue-specification and described hypermethylation of retinal transcription factors (i.e., PAX6, RAX, SIX6) in a tissue-dependent manner. Second, we have characterized the DNA methylome of visual disorders linked to internal and external environmental factors. Main conclusions allow certifying that crucial pathways related to Wnt-MAPK signaling pathways or neuroinflammation are epigenetically controlled in the fibrotic disorders involved in retinal detachment, but results also reinforced the contribution of neurovascularization (ETS1, HES5, PRDM16) in diabetic retinopathy. Finally, we had studied the methylome in the most frequent intraocular tumors in adults and children (uveal melanoma and retinoblastoma, respectively). We observed that hypermethylation of tumor suppressor genes is a frequent event in ocular tumors, but also unmethylation is associated with tumorogenesis. Interestingly, unmethylation of the proto-oncogen RAB31 was a predictor of metastasis risk in uveal melanoma. Loss of methylation of the oncogenic mir-17-92 cluster was detected in primary tissues but also in blood from patients.
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Affiliation(s)
- María Berdasco
- Cancer Epigenetics Group; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
| | - Antonio Gómez
- Cancer Epigenetics Group; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Marcos J Rubio
- Department of Ophthalmology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Jaume Català-Mora
- Hospital Sant Joan de Deu, Esplugues de Llobregat, Barcelona, Catalonia, Spain
| | - Vicente Zanón-Moreno
- Unidad de Epidemiología Molecular y Genética del Departamento de Medicina Preventiva y Salud Pública de la Facultad de Medicina y Odontología y Centro de Investigación en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Universidad de Valencia, Valencia, Spain
| | - Miguel Lopez
- Cancer Epigenetics Group; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Cristina Hernández
- Diabetes and Metabolism Research Unit, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Shigeo Yoshida
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takahito Nakama
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Keijiro Ishikawa
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Tatsuro Ishibashi
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Amina M Boubekeur
- Faculty of Life and Natural Science, Department of Applied Molecular Genetics, Laboratory of Medical Genetics, University of Science and Technology of Oran, Mohamed Boudiaf, Oran, Algeria
| | - Lotfi Louhibi
- Faculty of Life and Natural Science, Department of Applied Molecular Genetics, Laboratory of Medical Genetics, University of Science and Technology of Oran, Mohamed Boudiaf, Oran, Algeria
| | - Miguel A Pujana
- Cancer Systems Biology Group; Program Against Cancer Therapeutic Resistance (ProCURE); Catalan Institute of Oncology (ICO), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Sergi Sayols
- Cancer Epigenetics Group; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Fernando Setien
- Cancer Epigenetics Group; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Dolores Corella
- Unidad de Epidemiología Molecular y Genética del Departamento de Medicina Preventiva y Salud Pública de la Facultad de Medicina y Odontología y Centro de Investigación en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Universidad de Valencia, Valencia, Spain
| | - Carmen de Torres
- Hospital Sant Joan de Deu, Esplugues de Llobregat, Barcelona, Catalonia, Spain
| | - Andreu Parareda
- Hospital Sant Joan de Deu, Esplugues de Llobregat, Barcelona, Catalonia, Spain
| | - Jaume Mora
- Hospital Sant Joan de Deu, Esplugues de Llobregat, Barcelona, Catalonia, Spain
| | - Ling Zhao
- Shiley Eye Institute and Institute for Genomic Medicine, University of California, San Diego, La Jolla, United States
| | - Kang Zhang
- Shiley Eye Institute and Institute for Genomic Medicine, University of California, San Diego, La Jolla, United States
| | - Matilde E Lleonart
- Biomedical Research in Cancer Stem Cells Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Catalonia, Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rafael Simó
- Diabetes and Metabolism Research Unit, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Josep M Caminal
- Department of Ophthalmology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics Group; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain. .,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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140
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Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity. Proc Natl Acad Sci U S A 2017; 114:E8264-E8273. [PMID: 28900001 DOI: 10.1073/pnas.1707021114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Precise transcriptional regulation controlled by a transcription factor network is known to be crucial for establishing correct neuronal cell identities and functions in the CNS. In the retina, the expression of various cone and rod photoreceptor cell genes is regulated by multiple transcription factors; however, the role of epigenetic regulation in photoreceptor cell gene expression has been poorly understood. Here, we found that Samd7, a rod-enriched sterile alpha domain (SAM) domain protein, is essential for silencing nonrod gene expression through H3K27me3 regulation in rod photoreceptor cells. Samd7-null mutant mice showed ectopic expression of nonrod genes including S-opsin in rod photoreceptor cells and rod photoreceptor cell dysfunction. Samd7 physically interacts with Polyhomeotic homologs (Phc proteins), components of the Polycomb repressive complex 1 (PRC1), and colocalizes with Phc2 and Ring1B in Polycomb bodies. ChIP assays showed a significant decrease of H3K27me3 in the genes up-regulated in the Samd7-deficient retina, showing that Samd7 deficiency causes the derepression of nonrod gene expression in rod photoreceptor cells. The current study suggests that Samd7 is a cell type-specific PRC1 component epigenetically defining rod photoreceptor cell identity.
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141
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Wang WY, Wang YF, Ma P, Xu TP, Shu YQ. Taurine‑upregulated gene 1: A vital long non‑coding RNA associated with cancer in humans (Review). Mol Med Rep 2017; 16:6467-6471. [PMID: 28901436 DOI: 10.3892/mmr.2017.7472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 07/06/2017] [Indexed: 11/06/2022] Open
Abstract
It is widely reported that long non‑coding RNAs (lncRNAs) are involved in regulating cell differentiation, proliferation, apoptosis and other biological processes. Certain lncRNAs have been found to be crucial in various types of tumor. Taurine‑upregulated gene 1 (TUG1) has been shown to be expressed in a tissue‑specific pattern and exert oncogenic or tumor suppressive functions in different types of cancer in humans. According to previous studies, TUG1 is predominantly located in the nucleus and may regulate gene expression at the transcriptional level. It mediates chromosomal remodeling and coordinates with polycomb repressive complex 2 (PRC2) to regulate gene expression. Although the mechanisms of how TUG1 affects the tumor genesis process remain to be fully elucidated, increasing studies have suggested that TUG1 offers potential as a diagnostic and prognostic biomarker, and as a therapeutic target in certain types of tumor. This review aims to summarize current evidence concerning the characteristics, mechanisms and associations with cancer of TUG1.
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Affiliation(s)
- Wen-Yu Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yan-Fen Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Tong-Peng Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yong-Qian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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142
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Human Long Noncoding RNA Regulation of Stem Cell Potency and Differentiation. Stem Cells Int 2017; 2017:6374504. [PMID: 28951743 PMCID: PMC5603141 DOI: 10.1155/2017/6374504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/12/2017] [Accepted: 08/02/2017] [Indexed: 12/15/2022] Open
Abstract
Because of their capability of differentiation into lineage-specific cells, stem cells are an attractive therapeutic modality in regenerative medicine. To develop an effective stem cell-based therapeutic strategy with predictable results, deeper understanding of the underlying molecular mechanisms of stem cell differentiation and/or pluripotency maintenance is required. Thus, reviewing the key factors involved in the transcriptional and epigenetic regulation of stem cell differentiation and maintenance is important. Accumulating data indicate that long noncoding RNAs (lncRNAs) mediate numerous biological processes, including stem cell differentiation and maintenance. Here, we review recent findings on the human lncRNA regulation of stem cell potency and differentiation. Although the clinical implication of these lncRNAs is only beginning to be elucidated, it is anticipated that lncRNAs will become important therapeutic targets in the near future.
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143
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MacDonald RB, Charlton-Perkins M, Harris WA. Mechanisms of Müller glial cell morphogenesis. Curr Opin Neurobiol 2017; 47:31-37. [PMID: 28850820 DOI: 10.1016/j.conb.2017.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 08/11/2017] [Indexed: 02/07/2023]
Abstract
Müller Glia (MG), the radial glia cells of the retina, have spectacular morphologies subserving their enormous functional complexity. As early as 1892, the great neuroanatomist Santiago Ramon y Cajal studied the morphological development of MG, defining several steps in their morphogenesis [1,2]. However, the molecular cues controlling these developmental steps remain poorly understood. As MG have roles to play in every cellular and plexiform layer, this review discusses our current understanding on how MG morphology may be linked to their function, including the developmental mechanisms involved in MG patterning and morphogenesis. Uncovering the mechanisms governing glial morphogenesis, using transcriptomics and imaging, may provide shed new light on the pathophysiology and treatment of human neurological disorders.
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Affiliation(s)
- Ryan B MacDonald
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Mark Charlton-Perkins
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - William A Harris
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK.
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144
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Liu K, Kim J, Kim DW, Zhang YS, Bao H, Denaxa M, Lim SA, Kim E, Liu C, Wickersham IR, Pachnis V, Hattar S, Song J, Brown SP, Blackshaw S. Lhx6-positive GABA-releasing neurons of the zona incerta promote sleep. Nature 2017; 548:582-587. [PMID: 28847002 DOI: 10.1038/nature23663] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/19/2017] [Indexed: 01/21/2023]
Abstract
Multiple populations of wake-promoting neurons have been characterized in mammals, but few sleep-promoting neurons have been identified. Wake-promoting cell types include hypocretin and GABA (γ-aminobutyric-acid)-releasing neurons of the lateral hypothalamus, which promote the transition to wakefulness from non-rapid eye movement (NREM) and rapid eye movement (REM) sleep. Here we show that a subset of GABAergic neurons in the mouse ventral zona incerta, which express the LIM homeodomain factor Lhx6 and are activated by sleep pressure, both directly inhibit wake-active hypocretin and GABAergic cells in the lateral hypothalamus and receive inputs from multiple sleep-wake-regulating neurons. Conditional deletion of Lhx6 from the developing diencephalon leads to decreases in both NREM and REM sleep. Furthermore, selective activation and inhibition of Lhx6-positive neurons in the ventral zona incerta bidirectionally regulate sleep time in adult mice, in part through hypocretin-dependent mechanisms. These studies identify a GABAergic subpopulation of neurons in the ventral zona incerta that promote sleep.
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Affiliation(s)
- Kai Liu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Juhyun Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dong Won Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yi Stephanie Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hechen Bao
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Szu-Aun Lim
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Eileen Kim
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Chang Liu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ian R Wickersham
- The McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Samer Hattar
- National Institute of Mental Health, Bethesda, Maryland, USA
| | - Juan Song
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Solange P Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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145
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Nagar S, Trudler D, McKercher SR, Piña-Crespo J, Nakanishi N, Okamoto SI, Lipton SA. Molecular Pathway to Protection From Age-Dependent Photoreceptor Degeneration in Mef2 Deficiency. Invest Ophthalmol Vis Sci 2017; 58:3741-3749. [PMID: 28738418 PMCID: PMC5525556 DOI: 10.1167/iovs.17-21767] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Purpose Photoreceptor degeneration in the retina is a major cause of blindness in humans. Elucidating mechanisms of degenerative and neuroprotective pathways in photoreceptors should afford identification and development of therapeutic strategies. Methods We used mouse genetic models and improved methods for retinal explant cultures. Retinas were enucleated from Mef2d+/+ and Mef2d−/− mice, stained for MEF2 proteins and outer nuclear layer thickness, and assayed for apoptotic cells. Chromatin immunoprecipitation (ChIP) assays revealed MEF2 binding, and RT-qPCR showed levels of transcription factors. We used AAV2 and electroporation to express genes in retinal explants and electroretinograms to assess photoreceptor functionality. Results We identify a prosurvival MEF2D-PGC1α pathway that plays a neuroprotective role in photoreceptors. We demonstrate that Mef2d−/− mouse retinas manifest decreased expression of PGC1α and increased photoreceptor cell loss, resulting in the absence of light responses. Molecular repletion of PGC1α protects Mef2d−/− photoreceptors and preserves light responsivity. Conclusions These results suggest that the MEF2-PGC1α cascade may represent a new therapeutic target for drugs designed to protect photoreceptors from developmental- and age-dependent loss.
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Affiliation(s)
- Saumya Nagar
- Neuroscience and Aging Research Center and Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States
| | - Dorit Trudler
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, California, United States
| | - Scott R McKercher
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, California, United States
| | - Juan Piña-Crespo
- Neuroscience and Aging Research Center and Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States
| | - Nobuki Nakanishi
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, California, United States
| | - Shu-Ichi Okamoto
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, California, United States
| | - Stuart A Lipton
- Neuroscience and Aging Research Center and Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States 2Neurodegenerative Disease Center, Scintillon Institute, San Diego, California, United States 3Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, California, United States 4Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States
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146
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Aldiri I, Xu B, Wang L, Chen X, Hiler D, Griffiths L, Valentine M, Shirinifard A, Thiagarajan S, Sablauer A, Barabas ME, Zhang J, Johnson D, Frase S, Zhou X, Easton J, Zhang J, Mardis ER, Wilson RK, Downing JR, Dyer MA. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis. Neuron 2017; 94:550-568.e10. [PMID: 28472656 PMCID: PMC5508517 DOI: 10.1016/j.neuron.2017.04.022] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/15/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022]
Abstract
In the developing retina, multipotent neural progenitors undergo unidirectional differentiation in a precise spatiotemporal order. Here we profile the epigenetic and transcriptional changes that occur during retinogenesis in mice and humans. Although some progenitor genes and cell cycle genes were epigenetically silenced during retinogenesis, the most dramatic change was derepression of cell-type-specific differentiation programs. We identified developmental-stage-specific super-enhancers and showed that most epigenetic changes are conserved in humans and mice. To determine how the epigenome changes during tumorigenesis and reprogramming, we performed integrated epigenetic analysis of murine and human retinoblastomas and induced pluripotent stem cells (iPSCs) derived from murine rod photoreceptors. The retinoblastoma epigenome mapped to the developmental stage when retinal progenitors switch from neurogenic to terminal patterns of cell division. The epigenome of retinoblastomas was more similar to that of the normal retina than that of retina-derived iPSCs, and we identified retina-specific epigenetic memory.
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Affiliation(s)
- Issam Aldiri
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Lu Wang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Daniel Hiler
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Lyra Griffiths
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Marc Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Abbas Shirinifard
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Suresh Thiagarajan
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andras Sablauer
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Marie-Elizabeth Barabas
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jiakun Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Dianna Johnson
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Sharon Frase
- Cell and Tissue Imaging Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Elaine R Mardis
- Department of Genetics, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA; Department of Medicine, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA
| | - Richard K Wilson
- Department of Genetics, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA; Siteman Cancer Center, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA; Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
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147
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Todd L, Palazzo I, Squires N, Mendonca N, Fischer AJ. BMP- and TGFβ-signaling regulate the formation of Müller glia-derived progenitor cells in the avian retina. Glia 2017; 65:1640-1655. [PMID: 28703293 DOI: 10.1002/glia.23185] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/24/2017] [Accepted: 06/13/2017] [Indexed: 01/20/2023]
Abstract
Müller glia-derived progenitor cells (MGPCs) have the capability to regenerate neurons in the retinas of different vertebrate orders. The formation of MGPCs is regulated by a network of cell-signaling pathways. The purpose of this study was to investigate how BMP/Smad1/5/8- and TGFβ/Smad2/3-signaling are coordinated to influence the formation of MGPCs in the chick model system. We find that pSmad1/5/8 is selectively up-regulated in the nuclei of Müller glia following treatment with BMP4, FGF2, or NMDA-induced damage, and this up-regulation is blocked by a dorsomorphin analogue DMH1. By comparison, Smad2/3 is found in the nuclei of Müller glia in untreated retinas, and becomes localized to the cytoplasm following NMDA- or FGF2-treatment. These findings suggest a decrease in TGFβ- and increase in BMP-signaling when MGPCs are known to form. In both NMDA-damaged and FGF2-treated retinas, inhibition of BMP-signaling suppressed the proliferation of MGPCs, whereas inhibition of TGFβ-signaling stimulated the proliferation of MGPCs. Consistent with these findings, TGFβ2 suppressed the formation of MGPCs in NMDA-damaged retinas. Our findings indicate that BMP/TGFβ/Smad-signaling is recruited into the network of signaling pathways that controls the formation of proliferating MGPCs. We conclude that signaling through BMP4/Smad1/5/8 promotes the formation of MGPCs, whereas signaling through TGFβ/Smad2/3 suppresses the formation of MGPCs.
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Affiliation(s)
- Levi Todd
- Department of Neuroscience, College of Medicine, The Ohio State University, 4190 Graves Hall, 333 West 10th Ave, Columbus, Ohio, 43210
| | - Isabella Palazzo
- Department of Neuroscience, College of Medicine, The Ohio State University, 4190 Graves Hall, 333 West 10th Ave, Columbus, Ohio, 43210
| | - Natalie Squires
- Department of Neuroscience, College of Medicine, The Ohio State University, 4190 Graves Hall, 333 West 10th Ave, Columbus, Ohio, 43210
| | - Ninoshka Mendonca
- Department of Neuroscience, College of Medicine, The Ohio State University, 4190 Graves Hall, 333 West 10th Ave, Columbus, Ohio, 43210
| | - Andy J Fischer
- Department of Neuroscience, College of Medicine, The Ohio State University, 4190 Graves Hall, 333 West 10th Ave, Columbus, Ohio, 43210
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148
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Boudreau-Pinsonneault C, Cayouette M. Cell lineage tracing in the retina: Could material transfer distort conclusions? Dev Dyn 2017. [PMID: 28643368 DOI: 10.1002/dvdy.24535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recent studies reported the transfer of fluorescent labels between grafted and host cells after transplantation of photoreceptor precursor cells in the mouse retina. While clearly impacting the interpretation of transplantation studies in the retina, the potential impact of material transfer in other experimental paradigms using cell-specific labels remains uncertain. Here, we briefly review the evidence supporting material transfer in transplantation studies and discuss whether it might influence retinal cell lineage tracing experiments in developmental and regeneration studies. We also propose ways to control for the possible confounding occurrence of label exchange in such experiments. Developmental Dynamics 247:10-17, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Camille Boudreau-Pinsonneault
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada.,Integrated Program in Neuroscience, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada.,Integrated Program in Neuroscience, Department of Medicine, McGill University, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, QC, Canada.,Department of Anatomy and Cell Biology and Division of Experimental Medicine, McGill University, Montreal, QC, Canada
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149
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Park KU, Randazzo G, Jones KL, Brzezinski JA. Gsg1, Trnp1, and Tmem215 Mark Subpopulations of Bipolar Interneurons in the Mouse Retina. Invest Ophthalmol Vis Sci 2017; 58:1137-1150. [PMID: 28199486 PMCID: PMC5317276 DOI: 10.1167/iovs.16-19767] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose How retinal bipolar cell interneurons are specified and assigned to specialized subtypes is only partially understood. In part, this is due to a lack of early pan- and subtype-specific bipolar cell markers. To discover these factors, we identified genes that were upregulated in Blimp1 (Prdm1) mutant retinas, which exhibit precocious bipolar cell development. Methods Postnatal day (P)2 retinas from Blimp1 conditional knock-out (CKO) mice and controls were processed for RNA sequencing. Genes that increased at least 45% and were statistically different between conditions were considered candidate bipolar-specific factors. Candidates were further evaluated by RT-PCR, in situ hybridization, and immunohistochemistry. Knock-in Tmem215-LacZ mice were used to better trace retinal expression. Results A comparison between Blimp1 CKO and control RNA-seq datasets revealed approximately 40 significantly upregulated genes. We characterized the expression of three genes that have no known function in the retina, Gsg1 (germ cell associated gene), Trnp1 (TMF-regulated nuclear protein), and Tmem215 (a predicted transmembrane protein). Germ cell associated gene appeared restricted to a small subset of cone bipolars while Trnp1 was seen in all ON type bipolar cells. Using Tmem215-LacZ heterozygous knock-in mice, we observed that β-galactosidase expression started early in bipolar cell development. In adults, Tmem215 was expressed by a subset of ON and OFF cone bipolar cells. Conclusions We have identified Gsg1, Tmem215, and Trnp1 as novel bipolar subtype-specific genes. The spatial and temporal pattern of their expression is consistent with a role in controlling bipolar subtype fate choice, differentiation, or physiology.
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Affiliation(s)
- Ko Uoon Park
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Grace Randazzo
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Kenneth L Jones
- Department of Pediatrics, Section Hematology/Oncology, University of Colorado Denver, Aurora, Colorado, United States
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
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Li Q, Guindani M, Reich BJ, Bondell HD, Vannucci M. A Bayesian mixture model for clustering and selection of feature occurrence rates under mean constraints. Stat Anal Data Min 2017. [DOI: 10.1002/sam.11350] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qiwei Li
- Department of Statistics; Rice University; Houston Texas
| | - Michele Guindani
- Department of Statistics; University of California; Irvine California
| | - Brian J. Reich
- Department of Statistics; North Carolina State University; Raleigh North Carolina
| | - Howard D. Bondell
- Department of Statistics; North Carolina State University; Raleigh North Carolina
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