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Zhang Q, Zhong C, Shen J, Chen S, Jia Y, Duan S. Emerging role of LINC00461 in cancer. Biomed Pharmacother 2022; 152:113239. [PMID: 35679722 DOI: 10.1016/j.biopha.2022.113239] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
LINC00461 is located in the intergenic region between the protein-coding genes MEF2C and TMEM161B. LINC00461 upregulation was associated with the risk of 13 tumors and was strongly associated with clinicopathologic features and poor prognosis in 11 tumors. LINC00461 is involved in resistance to four anticancer drugs, including sunitinib for renal cell carcinoma, cisplatin for head and neck squamous cell carcinoma and rectal cancer, temozolomide for glioma, and docetaxel for breast cancer. LINC00461 can sponge 18 miRNAs to form a complex ceRNA network that regulates the expression of a large number of downstream genes. LINC00461 is involved in the MAPK/ERK signaling pathway and PI3K/AKT signaling pathway, thereby promoting tumorigenesis. Notably, knockdown of LINC00461 in exosomes antagonizes tumor cell proliferation in multiple myeloma. This article summarizes the diagnostic, prognostic, and therapeutic value of LINC00461 in various tumors, and systematically describes the ceRNA network and signaling pathways associated with LINC00461, providing potential directions for future LINC00461 research.
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Affiliation(s)
- Qiudan Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China; Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenming Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jinze Shen
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China
| | - Sang Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yunhua Jia
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China.
| | - Shiwei Duan
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, China.
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2
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Ross CJ, Ulitsky I. Discovering functional motifs in long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1708. [PMID: 34981665 DOI: 10.1002/wrna.1708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Caroline Jane Ross
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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3
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Ng KH, Subrayan V, Ramachandran V, Ismail F. Screening of single nucleotide polymorphisms among fuchs’ endothelial corneal dystrophy subjects in Malaysia. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00193-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The pathophysiology underlying Fuchs' Endothelial Corneal Dystrophy (FECD), especially in older individuals, remains unclear, with a genetic predisposition being reported as the single best predictor of the disease. Genetic studies have shown that several genes in various loci such as COL8A2, SLC4A11, TCF8/ZEB1 and TCF4 are associated with FECD in different populations and ethnicities. A case–control study was conducted to determine the association between genetic variants and FECD in a tertiary care setting in Malaysia. A total number of 12 patients with clinically diagnosed FECD and 12 age, gender and race matched control subjects were recruited. Extracted genomic DNA were genotyped using Infinium Global Screening Array (GSA)-24 version 1.0 BeadChip with iScan high-throughput system. Illumina GenomeStudio 2.0 Data Analysis and PLINK version 1.9 software were used to perform association tests and determine the distribution of obtained variants among the cases and controls.
Results
A significant novel genetic variant, rs11626651, a variant of the LOC105370676 gene or known as the LINC02320 gene, located at chromosome 14, has been identified as a suggestive association with FECD (p < 5 × 10−6). Further analysis in this study suggested that candidate genes such as COL8A2, ZEB1/TCF8, TCF4 and SLC4A11 had no significant associations with FECD.
Conclusions
The discovery of a novel variant may influence the underlying pathogenic basis of FECD in Malaysia. The current study is the first genetic study on FECD to use Infinium GSA. It is the first comprehensive report in Malaysia to provide genetic information of potential relevance to FECD, which may pave the way for new therapeutic strategies in the future. A detailed analysis with a larger sample size is recommended for further evaluation.
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4
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Dholpuria S, Kumar S, Kumar M, Sarwalia P, Kumar R, Datta TK. A novel lincRNA identified in buffalo oocytes with protein binding characteristics could hold the key for oocyte competence. Mol Biol Rep 2021; 48:3925-3934. [PMID: 34014469 DOI: 10.1007/s11033-021-06388-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/29/2021] [Indexed: 12/23/2022]
Abstract
Studying the maternal oocyte-specific genes, in farm animals is a significant step towards delineating the underlying mechanisms that regulate oocyte quality, early embryonic development and survival. With the creation of buffalo oocyte-specific subtracted cDNA library, it has raised new questions which need to be answered. The present study has characterized one of the ESTs selected from the library and highlighted its importance in the oocyte quality. The selected EST was made full length by RLM-RACE and four transcript variants were identified. Bioinformatics analysis indicated the novelty of full-length transcript along with conserved intergenic nature. The largest transcript was identified as long intergenic noncoding RNA based upon coding potential calculator output. The expression analysis at different hours of oocyte maturation showed a significant variation in developmentally competent oocytes to that of incompetent ones. Along with this, the transcript was also found to have protein binding ability which was confirmed by RNA electrophoretic mobility shift assay. The protein used in the experiment was isolated from oocyte and cumulus cells via sonication. A novel lincRNA has been reported here that might have an important role in maturation of oocytes, inferred from its relative gene expression study and protein binding characteristics.
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Affiliation(s)
- Sunny Dholpuria
- Department of Life Science, Sharda University, Greater Noida, India.
| | - Sandeep Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Manish Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Parul Sarwalia
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Rakesh Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Tirtha Kumar Datta
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India.
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5
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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6
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Carrella S, Banfi S, Karali M. Sophisticated Gene Regulation for a Complex Physiological System: The Role of Non-coding RNAs in Photoreceptor Cells. Front Cell Dev Biol 2021; 8:629158. [PMID: 33537317 PMCID: PMC7848107 DOI: 10.3389/fcell.2020.629158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/18/2020] [Indexed: 12/26/2022] Open
Abstract
Photoreceptors (PRs) are specialized neuroepithelial cells of the retina responsible for sensory transduction of light stimuli. In the highly structured vertebrate retina, PRs have a highly polarized modular structure to accommodate the demanding processes of phototransduction and the visual cycle. Because of their function, PRs are exposed to continuous cellular stress. PRs are therefore under pressure to maintain their function in defiance of constant environmental perturbation, besides being part of a highly sophisticated developmental process. All this translates into the need for tightly regulated and responsive molecular mechanisms that can reinforce transcriptional programs. It is commonly accepted that regulatory non-coding RNAs (ncRNAs), and in particular microRNAs (miRNAs), are not only involved but indeed central in conferring robustness and accuracy to developmental and physiological processes. Here we integrate recent findings on the role of regulatory ncRNAs (e.g., miRNAs, lncRNAs, circular RNAs, and antisense RNAs), and of their contribution to PR pathophysiology. We also outline the therapeutic implications of translational studies that harness ncRNAs to prevent PR degeneration and promote their survival and function.
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Affiliation(s)
- Sabrina Carrella
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marianthi Karali
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
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7
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Koffler-Brill T, Taiber S, Anaya A, Bordeynik-Cohen M, Rosen E, Kolla L, Messika-Gold N, Elkon R, Kelley MW, Ulitsky I, Avraham KB. Identification and characterization of key long non-coding RNAs in the mouse cochlea. RNA Biol 2020; 18:1160-1169. [PMID: 33131415 DOI: 10.1080/15476286.2020.1836456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The auditory system is a complex sensory network with an orchestrated multilayer regulatory programme governing its development and maintenance. Accumulating evidence has implicated long non-coding RNAs (lncRNAs) as important regulators in numerous systems, as well as in pathological pathways. However, their function in the auditory system has yet to be explored. Using a set of specific criteria, we selected four lncRNAs expressed in the mouse cochlea, which are conserved in the human transcriptome and are relevant for inner ear function. Bioinformatic characterization demonstrated a lack of coding potential and an absence of evolutionary conservation that represent properties commonly shared by their class members. RNAscope® analysis of the spatial and temporal expression profiles revealed specific localization to inner ear cells. Sub-cellular localization analysis presented a distinct pattern for each lncRNA and mouse tissue expression evaluation displayed a large variability in terms of level and location. Our findings establish the expression of specific lncRNAs in different cell types of the auditory system and present a potential pathway by which the lncRNA Gas5 acts in the inner ear. Studying lncRNAs and deciphering their functions may deepen our knowledge of inner ear physiology and morphology and may reveal the basis of as yet unresolved genetic hearing loss-related pathologies. Moreover, our experimental design may be employed as a reference for studying other inner ear-related lncRNAs, as well as lncRNAs expressed in other sensory systems.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Anaya
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Einat Rosen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Likhitha Kolla
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Naama Messika-Gold
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Matthew W Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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8
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Goyal V, DeVera C, Laurent V, Sellers J, Chrenek MA, Hicks D, Baba K, Iuvone PM, Tosini G. Dopamine 2 Receptor Signaling Controls the Daily Burst in Phagocytic Activity in the Mouse Retinal Pigment Epithelium. Invest Ophthalmol Vis Sci 2020; 61:10. [PMID: 32396631 PMCID: PMC7405625 DOI: 10.1167/iovs.61.5.10] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Purpose A burst in phagocytosis of spent photoreceptor outer fragments by RPE is a rhythmic process occurring 1 to 2 hours after the onset of light. This phenomenon is considered crucial for the health of the photoreceptors and RPE. We have recently reported that dopamine, via dopamine 2 receptor (D2R), shifts the circadian rhythm in the RPE. Methods Here, we first investigated the impact of the removal of D2R on the daily peak of phagocytosis by RPE and then we analyzed the function and morphology of retina and RPE in the absence of D2R. Results D2R knockout (KO) mice do not show a daily burst of phagocytic activity after the onset of light. RNA sequencing revealed a total of 394 differentially expressed genes (DEGs) between ZT 23 and ZT 1 in the control mice, whereas in D2R KO mice, we detected 1054 DEGs. Pathway analysis of the gene expression data implicated integrin signaling to be one of the upregulated pathways in control but not in D2R KO mice. Consistent with the gene expression data, phosphorylation of focal adhesion kinase (FAK) did not increase significantly in KO mice at ZT 1. No difference in retinal thickness, visual function, or morphology of RPE cells was observed between wild-type (WT) and D2R KO mice at the age of 3 and 12 months. Conclusions Our data suggest that removal of D2R prevents the burst of phagocytosis and a related increase in the phosphorylation of FAK after light onset. The pathway analysis points toward a putative role of D2R in controlling integrin signaling, which is known to play an important role in the control of the daily burst of phagocytosis by the RPE. Our data also indicate that the absence of the burst of phagocytic activity in the early morning does not produce any apparent deleterious effect on the retina or RPE up to 1 year of age.
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9
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Wang Y, Wang X, Wang YX, Ma Y, Di Y. Effect and mechanism of the long noncoding RNA MALAT1 on retinal neovascularization in retinopathy of prematurity. Life Sci 2020; 260:118299. [PMID: 32827542 DOI: 10.1016/j.lfs.2020.118299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/04/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022]
Abstract
AIMS The most typical pathological manifestation of retinopathy of prematurity (ROP) is Retinal neovascularization (RNV). Long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been reported to mediate angiogenesis. Our experiment aimed to research the effect and mechanism of the MALAT1 on RNV in ROP. MAIN METHODS C57 mice was used to establish oxygen-introduced retinopathy (OIR), and divided into control, hyperoxia, hyperoxia control siRNA, and hyperoxia MALAT1 siRNA groups. KEY FINDINGS It was shown that MALAT1 mRNA was high expressed in the retinas of OIR mice. Further studies revealed that after intravitreal injection of MALAT1 siRNA, the degree of retinopathy was significantly reduced compared with OIR group. In addition, the protein and mRNA expression levels of CCN1, AKT and VEGF were significantly decreased. This was accompanied by a decrease in inflammatory genes including IL-1β, IL-6, and TNF-α compared with the hyperoxia control siRNA mice. SIGNIFICANCE The result suggested that MALAT1 may be involved in the process of RNV in ROP and MALAT1 siRNA may be a promising agent for the treatment of ROP by inhibiting RNV.
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Affiliation(s)
- Yue Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Xue Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Yue-Xia Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Yuan Ma
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Yu Di
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China.
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10
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Sun L, Chen X, Jin Z. Emerging roles of non‐coding RNAs in retinal diseases: A review. Clin Exp Ophthalmol 2020; 48:1085-1101. [PMID: 32519377 DOI: 10.1111/ceo.13806] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Lan‐Fang Sun
- Laboratory of Stem Cell and Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital Wenzhou Medical University Wenzhou China
| | - Xue‐Jiao Chen
- Laboratory of Stem Cell and Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital Wenzhou Medical University Wenzhou China
| | - Zi‐Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory Beijing China
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11
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Maroñas O, García-Quintanilla L, Luaces-Rodríguez A, Fernández-Ferreiro A, Latorre-Pellicer A, Abraldes MJ, Lamas MJ, Carracedo A. Anti-VEGF Treatment and Response in Age-related Macular Degeneration: Disease's Susceptibility, Pharmacogenetics and Pharmacokinetics. Curr Med Chem 2020; 27:549-569. [PMID: 31296152 DOI: 10.2174/0929867326666190711105325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/03/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023]
Abstract
The current review is focussing different factors that contribute and directly correlate to the onset and progression of Age-related Macular Degeneration (AMD). In particular, the susceptibility to AMD due to genetic and non-genetic factors and the establishment of risk scores, based on the analysis of different genes to measure the risk of developing the disease. A correlation with the actual therapeutic landscape to treat AMD patients from the point of view of pharmacokinetics and pharmacogenetics is also exposed. Treatments commonly used, as well as different regimes of administration, will be especially important in trying to classify individuals as "responders" and "non-responders". Analysis of different genes correlated with drug response and also the emerging field of microRNAs (miRNAs) as possible biomarkers for early AMD detection and response will be also reviewed. This article aims to provide the reader a review of different publications correlated with AMD from the molecular and kinetic point of view as well as its commonly used treatments, major pitfalls and future directions that, to our knowledge, could be interesting to assess and follow in order to develop a personalized medicine model for AMD.
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Affiliation(s)
- Olalla Maroñas
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura García-Quintanilla
- Servicio de Farmacia, Xerencia de Xestión Integrada de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Andrea Luaces-Rodríguez
- Departamento de Farmacia e Tecnoloxia Farmaceutica e Instituto de Farmacia Industrial, Facultade de Farmacia, Universidade de Santiago de Compostela, Spain.,Grupo de Farmacoloxia Clínica, Instituto de Investigacion en Salud de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Anxo Fernández-Ferreiro
- Departamento de Farmacia e Tecnoloxia Farmaceutica e Instituto de Farmacia Industrial, Facultade de Farmacia, Universidade de Santiago de Compostela, Spain.,Grupo de Farmacoloxia Clínica, Instituto de Investigacion en Salud de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.,Departamento de Farmacia, Hospital Clínico Universitario de Santiago de Compostela (SERGAS) (CHUS), Santiago de Compostela, Spain
| | - Ana Latorre-Pellicer
- Unidad de Genetica Clínica y Genomica Funcional, Departamento de Farmacologia-Fisiología, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Maximino J Abraldes
- Servicio de Oftalmoloxía, Xerencia de Xestion Integrada de Santiago de Compostela, Santiago de Compostela, Spain.,Departamento de Ciruxía e Especialidades Médico- Quirúrxicas, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María J Lamas
- Grupo de Farmacoloxia Clínica, Instituto de Investigacion en Salud de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBER de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
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12
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Gao XR, Huang H, Kim H. Genome-wide association analyses identify 139 loci associated with macular thickness in the UK Biobank cohort. Hum Mol Genet 2019; 28:1162-1172. [PMID: 30535121 DOI: 10.1093/hmg/ddy422] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 11/13/2022] Open
Abstract
The macula, located near the center of the retina in the human eye, is responsible for providing critical functions, such as central, sharp vision. Structural changes in the macula are associated with many ocular diseases, including age-related macular degeneration (AMD) and glaucoma. Although macular thickness is a highly heritable trait, there are no prior reported genome-wide association studies (GWASs) of it. Here we describe the first GWAS of macular thickness, which was measured by spectral-domain optical coherence tomography using 68 423 participants from the UK Biobank cohort. We identified 139 genetic loci associated with macular thickness at genome-wide significance (P < 5 × 10-8). The most significant loci were LINC00461 (P = 5.1 × 10-120), TSPAN10 (P = 1.2 × 10-118), RDH5 (P = 9.2 × 10-105) and SLC6A20 (P = 1.4 × 10-71). Results from gene expression demonstrated that these genes are highly expressed in the retina. Other hits included many previously reported AMD genes, such as NPLOC4 (P = 1.7 × 10-103), RAD51B (P = 9.1 × 10-14) and SLC16A8 (P = 1.7 × 10-8), further providing functional significance of the identified loci. Through cross-phenotype analysis, these genetic loci also exhibited pleiotropic effects with myopia, neurodegenerative diseases (e.g. Parkinson's disease, schizophrenia and Alzheimer's disease), cancer (e.g. breast, ovarian and lung cancers) and metabolic traits (e.g. body mass index, waist circumference and type 2 diabetes). Our findings provide the first insight into the genetic architecture of macular thickness and may further elucidate the pathogenesis of related ocular diseases, such as AMD.
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Affiliation(s)
- X Raymond Gao
- Departments of Ophthalmology and Visual Science and Biomedical Informatics, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
| | - Hua Huang
- Departments of Ophthalmology and Visual Science and Biomedical Informatics, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
| | - Heejin Kim
- Departments of Ophthalmology and Visual Science and Biomedical Informatics, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
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13
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Retinal Gene Distribution and Functionality Implicated in Inherited Retinal Degenerations Can Reveal Disease-Relevant Pathways for Pharmacologic Intervention. Pharmaceuticals (Basel) 2019; 12:ph12020074. [PMID: 31108889 PMCID: PMC6631933 DOI: 10.3390/ph12020074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 01/17/2023] Open
Abstract
The advent of genetic therapies for inherited retinal diseases (IRDs) has spurred the need for precise diagnosis and understanding of pathways for therapeutic targeting. The majority of IRDs that are clinically diagnosed, however, lack an identifiable mutation in established disease-causing loci and thus can be investigated with limited rational drug discovery methods. Transcriptome profiling of the retina can reveal the functional state of the tissue, and geographic profiling can uncover the various clinical phenotypic presentations of IRDs and aid in pharmaceutical intervention. In this investigation, we detail the retinal geographic expression of known retinal disease-causing genes in the primate retina and functional targetable pathways in specific IRDs. Understanding the genetic basis as well as the resulting functional consequences will assist in the discovery of future therapeutic interventions and provide novel insights to medicinal chemists. Herein, we report that, despite the genetic heterogeneity of retinal diseases, potential functional pathways can be elucidated for therapeutic targeting and be used for predictive phenotypic and genotypic modeling of novel IRD presentations.
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14
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Volatile Evolution of Long Non-Coding RNA Repertoire in Retinal Pigment Epithelium: Insights from Comparison of Bovine and Human RNA Expression Profiles. Genes (Basel) 2019; 10:genes10030205. [PMID: 30857256 PMCID: PMC6471466 DOI: 10.3390/genes10030205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 11/17/2022] Open
Abstract
Currently, several long non-coding RNAs (lncRNAs) (TUG1, MALAT1, MEG3 and others) have been discovered to regulate normal visual function and may potentially contribute to dysfunction of the retina. We decided to extend these analyses of lncRNA genes to the retinal pigment epithelium (RPE) to determine whether there is conservation of RPE-expressed lncRNA between human and bovine genomes. We reconstructed bovine RPE lncRNAs based on genome-guided assembly. Next, we predicted homologous human transcripts based on whole genome alignment. We found a small set of conserved lncRNAs that could be involved in signature RPE functions that are conserved across mammals. However, the fraction of conserved lncRNAs in the overall pool of lncRNA found in RPE appeared to be very small (less than 5%), perhaps reflecting a fast and flexible adaptation of the mammalian eye to various environmental conditions.
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15
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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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16
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Mustafi D, Kevany BM, Bai X, Golczak M, Adams MD, Wynshaw-Boris A, Palczewski K. Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas. Hum Mol Genet 2018; 25:4376-4388. [PMID: 28172828 DOI: 10.1093/hmg/ddw268] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/26/2023] Open
Abstract
A defined set of genetic instructions encodes functionality in complex organisms. Delineating these unique genetic signatures is essential to understanding the formation and functionality of specialized tissues. Vision, one of the five central senses of perception, is initiated by the retina and has evolved over time to produce rod and cone photoreceptors that vary in a species-specific manner, and in some cases by geographical region resulting in higher order visual acuity in humans. RNA-sequencing and use of existing and de novo transcriptome assemblies allowed ocular transcriptome mapping from a diverse set of rodent and primate species. Global genomic refinements along with systems-based comparative and co-expression analyses of these transcriptome maps identified gene modules that correlated with specific features of rod versus cone retinal cellular composition. Organization of the ocular transcriptome demonstrated herein defines the molecular basis of photoreceptor architecture and functionality, providing a new paradigm for neurogenetic analyses of the mammalian retina in health and disease.
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Affiliation(s)
- Debarshi Mustafi
- Departments of Pharmacology and Cleveland Center for Membrane and Structural Biology
| | - Brian M Kevany
- Departments of Pharmacology and Cleveland Center for Membrane and Structural Biology
| | | | - Marcin Golczak
- Departments of Pharmacology and Cleveland Center for Membrane and Structural Biology
| | | | | | - Krzysztof Palczewski
- Departments of Pharmacology and Cleveland Center for Membrane and Structural Biology
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17
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Orban T, Leinonen H, Getter T, Dong Z, Sun W, Gao S, Veenstra A, Heidari-Torkabadi H, Kern TS, Kiser PD, Palczewski K. A Combination of G Protein-Coupled Receptor Modulators Protects Photoreceptors from Degeneration. J Pharmacol Exp Ther 2017; 364:207-220. [PMID: 29162627 DOI: 10.1124/jpet.117.245167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/20/2017] [Indexed: 02/03/2023] Open
Abstract
Degeneration of retinal photoreceptor cells can arise from environmental and/or genetic causes. Since photoreceptor cells, the retinal pigment epithelium (RPE), neurons, and glial cells of the retina are intimately associated, all cell types eventually are affected by retinal degenerative diseases. Such diseases often originate either in rod and/or cone photoreceptor cells or the RPE. Of these, cone cells located in the central retina are especially important for daily human activity. Here we describe the protection of cone cells by a combination therapy consisting of the G protein-coupled receptor modulators metoprolol, tamsulosin, and bromocriptine. These drugs were tested in Abca4-/-Rdh8-/- mice, a preclinical model for retinal degeneration. The specificity of these drugs was determined with an essentially complete panel of human G protein-coupled receptors. Significantly, the combination of metoprolol, tamsulosin, and bromocriptine had no deleterious effects on electroretinographic responses of wild-type mice. Moreover, putative G protein-coupled receptor targets of these drugs were shown to be expressed in human and mouse eyes by RNA sequencing and quantitative polymerase chain reaction. Liquid chromatography together with mass spectrometry using validated internal standards confirmed that metoprolol, tamsulosin, and bromocriptine individually or together penetrate the eye after either intraperitoneal delivery or oral gavage. Collectively, these findings support human trials with combined therapy composed of lower doses of metoprolol, tamsulosin, and bromocriptine designed to safely impede retinal degeneration associated with certain genetic diseases (e.g., Stargardt disease). The same low-dose combination also could protect the retina against diseases with complex or unknown etiologies such as age-related macular degeneration.
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Affiliation(s)
- Tivadar Orban
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Henri Leinonen
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Tamar Getter
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Zhiqian Dong
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Wenyu Sun
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Songqi Gao
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Alexander Veenstra
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Hossein Heidari-Torkabadi
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Timothy S Kern
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Philip D Kiser
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
| | - Krzysztof Palczewski
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (T.O., H.L., T.G., S.G., A.V., H.H.-T., T.S.K., P.D.K., K.P.); Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio (T.S.K., P.D.K.); and Polgenix Inc., Cleveland, Ohio (Z.D., W.S.)
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18
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Liu WH, Tsai ZTY, Tsai HK. Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs. BMC Genomics 2017; 18:786. [PMID: 29037146 PMCID: PMC5644071 DOI: 10.1186/s12864-017-4156-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 10/02/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The regulatory roles of long intergenic noncoding RNAs (lincRNAs) in humans have been revealed through the use of advanced sequencing technology. Recently, three possible scenarios of lincRNA origins have been proposed: de novo origination from intergenic regions, duplication from other long noncoding RNAs, and pseudogenization from protein-coding genes. The first two scenarios are largely studied and supported, yet few studies focused on the evolution from pseudogenized protein-coding sequence to lincRNA. Due to the non-mutually exclusive nature of these three scenarios and the need of systematic investigation of lincRNA origination, we conducted a comparative genomics study to investigate the evolution of human lincRNAs. RESULTS Combining with syntenic analysis and stringent Blastn e-value cutoff, we found that the majority of lincRNAs are aligned to intergenic regions of other species. Interestingly, 193 human lincRNAs could have protein-coding orthologs in at least two of nine vertebrates. Transposable elements in these conserved regions in human genome are much less than expectation. Moreover, 19% of these lincRNAs have overlaps with or are close to pseudogenes in the human genome. CONCLUSIONS We suggest that a notable portion of lincRNAs could be derived from pseudogenized protein-coding genes. Furthermore, based on our computational analysis, we hypothesize that a subset of these lincRNAs could have potential to regulate their paralogs by functioning as competing endogenous RNAs. Our results provide evolutionary evidence of the relationship between human lincRNAs and protein-coding genes.
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Affiliation(s)
- Wan-Hsin Liu
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Zing Tsung-Yeh Tsai
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Huai-Kuang Tsai
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.
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19
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Zelinger L, Karakülah G, Chaitankar V, Kim JW, Yang HJ, Brooks MJ, Swaroop A. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Invest Ophthalmol Vis Sci 2017; 58:4422-4435. [PMID: 28863214 PMCID: PMC5584472 DOI: 10.1167/iovs.17-21805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023] Open
Abstract
Purpose Transcriptome analysis by next generation sequencing allows qualitative and quantitative profiling of expression patterns associated with development and disease. However, most transcribed sequences do not encode proteins, and little is known about the functional relevance of noncoding (nc) transcriptome in neuronal subtypes. The goal of this study was to perform a comprehensive analysis of long noncoding (lncRNAs) and antisense (asRNAs) RNAs expressed in mouse retinal photoreceptors. Methods Transcriptomic profiles were generated at six developmental time points from flow-sorted Nrlp-GFP (rods) and Nrlp-GFP;Nrl-/- (S-cone like) mouse photoreceptors. Bioinformatic analysis was performed to identify novel noncoding transcripts and assess their regulation by rod differentiation factor neural retina leucine zipper (NRL). In situ hybridization (ISH) was used for validation and cellular localization. Results NcRNA profiles demonstrated dynamic yet specific expression signature and coexpression clusters during rod development. In addition to currently annotated 586 lncRNAs and 454 asRNAs, we identified 1037 lncRNAs and 243 asRNAs by de novo assembly. Of these, 119 lncRNAs showed altered expression in the absence of NRL and included NRL binding sites in their promoter/enhancer regions. ISH studies validated the expression of 24 lncRNAs (including 12 previously unannotated) and 4 asRNAs in photoreceptors. Coexpression analysis demonstrated 63 functional modules and 209 significant antisense-gene correlations, allowing us to predict possible role of these lncRNAs in rods. Conclusions Our studies reveal coregulation of coding and noncoding transcripts in rod photoreceptors by NRL and establish the framework for deciphering the function of ncRNAs during retinal development.
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Affiliation(s)
- Lina Zelinger
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Gökhan Karakülah
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Vijender Chaitankar
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Matthew J. Brooks
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
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20
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Au ED, Fernandez-Godino R, Kaczynksi TJ, Sousa ME, Farkas MH. Characterization of lincRNA expression in the human retinal pigment epithelium and differentiated induced pluripotent stem cells. PLoS One 2017; 12:e0183939. [PMID: 28837677 PMCID: PMC5570510 DOI: 10.1371/journal.pone.0183939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/14/2017] [Indexed: 11/29/2022] Open
Abstract
Long intervening non-coding RNAs (lincRNAs) are increasingly being implicated as important factors in many aspects of cellular development, function, and disease, but remain poorly understood. In this study, we examine the human retinal pigment epithelium (RPE) lincRNA transcriptome using RNA-Seq data generated from human fetal RPE (fRPE), RPE derived from human induced pluripotent stem cells (iPS-RPE), and undifferentiated iPS (iPS). In addition, we determine the suitability of iPS-RPE, from a transcriptome standpoint, as a model for use in future studies of lincRNA structure and function. A comparison of gene and isoform expression across the whole transcriptome shows only minimal differences between all sample types, though fRPE and iPS-RPE show higher concordance than either shows with iPS. Notably, RPE signature genes show the highest degree of fRPE to iPS-RPE concordance, indicating that iPS-RPE cells provide a suitable model for use in future studies. An analysis of lincRNAs demonstrates high concordance between fRPE and iPS-RPE, but low concordance between either RPE and iPS. While most lincRNAs are expressed at low levels (RPKM < 10), there is a high degree of concordance among replicates within each sample type, suggesting the expression is consistent, even at levels subject to high variability. Finally, we identified and annotated 180 putative novel genes in the fRPE samples, a majority of which are also expressed in the iPS-RPE. Overall, this study represents the first characterization of lincRNA expression in the human RPE, and provides a model for studying the role lincRNAs play in RPE development, function, and disease.
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Affiliation(s)
- Elizabeth D. Au
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
| | - Rosario Fernandez-Godino
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States of America
| | - Tadeusz J. Kaczynksi
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
| | - Maria E. Sousa
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
| | - Michael H. Farkas
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
- * E-mail:
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21
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Yang Y, Ren M, Song C, Li D, Soomro SH, Xiong Y, Zhang H, Fu H. LINC00461, a long non-coding RNA, is important for the proliferation and migration of glioma cells. Oncotarget 2017; 8:84123-84139. [PMID: 29137410 PMCID: PMC5663582 DOI: 10.18632/oncotarget.20340] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/25/2017] [Indexed: 12/31/2022] Open
Abstract
An increasing number of reports have revealed that long non-coding RNAs are important players in tumorigenesis. Here we showed that long non-coding RNA LINC00461 is highly expressed in glioma tissues compared to non-neoplastic brain tissues. The knockdown of LINC00461 suppressed cyclinD1/A/E expression which led to G0/G1 cell cycle arrest and inhibited cell proliferation in glioma cells. LINC00461 suppression also inhibited glioma cell migration and invasion. The function of LINC00461 in glioma cells is partially mediated by MAPK/ERK and PI3K/AKT signaling pathways as down-regulation of LINC00461 expression suppressed ERK1/2 and AKT activities. Moreover, LINC00461 knockdown decreased expression levels of microRNA miR-9 and flanking genes MEF2C and TMEM161B. Taken together, our results demonstrate that LINC00461 is important for glioma progression affecting cell proliferation, migration and invasion via MAPK/ERK, PI3K/AKT, and possibly other signaling pathways.
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Affiliation(s)
- Yali Yang
- Department of Anatomy and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Mingxin Ren
- Department of Anatomy and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Chao Song
- Department of Anatomy and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Dan Li
- Department of Anatomy and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shahid Hussain Soomro
- Department of Anatomy and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yajie Xiong
- Department of Anatomy and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Hongfeng Zhang
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Hui Fu
- Department of Anatomy and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
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22
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Ushakov K, Koffler-Brill T, Rom A, Perl K, Ulitsky I, Avraham KB. Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems. Sci Rep 2017; 7:8637. [PMID: 28819115 PMCID: PMC5561060 DOI: 10.1038/s41598-017-08320-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction. To help address this need, we performed a whole-genome identification of lncRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 3,239 lncRNA genes, most of which were intergenic (lincRNAs) and 721 are novel. We examined temporal and tissue specificity by analyzing the developmental profiles on embryonic day 16.5 and at birth. The spatial and temporal patterns of three lncRNAs, two of which are in proximity to genes associated with hearing and deafness, were explored further. Our findings indicate that lncRNAs are prevalent in the sensory epithelium of the mouse inner ear and are likely to play key roles in regulating critical pathways for hearing and balance.
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Affiliation(s)
- Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Kobi Perl
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.,Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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23
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Wan P, Su W, Zhuo Y. Precise long non-coding RNA modulation in visual maintenance and impairment. J Med Genet 2017; 54:450-459. [PMID: 28003323 PMCID: PMC5502309 DOI: 10.1136/jmedgenet-2016-104266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) are remarkably powerful, flexible and pervasive cellular regulators. With the help of cheaper RNA-seq, high-throughput screening of lncRNAs has become widely applied and has identified large numbers of specific lncRNAs in various physiological or pathological processes. Vision is known to be a complex and vital perception that comprises 80% of the sensory information we receive. A consensus has been reached that normal visual maintenance and impairment are primarily driven by gene regulation. Recently, it has become understood that lncRNAs are key regulators in most biological processes, including cell proliferation, apoptosis, differentiation, immune responses, oxidative stress and inflammation. Our review is intended to provide insight towards a comprehensive view of the precise modulation of lncRNAs in visual maintenance and impairment. We also highlight the challenges and future directions in conducting lncRNA studies, particularly in patients whose lncRNAs may hold expanded promise for diagnostic, prognostic and therapeutic applications.
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Affiliation(s)
- Peixing Wan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
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24
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Van Cauwenbergh C, Van Schil K, Cannoodt R, Bauwens M, Van Laethem T, De Jaegere S, Steyaert W, Sante T, Menten B, Leroy BP, Coppieters F, De Baere E. arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs. Genet Med 2016; 19:457-466. [PMID: 27608171 PMCID: PMC5392597 DOI: 10.1038/gim.2016.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Purpose: Our goal was to design a customized microarray, arrEYE, for high-resolution copy number variant (CNV) analysis of known and candidate genes for inherited retinal dystrophy (iRD) and retina-expressed noncoding RNAs (ncRNAs). Methods: arrEYE contains probes for the full genomic region of 106 known iRD genes, including those implicated in retinitis pigmentosa (RP) (the most frequent iRD), cone–rod dystrophies, macular dystrophies, and an additional 60 candidate iRD genes and 196 ncRNAs. Eight CNVs in iRD genes identified by other techniques were used as positive controls. The test cohort consisted of 57 patients with autosomal dominant, X-linked, or simplex RP. Results: In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delinsAGAATATG, p.(Glu212Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(Ala615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs. Conclusion: The arrEYE platform revealed subtle single-exon to larger CNVs in iRD genes that could be characterized at the nucleotide level, facilitated by the high resolution of the platform. We report the first CNV in HGSNAT that, combined with another mutation, leads to RP, further supporting its recently identified role in nonsyndromic iRD. Genet Med19 4, 457–466.
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Affiliation(s)
- Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kristof Van Schil
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robrecht Cannoodt
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Data Mining and Modeling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
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25
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Ulitsky I. Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat Rev Genet 2016; 17:601-14. [DOI: 10.1038/nrg.2016.85] [Citation(s) in RCA: 373] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Babino D, Palczewski G, Widjaja-Adhi MAK, Kiser PD, Golczak M, von Lintig J. Characterization of the Role of β-Carotene 9,10-Dioxygenase in Macular Pigment Metabolism. J Biol Chem 2015; 290:24844-57. [PMID: 26307071 DOI: 10.1074/jbc.m115.668822] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 12/22/2022] Open
Abstract
A family of enzymes collectively referred to as carotenoid cleavage oxygenases is responsible for oxidative conversion of carotenoids into apocarotenoids, including retinoids (vitamin A and its derivatives). A member of this family, the β-carotene 9,10-dioxygenase (BCO2), converts xanthophylls to rosafluene and ionones. Animals deficient in BCO2 highlight the critical role of the enzyme in carotenoid clearance as accumulation of these compounds occur in tissues. Inactivation of the enzyme by a four-amino acid-long insertion has recently been proposed to underlie xanthophyll concentration in the macula of the primate retina. Here, we focused on comparing the properties of primate and murine BCO2s. We demonstrate that the enzymes display a conserved structural fold and subcellular localization. Low temperature expression and detergent choice significantly affected binding and turnover rates of the recombinant enzymes with various xanthophyll substrates, including the unique macula pigment meso-zeaxanthin. Mice with genetically disrupted carotenoid cleavage oxygenases displayed adipose tissue rather than eye-specific accumulation of supplemented carotenoids. Studies in a human hepatic cell line revealed that BCO2 is expressed as an oxidative stress-induced gene. Our studies provide evidence that the enzymatic function of BCO2 is conserved in primates and link regulation of BCO2 gene expression with oxidative stress that can be caused by excessive carotenoid supplementation.
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Affiliation(s)
- Darwin Babino
- From the Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106 and
| | - Grzegorz Palczewski
- From the Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106 and
| | - M Airanthi K Widjaja-Adhi
- From the Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106 and
| | - Philip D Kiser
- From the Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106 and the Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Marcin Golczak
- From the Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106 and
| | - Johannes von Lintig
- From the Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106 and
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27
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Evolutionary annotation of conserved long non-coding RNAs in major mammalian species. SCIENCE CHINA-LIFE SCIENCES 2015; 58:787-98. [DOI: 10.1007/s11427-015-4881-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 04/17/2015] [Indexed: 12/18/2022]
Abstract
Abstract
Mammalian genomes contain tens of thousands of long non-coding RNAs (lncRNAs) that have been implicated in diverse biological processes. However, the lncRNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lncRNA catalogs (4,142–42,558 lncRNAs) covering the major mammalian species. Compared to protein- coding RNAs, expression of lncRNAs exhibits striking lineage specificity. Notably, although 30%–99% human lncRNAs are conserved across different species on DNA locus level, only 20%–27% of these conserved lncRNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes (48%–80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lncRNAs. Moreover, we constructed lncRNA expression phylogenetic trees across nine mammals and demonstrated that lncRNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lncRNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lncRNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named PhyloNONCODE (http://www.bioinfo.org/phyloNoncode). Our work starts to place mammalian lncRNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.
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28
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Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015; 46:1-30. [PMID: 25668385 PMCID: PMC4402139 DOI: 10.1016/j.preteyeres.2015.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/10/2023]
Abstract
Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.
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Affiliation(s)
- Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA.
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Integrative transcriptome-wide analyses reveal critical HER2-regulated mRNAs and lincRNAs in HER2+ breast cancer. Breast Cancer Res Treat 2015; 150:321-34. [PMID: 25749757 DOI: 10.1007/s10549-015-3327-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/28/2015] [Indexed: 01/27/2023]
Abstract
Breast cancer is a major health problem affecting millions of women worldwide. Over 200,000 new cases are diagnosed annually in the USA, with approximately 40,000 of these cases resulting in death. HER2-positive (HER2+) breast tumors, representing 20-30 % of early-stage breast cancer diagnoses, are characterized by the amplification of the HER2 gene. However, the critical genes and pathways that become affected by HER2 amplification in humans are yet to be specifically identified. Furthermore, it is yet to be determined if HER2 amplification also affects the expression of long intervening non-coding (linc)RNAs, which are involved in the epigenetic regulation of gene expression. We examined changes in gene expression by next generation RNA sequencing in human tumors pre- and post- HER2 inhibition by trastuzumab in vivo, and changes in gene expression in response to HER2 knock down in cell culture models. We integrated our results with gene expression analysis of HER2+ tumors vs matched normal tissue from The Cancer Genome Atlas. The integrative analyses of these datasets led to the identification of a small set of mRNAs, and the associated biological pathways that become deregulated by HER2 amplification. Furthermore, our analyses identified three lincRNAs that become deregulated in response to HER2 amplification both in vitro and in vivo. Our results should provide the foundation for functional studies of these candidate mRNAs and lincRNAs to further our understanding of how HER2 amplification results in tumorigenesis. Also, the identified lincRNAs could potentially open the door for future RNA-based biomarkers and therapeutics in HER2+ breast cancer.
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30
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Hoang TV, Kumar PKR, Sutharzan S, Tsonis PA, Liang C, Robinson ML. Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses with RNA sequencing. Mol Vis 2014; 20:1491-517. [PMID: 25489224 PMCID: PMC4225139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 11/02/2014] [Indexed: 11/19/2022] Open
Abstract
PURPOSE The ocular lens contains only two cell types: epithelial cells and fiber cells. The epithelial cells lining the anterior hemisphere have the capacity to continuously proliferate and differentiate into lens fiber cells that make up the large proportion of the lens mass. To understand the transcriptional changes that take place during the differentiation process, high-throughput RNA-Seq of newborn mouse lens epithelial cells and lens fiber cells was conducted to comprehensively compare the transcriptomes of these two cell types. METHODS RNA from three biologic replicate samples of epithelial and fiber cells from newborn FVB/N mouse lenses was isolated and sequenced to yield more than 24 million reads per sample. Sequence reads that passed quality filtering were mapped to the reference genome using Genomic Short-read Nucleotide Alignment Program (GSNAP). Transcript abundance and differential gene expression were estimated using the Cufflinks and DESeq packages, respectively. Gene Ontology enrichment was analyzed using GOseq. RNA-Seq results were compared with previously published microarray data. The differential expression of several biologically important genes was confirmed using reverse transcription (RT)-quantitative PCR (qPCR). RESULTS Here, we present the first application of RNA-Seq to understand the transcriptional changes underlying the differentiation of epithelial cells into fiber cells in the newborn mouse lens. In total, 6,022 protein-coding genes exhibited differential expression between lens epithelial cells and lens fiber cells. To our knowledge, this is the first study identifying the expression of 254 long intergenic non-coding RNAs (lincRNAs) in the lens, of which 86 lincRNAs displayed differential expression between the two cell types. We found that RNA-Seq identified more differentially expressed genes and correlated with RT-qPCR quantification better than previously published microarray data. Gene Ontology analysis showed that genes upregulated in the epithelial cells were enriched for extracellular matrix production, cell division, migration, protein kinase activity, growth factor binding, and calcium ion binding. Genes upregulated in the fiber cells were enriched for proteosome complexes, unfolded protein responses, phosphatase activity, and ubiquitin binding. Differentially expressed genes involved in several important signaling pathways, lens structural components, organelle loss, and denucleation were also highlighted to provide insights into lens development and lens fiber differentiation. CONCLUSIONS RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of protein-coding and non-coding transcripts from lens epithelial cells and lens fiber cells. This information provides a valuable resource for studying lens development, nuclear degradation, and organelle loss during fiber differentiation, and associated diseases.
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Affiliation(s)
| | | | | | - Panagiotis A. Tsonis
- Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, OH
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH
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31
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Dey BK, Mueller AC, Dutta A. Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription 2014; 5:e944014. [PMID: 25483404 DOI: 10.4161/21541272.2014.944014] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A significant portion of the mammalian genome encodes numerous transcripts that are not translated into proteins, termed long non-coding RNAs. Initial studies identifying long non-coding RNAs inferred these RNA sequences were a consequence of transcriptional noise or promiscuous RNA polymerase II activity. However, the last decade has seen a revolution in the understanding of regulation and function of long non-coding RNAs. Now it has become apparent that long non-coding RNAs play critical roles in a wide variety of biological processes. In this review, we describe the current understanding of long non-coding RNA-mediated regulation of cellular processes: differentiation, development, and disease.
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Key Words
- Bvht, braveheart
- CDT, C-terminal domain
- DBE-T, D4Z4-binding element
- DMD, Duchenne muscular dystrophy
- ES, embryonic stem
- FSHD, facioscapulohumeral muscular dystrophy
- Fendrr, Foxf1a called fetal-lethal non-coding developmental regulatory RNA
- MEF2, myocyte enhancer factor-2
- MRFs, myogenic regulatory factors
- Malat1, metastasis associated lung adenocarcinoma transcript 1
- Mesp1, mesoderm progenitor 1
- Neat2, nuclear-enriched abundant transcript 2
- PRC2, polycomb group repressive complex 2
- RNAP II, RNA polymerase II
- SINE, short interspersed element
- SR, serine arginine
- SRA, steroid receptor activator
- SRY, sex-determining region Y
- YAM 1-4, YY1-associated muscle 1-4
- ceRNAs, competing endogenous RNAs
- ciRS-7, circular RNA sponge for miR-7
- development
- differentiation
- disease
- gene expression
- iPS, induced pluripotent stem
- lncRNAs, long non-coding RNAs
- long non-coding RNAs
- ncRNAa, non-coding RNA activating
- skeletal muscle
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Affiliation(s)
- Bijan K Dey
- a Department of Biochemistry and Molecular Genetics ; University of Virginia School of Medicine ; Charlottesville , VA USA
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Palczewski K. Chemistry and biology of the initial steps in vision: the Friedenwald lecture. Invest Ophthalmol Vis Sci 2014; 55:6651-72. [PMID: 25338686 DOI: 10.1167/iovs.14-15502] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Visual transduction is the process in the eye whereby absorption of light in the retina is translated into electrical signals that ultimately reach the brain. The first challenge presented by visual transduction is to understand its molecular basis. We know that maintenance of vision is a continuous process requiring the activation and subsequent restoration of a vitamin A-derived chromophore through a series of chemical reactions catalyzed by enzymes in the retina and retinal pigment epithelium (RPE). Diverse biochemical approaches that identified key proteins and reactions were essential to achieve a mechanistic understanding of these visual processes. The three-dimensional arrangements of these enzymes' polypeptide chains provide invaluable insights into their mechanisms of action. A wealth of information has already been obtained by solving high-resolution crystal structures of both rhodopsin and the retinoid isomerase from pigment RPE (RPE65). Rhodopsin, which is activated by photoisomerization of its 11-cis-retinylidene chromophore, is a prototypical member of a large family of membrane-bound proteins called G protein-coupled receptors (GPCRs). RPE65 is a retinoid isomerase critical for regeneration of the chromophore. Electron microscopy (EM) and atomic force microscopy have provided insights into how certain proteins are assembled to form much larger structures such as rod photoreceptor cell outer segment membranes. A second challenge of visual transduction is to use this knowledge to devise therapeutic approaches that can prevent or reverse conditions leading to blindness. Imaging modalities like optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO) applied to appropriate animal models as well as human retinal imaging have been employed to characterize blinding diseases, monitor their progression, and evaluate the success of therapeutic agents. Lately two-photon (2-PO) imaging, together with biochemical assays, are revealing functional aspects of vision at a new molecular level. These multidisciplinary approaches combined with suitable animal models and inbred mutant species can be especially helpful in translating provocative cell and tissue culture findings into therapeutic options for further development in animals and eventually in humans. A host of different approaches and techniques is required for substantial progress in understanding fundamental properties of the visual system.
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Affiliation(s)
- Krzysztof Palczewski
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States
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33
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Yan B, Yao J, Tao ZF, Jiang Q. Epigenetics and ocular diseases: from basic biology to clinical study. J Cell Physiol 2014; 229:825-33. [PMID: 24318407 DOI: 10.1002/jcp.24522] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/02/2013] [Indexed: 12/23/2022]
Abstract
Epigenetics is an emerging field in ophthalmology and has opened a new avenue for understanding ocular development and ocular diseases related to aging and environment. Epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and deployment of non-coding RNAs, result in the heritable silencing of gene expression without any change in DNA sequence. Accumulating evidence suggests a potential link between gene expression, chromatin structure, non-coding RNAs, and cellular differentiation during ocular development. Disruption of the balance of epigenetic networks could become the etiology of several ocular diseases. Here, we summarized the current knowledge about epigenetic regulatory mechanisms in ocular development and diseases.
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Affiliation(s)
- Biao Yan
- Eye Hospital, Nanjing Medical University, Nanjing, China
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Ushakov K, Rudnicki A, Avraham KB. MicroRNAs in sensorineural diseases of the ear. Front Mol Neurosci 2013; 6:52. [PMID: 24391537 PMCID: PMC3870287 DOI: 10.3389/fnmol.2013.00052] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/04/2013] [Indexed: 12/30/2022] Open
Abstract
Non-coding microRNAs (miRNAs) have a fundamental role in gene regulation and expression in almost every multicellular organism. Only discovered in the last decade, miRNAs are already known to play a leading role in many aspects of disease. In the vertebrate inner ear, miRNAs are essential for controlling development and survival of hair cells. Moreover, dysregulation of miRNAs has been implicated in sensorineural hearing impairment, as well as in other ear diseases such as cholesteatomas, vestibular schwannomas, and otitis media. Due to the inaccessibility of the ear in humans, animal models have provided the optimal tools to study miRNA expression and function, in particular mice and zebrafish. A major focus of current research has been to discover the targets of the miRNAs expressed in the inner ear, in order to determine the regulatory pathways of the auditory and vestibular systems. The potential for miRNAs manipulation in development of therapeutic tools for hearing impairment is as yet unexplored, paving the way for future work in the field.
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Affiliation(s)
- Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Anya Rudnicki
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
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Mustafi D, Kevany BM, Genoud C, Bai X, Palczewski K. Photoreceptor phagocytosis is mediated by phosphoinositide signaling. FASEB J 2013; 27:4585-95. [PMID: 23913857 DOI: 10.1096/fj.13-237537] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Circadian oscillations in peripheral tissues, such as the retinal compartment of the eye, are critical to anticipating changing metabolic demands. Circadian shedding of retinal photoreceptor cell discs with subsequent phagocytosis by the neighboring retinal pigmented epithelium (RPE) is essential for removal of toxic metabolites and lifelong survival of these postmitotic neurons. Defects in photoreceptor phagocytosis can lead to severe retinal pathology, but the biochemical mechanisms remain poorly defined. By first documenting a 2.8-fold burst of photoreceptor phagocytosis events in the mouse eye in the morning compared with the afternoon by serial block face imaging, we established time points to assess transcriptional readouts by RNA sequencing (RNA-Seq). We identified 365 oscillating protein-coding transcripts that implicated the phosphoinositide lipid signaling network mediating the discrete steps of photoreceptor phagocytosis. Moreover, examination of overlapping cistromic sites by core clock transcription factors and promoter elements of these effector genes provided a functional basis for the circadian cycling of these transcripts. RNA-Seq also revealed oscillating expression of 16 long intergenic noncoding RNAs and key histone modifying enzymes critical for circadian gene expression. Our phenotypic and genotypic characterization reveals a complex global landscape of overlapping and temporally controlled networks driving the essential circadian process in the eye.
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Affiliation(s)
- Debarshi Mustafi
- 1Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106-4965, USA.
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