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Kocherlakota S, Baes M. Benefits and Caveats in the Use of Retinal Pigment Epithelium-Specific Cre Mice. Int J Mol Sci 2024; 25:1293. [PMID: 38279294 PMCID: PMC10816505 DOI: 10.3390/ijms25021293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
The retinal pigment epithelium (RPE) is an important monolayer of cells present in the outer retina, forming a major part of the blood-retina barrier (BRB). It performs many tasks essential for the maintenance of retinal integrity and function. With increasing knowledge of the retina, it is becoming clear that both common retinal disorders, like age-related macular degeneration, and rare genetic disorders originate in the RPE. This calls for a better understanding of the functions of various proteins within the RPE. In this regard, mice enabling an RPE-specific gene deletion are a powerful tool to study the role of a particular protein within the RPE cells in their native environment, simultaneously negating any potential influences of systemic changes. Moreover, since RPE cells interact closely with adjacent photoreceptors, these mice also provide an excellent avenue to study the importance of a particular gene function within the RPE to the retina as a whole. In this review, we outline and compare the features of various Cre mice created for this purpose, which allow for inducible or non-inducible RPE-specific knockout of a gene of interest. We summarize the various benefits and caveats involved in the use of such mouse lines, allowing researchers to make a well-informed decision on the choice of Cre mouse to use in relation to their research needs.
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Affiliation(s)
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
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2
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Seruggia D, Josa S, Fernández A, Montoliu L. The structure and function of the mouse tyrosinase locus. Pigment Cell Melanoma Res 2020; 34:212-221. [DOI: 10.1111/pcmr.12942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 10/14/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Davide Seruggia
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
- Division of Hematology/Oncology Boston Children's HospitalHarvard Medical School Boston MA USA
| | - Santiago Josa
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
| | - Almudena Fernández
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
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3
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Seruggia D, Fernández A, Cantero M, Fernández-Miñán A, Gomez-Skarmeta JL, Pelczar P, Montoliu L. Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression. Sci Rep 2020; 10:15494. [PMID: 32968154 PMCID: PMC7511308 DOI: 10.1038/s41598-020-72543-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022] Open
Abstract
Control of gene expression is dictated by cell-type specific regulatory sequences that physically organize the structure of chromatin, including promoters, enhancers and insulators. While promoters and enhancers convey cell-type specific activating signals, insulators prevent the cross-talk of regulatory elements within adjacent loci and safeguard the specificity of action of promoters and enhancers towards their targets in a tissue specific manner. Using the mouse tyrosinase (Tyr) locus as an experimental model, a gene whose mutations are associated with albinism, we described the chromatin structure in cells at two distinct transcriptional states. Guided by chromatin structure, through the use of Chromosome Conformation Capture (3C), we identified sequences at the 5' and 3' boundaries of this mammalian gene that function as enhancers and insulators. By CRISPR/Cas9-mediated chromosomal deletion, we dissected the functions of these two regulatory elements in vivo in the mouse, at the endogenous chromosomal context, and proved their mechanistic role as genomic insulators, shielding the Tyr locus from the expression patterns of adjacent genes.
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Affiliation(s)
- Davide Seruggia
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
- CIBERER-ISCIII, Madrid, Spain
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Almudena Fernández
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
- CIBERER-ISCIII, Madrid, Spain
| | - Marta Cantero
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
- CIBERER-ISCIII, Madrid, Spain
| | - Ana Fernández-Miñán
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - José Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Pawel Pelczar
- Center for Transgenic Models, University of Basel, Basel, Switzerland
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain.
- CIBERER-ISCIII, Madrid, Spain.
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4
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Schneider S, Hotaling N, Campos M, Patnaik SR, Bharti K, May-Simera HL. Generation of an inducible RPE-specific Cre transgenic-mouse line. PLoS One 2018; 13:e0207222. [PMID: 30440011 PMCID: PMC6237357 DOI: 10.1371/journal.pone.0207222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/26/2018] [Indexed: 11/19/2022] Open
Abstract
The retinal pigment epithelium (RPE) is an epithelial monolayer in the back of the vertebrate eye. RPE dysfunction is associated with retinal degeneration and blindness. In order to fully understand how dysregulation affects visual function, RPE-specific gene knockouts are indispensable. Since the currently available RPE-specific Cre recombinases show lack of specificity or poor recombination, we sought to generate an alternative. We generated a tamoxifen-inducible RPE-specific Cre transgenic mouse line under transcriptional control of an RPE-specific Tyrosinase enhancer. We characterized the Cre-mediated recombinant expression by crossing our RPE-Tyrosinase-CreErT2 mouse line with the tdTomato reporter line, Ai14. Detected fluorescence was quantified via high-content image analysis. Recombination was predominantly observed in the RPE and adjacent ciliary body. RPE flatmount preparations revealed a high level of recombination in adult mice (47.25-69.48%). Regional analysis of dorsal, ventral, nasal and temporal areas did not show significant changes in recombination. However, recombination was higher in the central RPE compared to the periphery. Higher levels of Cre-mediated recombinant expression was observed in embryonic RPE (~83%). Compared to other RPE-specific Cre transgenic mouse lines, this newly generated RPE-Tyrosinase-CreErT2 line shows a more uniform and higher level of recombination with the advantage to initiate recombination in both, prenatal and postnatal animals. This line can serve as a valuable tool for researches exploring the role of individual gene functions, in both developing and differentiated RPE.
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Affiliation(s)
- Sandra Schneider
- Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, Germany
| | - Nathan Hotaling
- National Eye Institute, NIH, Bethesda, MD, United States of America
| | - Maria Campos
- National Eye Institute, NIH, Bethesda, MD, United States of America
| | - Sarita Rani Patnaik
- Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, Germany
| | - Kapil Bharti
- National Eye Institute, NIH, Bethesda, MD, United States of America
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5
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Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G. Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol 2018; 19:47. [PMID: 29622030 PMCID: PMC5887227 DOI: 10.1186/s13059-018-1426-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS We use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body system. We present a cellular-state landscape for hPSC early differentiation that covers multiple cellular lineages, including neural, muscle, endothelial, stromal, liver, and epithelial cells. Through pseudotime analysis, we construct the developmental trajectories of these progenitor cells and reveal the gene expression dynamics in the process of cell differentiation. We further reprogram primed H9 cells into naïve-like H9 cells to study the cellular-state transition process. We find that genes related to hemogenic endothelium development are enriched in naïve-like H9. Functionally, naïve-like H9 show higher potency for differentiation into hematopoietic lineages than primed cells. CONCLUSIONS Our single-cell analysis reveals the cellular-state landscape of hPSC early differentiation, offering new insights that can be harnessed for optimization of differentiation protocols.
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Affiliation(s)
- Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Hangzhou, 310058, China. .,College of Animal Science, Zhejiang University, Hangzhou, 310058, China.
| | - Daosheng Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Huidong Chen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA.,Department of Computer Science and Technology, Tongji University, Shanghai, 201804, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chen Cheng
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - He Huang
- Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Hangzhou, 310058, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China.
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6
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In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites. Adv Bioinformatics 2016; 2016:1286510. [PMID: 27698666 PMCID: PMC5028829 DOI: 10.1155/2016/1286510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 03/17/2016] [Accepted: 06/02/2016] [Indexed: 12/22/2022] Open
Abstract
Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.
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7
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de Assis LVM, Moraes MN, da Silveira Cruz-Machado S, Castrucci AML. The effect of white light on normal and malignant murine melanocytes: A link between opsins, clock genes, and melanogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1119-33. [PMID: 26947915 DOI: 10.1016/j.bbamcr.2016.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 02/29/2016] [Accepted: 03/02/2016] [Indexed: 11/26/2022]
Abstract
The skin possesses a photosensitive system comprised of opsins whose function is not fully understood, and clock genes which exert an important regulatory role in skin biology. Here, we evaluated the presence of opsins in normal (Melan-a cells) and malignant (B16-F10 cells) murine melanocytes. Both cell lines express Opn2, Opn4--for the first time reported in these cell types--as well as S-opsin. OPN4 protein was found in a small area capping the cell nuclei of B16-F10 cells kept in constant dark (DD); twenty-four hours after the white light pulse (WLP), OPN4 was found in the cell membrane. Despite the fact that B16-F10 cells expressed less Opn2 and Opn4 than Melan-a cells, our data indicate that the malignant melanocytes exhibited increased photoresponsiveness. The clock gene machinery is also severely downregulated in B16-F10 cells as compared to Melan-a cells. Per1, Per2, and Bmal1 expression increased in B16-F10 cells in response to WLP. Although no response in clock gene expression to WLP was observed in Melan-a cells, gene correlational data suggest a minor effect of WLP. In contrast to opsins and clock genes, melanogenesis is significantly upregulated in malignant melanocytes in comparison to Melan-a cells. Tyrosinase expression increased after WLP only in B16-F10 cells; however no increase in melanin content after WLP was seen in either cell line. Our findings may prove useful in the treatment and the development of new pharmacological approaches of depigmentation diseases and skin cancer.
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Affiliation(s)
- L V M de Assis
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - M N Moraes
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - S da Silveira Cruz-Machado
- Laboratory of Chronopharmacology, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - A M L Castrucci
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.
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8
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Small-molecule-directed, efficient generation of retinal pigment epithelium from human pluripotent stem cells. Proc Natl Acad Sci U S A 2015; 112:10950-5. [PMID: 26269569 DOI: 10.1073/pnas.1422818112] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Age-related macular degeneration (AMD) is associated with dysfunction and death of retinal pigment epithelial (RPE) cells. Cell-based approaches using RPE-like cells derived from human pluripotent stem cells (hPSCs) are being developed for AMD treatment. However, most efficient RPE differentiation protocols rely on complex, stepwise treatments and addition of growth factors, whereas small-molecule-only approaches developed to date display reduced yields. To identify new compounds that promote RPE differentiation, we developed and performed a high-throughput quantitative PCR screen complemented by a novel orthogonal human induced pluripotent stem cell (hiPSC)-based RPE reporter assay. Chetomin, an inhibitor of hypoxia-inducible factors, was found to strongly increase RPE differentiation; combination with nicotinamide resulted in conversion of over one-half of the differentiating cells into RPE. Single passage of the whole culture yielded a highly pure hPSC-RPE cell population that displayed many of the morphological, molecular, and functional characteristics of native RPE.
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9
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Seruggia D, Fernández A, Cantero M, Pelczar P, Montoliu L. Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR-Cas9-mediated mutagenesis. Nucleic Acids Res 2015; 43:4855-67. [PMID: 25897126 PMCID: PMC4446435 DOI: 10.1093/nar/gkv375] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 04/08/2015] [Indexed: 12/26/2022] Open
Abstract
Newly developed genome-editing tools, such as the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system, allow simple and rapid genetic modification in most model organisms and human cell lines. Here, we report the production and analysis of mice carrying the inactivation via deletion of a genomic insulator, a key non-coding regulatory DNA element found 5' upstream of the mouse tyrosinase (Tyr) gene. Targeting sequences flanking this boundary in mouse fertilized eggs resulted in the efficient deletion or inversion of large intervening DNA fragments delineated by the RNA guides. The resulting genome-edited mice showed a dramatic decrease in Tyr gene expression as inferred from the evident decrease of coat pigmentation, thus supporting the functionality of this boundary sequence in vivo, at the endogenous locus. Several potential off-targets bearing sequence similarity with each of the two RNA guides used were analyzed and found to be largely intact. This study reports how non-coding DNA elements, even if located in repeat-rich genomic sequences, can be efficiently and functionally evaluated in vivo and, furthermore, it illustrates how the regulatory elements described by the ENCODE and EPIGENOME projects, in the mouse and human genomes, can be systematically validated.
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Affiliation(s)
- Davide Seruggia
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus Cantoblanco, Darwin 3, 28049 Madrid, Spain CIBERER-ISCIII, Madrid, Spain
| | - Almudena Fernández
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus Cantoblanco, Darwin 3, 28049 Madrid, Spain CIBERER-ISCIII, Madrid, Spain
| | - Marta Cantero
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus Cantoblanco, Darwin 3, 28049 Madrid, Spain CIBERER-ISCIII, Madrid, Spain
| | - Pawel Pelczar
- Institute of Laboratory Animal Science, University of Zurich, Zurich, Switzerland
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus Cantoblanco, Darwin 3, 28049 Madrid, Spain CIBERER-ISCIII, Madrid, Spain
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10
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Sarode B, Nowell CS, Ihm J, Kostic C, Arsenijevic Y, Moulin AP, Schorderet DF, Beermann F, Radtke F. Notch signaling in the pigmented epithelium of the anterior eye segment promotes ciliary body development at the expense of iris formation. Pigment Cell Melanoma Res 2014; 27:580-9. [DOI: 10.1111/pcmr.12236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 03/12/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Bhushan Sarode
- School of Life Science; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC); Lausanne Switzerland
| | - Craig S. Nowell
- School of Life Science; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC); Lausanne Switzerland
| | - JongEun Ihm
- School of Life Science; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Corinne Kostic
- Unit of Gene Therapy and Stem Cell Biology; Jules-Gonin Eye Hospital; University of Lausanne; Lausanne Switzerland
- Eye Pathology Laboratory; Jules-Gonin Eye Hospital; University of Lausanne; Lausanne Switzerland
| | - Yvan Arsenijevic
- Unit of Gene Therapy and Stem Cell Biology; Jules-Gonin Eye Hospital; University of Lausanne; Lausanne Switzerland
- Eye Pathology Laboratory; Jules-Gonin Eye Hospital; University of Lausanne; Lausanne Switzerland
| | - Alexandre P. Moulin
- Eye Pathology Laboratory; Jules-Gonin Eye Hospital; University of Lausanne; Lausanne Switzerland
| | - Daniel F. Schorderet
- School of Life Science; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
- Eye Pathology Laboratory; Jules-Gonin Eye Hospital; University of Lausanne; Lausanne Switzerland
- IRO - Institute for Research in Ophthalmology; Sion Switzerland
| | - Friedrich Beermann
- School of Life Science; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC); Lausanne Switzerland
| | - Freddy Radtke
- School of Life Science; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC); Lausanne Switzerland
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11
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Bharti K, Gasper M, Ou J, Brucato M, Clore-Gronenborn K, Pickel J, Arnheiter H. A regulatory loop involving PAX6, MITF, and WNT signaling controls retinal pigment epithelium development. PLoS Genet 2012; 8:e1002757. [PMID: 22792072 PMCID: PMC3390378 DOI: 10.1371/journal.pgen.1002757] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 04/20/2012] [Indexed: 01/13/2023] Open
Abstract
The separation of the optic neuroepithelium into future retina and retinal pigment epithelium (RPE) is a critical event in early eye development in vertebrates. Here we show in mice that the transcription factor PAX6, well-known for its retina-promoting activity, also plays a crucial role in early pigment epithelium development. This role is seen, however, only in a background genetically sensitized by mutations in the pigment cell transcription factor MITF. In fact, a reduction in Pax6 gene dose exacerbates the RPE-to-retina transdifferentiation seen in embryos homozygous for an Mitf null allele, and it induces such a transdifferentiation in embryos that are either heterozygous for the Mitf null allele or homozygous for an RPE–specific hypomorphic Mitf allele generated by targeted mutation. Conversely, an increase in Pax6 gene dose interferes with transdifferentiation even in homozygous Mitf null embryos. Gene expression analyses show that, together with MITF or its paralog TFEC, PAX6 suppresses the expression of Fgf15 and Dkk3. Explant culture experiments indicate that a combination of FGF and DKK3 promote retina formation by inhibiting canonical WNT signaling and stimulating the expression of retinogenic genes, including Six6 and Vsx2. Our results demonstrate that in conjunction with Mitf/Tfec Pax6 acts as an anti-retinogenic factor, whereas in conjunction with retinogenic genes it acts as a pro-retinogenic factor. The results suggest that careful manipulation of the Pax6 regulatory circuit may facilitate the generation of retinal and pigment epithelium cells from embryonic or induced pluripotent stem cells. The retinal pigment epithelium or RPE in the back of the eye is critical for the normal function of the retina, and its abnormalities can lead to retinal disorders such as adult-onset macular degeneration. Insights into the pathogenesis of such disorders, and potential therapies, may come from using RPE cells generated in vitro from induced pluripotent stem cells. To obtain authentic RPE cells in vitro, we need to thoroughly understand the normal process of their development in vivo. Here we find that the potent retina-inducing transcription factor PAX6 plays a critical anti-retinogenic role in the RPE of mice. But how can PAX6 be pro-retinogenic in the retina and anti-retinogenic in the RPE? To address this question, we used gene expression studies and combined them with chromatin immunoprecipitation assays, which analyze the interaction of transcription factors with chromatin in vivo. Our findings show that, in the RPE, PAX6 cooperates with either one (or both) of two related RPE transcription factors, MITF and TFEC, to suppress extracellular signals that in the normal retina induce a signaling cascade promoting retina formation. Hence, this study provides mechanistic insights into RPE development that may become important for the efficient generation of retina and RPE from induced pluripotent stem cells.
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Affiliation(s)
- Kapil Bharti
- Mammalian Development Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America.
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12
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Barolo S. Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy. Bioessays 2012; 34:135-41. [PMID: 22083793 PMCID: PMC3517143 DOI: 10.1002/bies.201100121] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper, in the form of a frequently asked questions page (FAQ), addresses outstanding questions about "shadow enhancers", quasi-redundant cis-regulatory elements, and their proposed roles in transcriptional control. Questions include: What exactly are shadow enhancers? How many genes have shadow/redundant/distributed enhancers? How redundant are these elements? What is the function of distributed enhancers? How modular are enhancers? Is it useful to study a single enhancer in isolation? In addition, a revised definition of "shadow enhancers" is proposed, and possible mechanisms of shadow enhancer function and evolution are discussed.
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Affiliation(s)
- Scott Barolo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
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13
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Biesemeier A, Julien S, Kokkinou D, Schraermeyer U, Eibl O. A low zinc diet leads to loss of Zn in melanosomes of the RPE but not in melanosomes of the choroidal melanocytes. Metallomics 2012; 4:323-32. [DOI: 10.1039/c2mt00187j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Aydin IT, Beermann F. A mart-1::Cre transgenic line induces recombination in melanocytes and retinal pigment epithelium. Genesis 2011; 49:403-9. [PMID: 21309074 DOI: 10.1002/dvg.20725] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The number of transgenic mouse lines expressing Cre in either type of pigment cells (melanocytes and retinal pigment epithelium, RPE) is limited, and the available lines do not always offer sufficient specificity. In this study, we addressed this issue and we report on the generation of a MART-1::Cre BAC transgenic mouse line, in which the expression of Cre recombinase is controlled by regulatory elements of the pigment cell-specific gene MART-1 (mlana). When MART-1::Cre BAC transgenic mice were bred with the ROSA26-R reporter line, ß-galactosidase expression was observed in RPE from E12.5 onwards, and in melanocyte precursors from E17.5, indicating that the MART-1::Cre line provides Cre recombinase activity in pigment-producing cells rather than in a particular lineage. In addition, breeding of this mouse line to mice carrying a conditional allele of RBP-Jκ corroborated the reported phenotypes in both pigment cell lineages, inducing hair greying and microphthalmia. Our results thus suggest, that the MART-1::Cre line may serve as a novel and useful tool for functional studies in melanocytes and the RPE.genesis 49:403-409, 2011.
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Affiliation(s)
- Iraz T Aydin
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland
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Aruta C, Giordano F, De Marzo A, Comitato A, Raposo G, Nandrot EF, Marigo V. In vitro differentiation of retinal pigment epithelium from adult retinal stem cells. Pigment Cell Melanoma Res 2011; 24:233-40. [PMID: 21232026 DOI: 10.1111/j.1755-148x.2010.00793.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the limitations in molecular and functional studies of the retinal pigment epithelium (RPE) has been the lack of an in vitro system retaining all the features of in vivo RPE cells. Retinal pigment epithelium cell lines do not show characteristics typical of a functional RPE, such as pigmentation and expression of specific markers. The present study was aimed at the development of culture conditions to differentiate, in vitro, retinal stem cells (RSC), derived from the adult ciliary body, into a functional RPE. Retinal stem cells were purified from murine eyes, grown as pigmented neurospheres and induced to differentiate into RPE on an extracellular matrix substrate using specific culture conditions. After 7-15 days of culture, pigmented cells with an epithelial morphology showed a polarized organization and a capacity for phagocytosis. We detected different stages of melanogenesis in cells at 7 days of differentiation, whereas RPE at 15 days contained only mature melanosomes. These data suggest that our protocol to differentiate RPE in vitro can provide a useful model for molecular and functional studies.
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Affiliation(s)
- Claudia Aruta
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy
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16
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Schouwey K, Aydin IT, Radtke F, Beermann F. RBP-Jκ-dependent Notch signaling enhances retinal pigment epithelial cell proliferation in transgenic mice. Oncogene 2010; 30:313-22. [DOI: 10.1038/onc.2010.428] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Biesemeier A, Kreppel F, Kochanek S, Schraermeyer U. The classical pathway of melanogenesis is not essential for melanin synthesis in the adult retinal pigment epithelium. Cell Tissue Res 2010; 339:551-60. [PMID: 20140456 DOI: 10.1007/s00441-009-0920-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 12/15/2009] [Indexed: 11/29/2022]
Abstract
Premelanosomes are presumed to be essential for melanogenesis in melanocytes and pre-natal retinal pigment epithelium (RPE) cells. We analysed melanin synthesis in adenoviral-transduced tyrosinase-gene-expressing amelanotic RPE (ARPE) 19 cells to determine whether premelanosome formation is needed for post-natal melanogenesis. The synthesis of melanogenic proteins and melanin granules was investigated by immunocytochemistry and light and electron microscopy. The occurrence of tyrosinase was analysed ultrastructurally by dihydroxyphenylalanine histochemistry. The viability of transduced cell cultures was examined via MTT assay. We found active tyrosinase in small granule-like vesicles throughout the cytoplasm and in the endoplasmic reticulum and nuclear membrane. Tyrosinase was also associated with multi-vesicular and multi-lamellar organelles. Typical premelanosomes, structural protein PMEL17, tyrosinase-related protein 1 and classic melanosomal stages I-IV were not detected. Instead, melanogenesis took place inside multi-vesicular and multi-lamellar bodies of unknown origin. Viability was not affected up to 10 days after transduction. We thus demonstrate a pathway of melanin formation lacking typical hallmarks of melanogenesis.
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Affiliation(s)
- Antje Biesemeier
- Department for Experimental Vitreoretinal Surgery, University Eye Hospital Tübingen, Germany.
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Dhomen N, Da Rocha Dias S, Hayward R, Ogilvie L, Hedley D, Delmas V, McCarthy A, Henderson D, Springer CJ, Pritchard C, Larue L, Marais R. Inducible expression of (V600E) Braf using tyrosinase-driven Cre recombinase results in embryonic lethality. Pigment Cell Melanoma Res 2009; 23:112-20. [PMID: 20002887 DOI: 10.1111/j.1755-148x.2009.00662.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We recently demonstrated that expression of (V600E)Braf in mature mouse melanocytes induces melanoma. Here, we show that expression of (V600E)Braf using the tyrosinase promoter leads to an unexpected embryonic lethality, with the animals dying before, at, or shortly after birth. The mice suffer from a range of developmental defects in the skin, the brain, the eyes and the heart, tissues that are normally colonized by melanocytes. We show that the (V600E)Braf expressing cells are potential melanocytic precursors that are fully transformed, suggesting that (V600E)Braf stimulates proliferation and blocks differentiation of these cells. Our data suggests that the presence of these cells in the organs that are normally occupied by melanocytes leads to severe developmental disruption, resulting in catastrophic defects and leading to death of the individual.
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Affiliation(s)
- Nathalie Dhomen
- The Institute of Cancer Research, Signal Transduction Team, Cancer Research UK Centre for Cell and Molecular Biology, London, UK
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Aydin IT, Beermann F. Melanocyte and RPE-specific expression in transgenic mice by mouse MART-1/Melan-A/mlanaregulatory sequences. Pigment Cell Melanoma Res 2009; 22:854-6. [DOI: 10.1111/j.1755-148x.2009.00629.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cho IH, Lü ZR, Yu JR, Park YD, Yang JM, Hahn MJ, Zou F. Towards Profiling the Gene Expression of Tyrosinase-induced Melanogenesis in HEK293 Cells: a Functional DNA Chip Microarray and Interactomics Studies. J Biomol Struct Dyn 2009; 27:331-46. [DOI: 10.1080/07391102.2009.10507320] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Kopp A. Metamodels and phylogenetic replication: a systematic approach to the evolution of developmental pathways. Evolution 2009; 63:2771-89. [PMID: 19545263 DOI: 10.1111/j.1558-5646.2009.00761.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Molecular genetic analysis of phenotypic variation has revealed many examples of evolutionary change in the developmental pathways that control plant and animal morphology. A major challenge is to integrate the information from diverse organisms and traits to understand the general patterns of developmental evolution. This integration can be facilitated by evolutionary metamodels-traits that have undergone multiple independent changes in different species and whose development is controlled by well-studied regulatory pathways. The metamodel approach provides the comparative equivalent of experimental replication, allowing us to test whether the evolution of each developmental pathway follows a consistent pattern, and whether different pathways are predisposed to different modes of evolution by their intrinsic organization. A review of several metamodels suggests that the structure of developmental pathways may bias the genetic basis of phenotypic evolution, and highlights phylogenetic replication as a value-added approach that produces deeper insights into the mechanisms of evolution than single-species analyses.
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Affiliation(s)
- Artyom Kopp
- Department of Evolution and Ecology, University of California-Davis, Davis, California 95616, USA.
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Murisier F, Aydin IT, Guichard S, Brunschwiler S, Beermann F. Expression from a bacterial artificial chromosome containing the Dct gene locus. Pigment Cell Melanoma Res 2008; 21:212-5. [PMID: 18426415 DOI: 10.1111/j.1755-148x.2008.00449.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Ning A, Cui J, To E, Ashe KH, Matsubara J. Amyloid-beta deposits lead to retinal degeneration in a mouse model of Alzheimer disease. Invest Ophthalmol Vis Sci 2008; 49:5136-43. [PMID: 18566467 PMCID: PMC3947384 DOI: 10.1167/iovs.08-1849] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To compare the temporal and spatial expression patterns of amyloid precursor protein (APP), amyloid-beta deposits, inflammatory chemokines, and apoptosis in the retina of a mouse model of Alzheimer disease (AD). METHODS Retinas of transgenic mice harboring a mutant presenilin (PS1) and a mutant APP gene were processed for TUNEL and immunohistochemistry with antibodies against APP, amyloid-beta, monocyte chemotactic protein (MCP)-1, and F4/80. Comparisons were made between age groups and between transgenic and wild-type congeners. RESULTS The neuroretina demonstrated age-dependent increases in APP in the ganglion cells (RGCs) and in neurons of the inner nuclear layer (INL). Amyloid-beta demonstrated significant age-dependent deposition in the nerve fiber layer (NFL). TUNEL-positive RGC increased in an age-dependent fashion and in transgenic compared with wild-type congeners. Concomitant overexpression of MCP-1 and intense immunoreactivity for F4/80 suggested that RGCs upregulate MCP-1 in response to amyloid-beta. Activated microglia proliferated in response to MCP-1. In the outer retina, retinal pigment epithelium (RPE) demonstrated moderate age-dependent APP immunoreactivity, but nearby drusenlike deposits were not present. Amyloid-beta was observed in the choriocapillaris of the older animals. CONCLUSIONS Amyloid-beta deposits accumulate with age in the retina of a transgenic mouse model of AD. The amyloid-beta loads are accompanied by increased immunoreactivity for MCP-1, F4/80, and TUNEL-positive profiles in the RGC layer. The results suggest that amyloid-beta causes neurodegeneration in the retina of the doubly mutant transgenic mouse model of AD.
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Affiliation(s)
- Allison Ning
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jing Cui
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Eleanor To
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Karen Hsiao Ashe
- Department of Neurology, University of Minnesota, Minneapolis, Minnesota
| | - Joanne Matsubara
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada
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Vogel P, Read RW, Vance RB, Platt KA, Troughton K, Rice DS. Ocular albinism and hypopigmentation defects in Slc24a5-/- mice. Vet Pathol 2008; 45:264-79. [PMID: 18424845 DOI: 10.1354/vp.45-2-264] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
As part of a high-throughput mutagenesis and phenotyping process designed to discover novel drug targets, we generated and characterized mice with a targeted mutation in Slc24a5, a gene encoding a putative cation exchanger. Upon macroscopic examination, Slc24a5-/- mice were viable, fertile, and indistinguishable by coat color from their heterozygous and wild-type litter mates. Ophthalmoscopic examination revealed diffuse retinal hypopigmentation, and a histologic examination of the eye confirmed the presence of moderate-to-marked hypopigmentation of the retinal pigmented epithelium (RPE), ciliary body, and iris pigment epithelium (IPE). Hypopigmentation was most severe in the anterior layer cells of the IPE, where melanosomes were smaller, paler, and more indistinct than those of the anterior stroma and posterior IPE. The pigment granules of the posterior IPE appeared to be nearly as dark as those in stromal melanocytes; however, both cell layers were thinner and paler than corresponding layers in wild-type mice. Ultrastructural analysis of the RPE, IPE, and ciliary body pigmented cells confirmed that mutation of Slc24a5 results in marked hypopigmentation of melanosomes in optic cup-derived pigmented neuroepithelium in the eyes. Milder reductions in melanosome size and pigmentation were noted in neural crest-derived melanocytes. The severe hypopigmentation of neuroepithelium-derived cells in the eyes resulted in a novel form of ocular albinism in Slc24a5-/- mice. Our findings suggest that SLC24A5 may be a candidate gene for some forms of ocular albinism and for the BEY1/EYCL2 locus previously associated with central brown eye color in humans.
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Affiliation(s)
- P Vogel
- Lexicon Pharmaceuticals Inc., 8800 Technology Forest Place, The Woodlands, TX 77381-1160, USA.
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Käsmann-Kellner B, Seitz B. [Phenotype of the visual system in oculocutaneous and ocular albinism]. Ophthalmologe 2007; 104:648-61. [PMID: 17684749 DOI: 10.1007/s00347-007-1571-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In spite of albinism being one of the visual impairments which has been known for over a century, it has only been known for a few decades that albinism is correlated to severe cerebral morphological developmental alterations. The increasing knowledge about the role of melanin in the development and orientation of cerebral neurons not only renders more insight into albinism, but also a greater insight in the physiological neuronal and cerebral development in man. Concerning the morphological and visual phenotype there are new clinical findings which enlarge the known spectrum of albinism. In a representative group of 506 persons with oculocutaneous and ocular albinism who are in care at the Department of Ophthalmology at the University of Saarland (UKS), we present a staging of morphological findings of the iris, retinal pigment epithelium and macula, and of the optic nerve head which has been in use for 10 years. Albinism may present with a remarkably mild ocular phenotype and a near to normal functional phenotype. We present correlations between molecular genetic types of albinism, ocular phenotype and visual function. Of great importance concerning later visual acuity is the dysplasia of the optic nerve head (ONH), which is a frequent finding in albinism. The appearance of the ONH should always be included in any clinical description of an albinism patient. It is highly possible that due to a moderate phenotype there are still many patients who have not been diagnosed yet. Visual acuity of 30/20 to 20/20 and no nystagmus do not rule out albinism. In addition, when performing albino VEPs in phenotypically normal children with infantile strabismus, small ONHs, but normal visual acuity and no nystagmus, the classical atypical chiasmal crossing is sometimes found. Therefore, the number of persons having undiagnosed albinism is probably quite high, perhaps there even is a very broad transition zone from normal to albinotic.
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Affiliation(s)
- B Käsmann-Kellner
- Klinik für Augenheilkunde im Universitätsklinikum des Saarlandes UKS, Kirrbergerstrasse 1, 66424, Homburg (Saar), Deutschland.
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Murisier F, Guichard S, Beermann F. The tyrosinase enhancer is activated by Sox10 and Mitf in mouse melanocytes. ACTA ACUST UNITED AC 2007; 20:173-84. [PMID: 17516925 DOI: 10.1111/j.1600-0749.2007.00368.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The terminal differentiation of melanocytes is associated with the transcriptional activation of genes responsible for pigment production such as tyrosinase. Pigment cell-specific transcription factors, such as Mitf, as well as specific proximal and distal regulatory elements (DRE) are implicated in the tight control of tyrosinase expression during development and adulthood. Proper tyrosinase expression in melanocytes depends upon the presence of a DRE that is located at -15 kb and provides enhancer activity via a central element termed core-enhancer. In this report, we show that the transcription factors Sox10, Mitf and USF-1 are able to activate the core-enhancer in luciferase reporter assays. Comparative sequence analysis identified evolutionarily motifs resembling Sox10 binding sites that were required for full enhancer activity in melanoma cells and in tyrosinase::lacZ transgenic mice. Sox10 was able to bind the DRE in vitro and mutation of the conserved motifs abolished the enhancer transactivation mediated by Sox10. In addition, two highly conserved CAGCTG E-box motifs were identified that were also required for enhancer activity and for transactivation by Mitf. The results suggest that Sox10 directly, and Mitf, most likely indirectly, activate the tyrosinase enhancer, underlining the contribution of Sox10 to tyrosinase gene regulation in melanocytes.
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Affiliation(s)
- Fabien Murisier
- Swiss Institute for Experimental Cancer Research (ISREC), National Center of Competence in Research (NCCR) Molecular Oncology, Chemin des Boveresses 155, 1066 Epalinges, Switzerland
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Abstract
The elucidation of a growing number of species' genomes heralds an unprecedented opportunity to ascertain functional attributes of non-coding sequences. In particular, cis regulatory modules (CRMs) controlling gene expression constitute a rich treasure trove of data to be defined and experimentally validated. Such information will provide insight into cell lineage determination and differentiation and the genetic basis of heritable diseases as well as the development of novel tools for restricting the inactivation of genes to specific cell types or conditions. Historically, the study of CRMs and their individual transcription factor binding sites has been limited to proximal regions around gene loci. Two important by-products of the genomics revolution, artificial chromosome vectors and comparative genomics, have fueled efforts to define an increasing number of CRMs acting remotely to control gene expression. Such regulation from a distance has challenged our perspectives of gene expression control and perhaps the very definition of a gene. This review summarizes current approaches to characterize remote control of gene expression in transgenic mice and inherent limitations for accurately interpreting the essential nature of CRM activity.
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Affiliation(s)
- Xiaochun Long
- Cardiovascular Research Institute, University of Rochester School of Medicine, Rochester, New York 14642, USA
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