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Machado JP, Philip S, Maldonado E, O'Brien SJ, Johnson WE, Antunes A. Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. Genome Biol Evol 2016; 8:2748-59. [PMID: 27613398 PMCID: PMC5630915 DOI: 10.1093/gbe/evw200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A diverse group of genes are involved in the tooth development of mammals. Several studies, focused mainly on mice and rats, have provided a detailed depiction of the processes coordinating tooth formation and shape. Here we surveyed 236 tooth-associated genes in 39 mammalian genomes and tested for signatures of selection to assess patterns of molecular adaptation in genes regulating mammalian dentition. Of the 236 genes, 31 (∼13.1%) showed strong signatures of positive selection that may be responsible for the phenotypic diversity observed in mammalian dentition. Mammalian-specific tooth-associated genes had accelerated mutation rates compared with older genes found across all vertebrates. More recently evolved genes had fewer interactions (either genetic or physical), were associated with fewer Gene Ontology terms and had faster evolutionary rates compared with older genes. The introns of these positively selected genes also exhibited accelerated evolutionary rates, which may reflect additional adaptive pressure in the intronic regions that are associated with regulatory processes that influence tooth-gene networks. The positively selected genes were mainly involved in processes like mineralization and structural organization of tooth specific tissues such as enamel and dentin. Of the 236 analyzed genes, 12 mammalian-specific genes (younger genes) provided insights on diversification of mammalian teeth as they have higher evolutionary rates and exhibit different expression profiles compared with older genes. Our results suggest that the evolution and development of mammalian dentition occurred in part through positive selection acting on genes that previously had other functions.
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Affiliation(s)
- João Paulo Machado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Siby Philip
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Emanuel Maldonado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia Oceanographic Center, Nova Southeastern University, Ft Lauderdale
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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Rothe M, Monteiro F, Dietmann P, Kühl SJ. Comparative expression study of sipa family members during early Xenopus laevis development. Dev Genes Evol 2016; 226:369-82. [DOI: 10.1007/s00427-016-0556-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/28/2016] [Indexed: 01/20/2023]
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Dash S, Siddam AD, Barnum CE, Janga SC, Lachke SA. RNA-binding proteins in eye development and disease: implication of conserved RNA granule components. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:527-57. [PMID: 27133484 DOI: 10.1002/wrna.1355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/21/2016] [Indexed: 01/16/2023]
Abstract
The molecular biology of metazoan eye development is an area of intense investigation. These efforts have led to the surprising recognition that although insect and vertebrate eyes have dramatically different structures, the orthologs or family members of several conserved transcription and signaling regulators such as Pax6, Six3, Prox1, and Bmp4 are commonly required for their development. In contrast, our understanding of posttranscriptional regulation in eye development and disease, particularly regarding the function of RNA-binding proteins (RBPs), is limited. We examine the present knowledge of RBPs in eye development in the insect model Drosophila as well as several vertebrate models such as fish, frog, chicken, and mouse. Interestingly, of the 42 RBPs that have been investigated for their expression or function in vertebrate eye development, 24 (~60%) are recognized in eukaryotic cells as components of RNA granules such as processing bodies, stress granules, or other specialized ribonucleoprotein (RNP) complexes. We discuss the distinct developmental and cellular events that may necessitate potential RBP/RNA granule-associated RNA regulon models to facilitate posttranscriptional control of gene expression in eye morphogenesis. In support of these hypotheses, three RBPs and RNP/RNA granule components Tdrd7, Caprin2, and Stau2 are linked to ocular developmental defects such as congenital cataract, Peters anomaly, and microphthalmia in human patients or animal models. We conclude by discussing the utility of interdisciplinary approaches such as the bioinformatics tool iSyTE (integrated Systems Tool for Eye gene discovery) to prioritize RBPs for deriving posttranscriptional regulatory networks in eye development and disease. WIREs RNA 2016, 7:527-557. doi: 10.1002/wrna.1355 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University & Purdue University Indianapolis, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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Anand D, Lachke SA. Systems biology of lens development: A paradigm for disease gene discovery in the eye. Exp Eye Res 2016; 156:22-33. [PMID: 26992779 DOI: 10.1016/j.exer.2016.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/19/2022]
Abstract
Over the past several decades, the biology of the developing lens has been investigated using molecular genetics-based approaches in various vertebrate model systems. These efforts, involving target gene knockouts or knockdowns, have led to major advances in our understanding of lens morphogenesis and the pathological basis of cataracts, as well as of other lens related eye defects. In particular, we now have a functional understanding of regulators such as Pax6, Six3, Sox2, Oct1 (Pou2f1), Meis1, Pnox1, Zeb2 (Sip1), Mab21l1, Foxe3, Tfap2a (Ap2-alpha), Pitx3, Sox11, Prox1, Sox1, c-Maf, Mafg, Mafk, Hsf4, Fgfrs, Bmp7, and Tdrd7 in this tissue. However, whether these individual regulators interact or their targets overlap, and the significance of such interactions during lens morphogenesis, is not well defined. The arrival of high-throughput approaches for gene expression profiling (microarrays, RNA-sequencing (RNA-seq), etc.), which can be coupled with chromatin immunoprecipitation (ChIP) or RNA immunoprecipitation (RIP) assays, along with improved computational resources and publically available datasets (e.g. those containing comprehensive protein-protein, protein-DNA information), presents new opportunities to advance our understanding of the lens tissue on a global systems level. Such systems-level knowledge will lead to the derivation of the underlying lens gene regulatory network (GRN), defined as a circuit map of the regulator-target interactions functional in lens development, which can be applied to expedite cataract gene discovery. In this review, we cover the various systems-level approaches such as microarrays, RNA-seq, and ChIP that are already being applied to lens studies and discuss strategies for assembling and interpreting these vast amounts of high-throughput information for effective dispersion to the scientific community. In particular, we discuss strategies for effective interpretation of this new information in the context of the rich knowledge obtained through the application of traditional single-gene focused experiments on the lens. Finally, we discuss our vision for integrating these diverse high-throughput datasets in a single web-based user-friendly tool iSyTE (integrated Systems Tool for Eye gene discovery) - a resource that is already proving effective in the identification and characterization of genes linked to lens development and cataract. We anticipate that application of a similar approach to other ocular tissues such as the retina and the cornea, and even other organ systems, will significantly impact disease gene discovery.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
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55
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Rothe M, Kanwal N, Dietmann P, Seigfried F, Hempel A, Schütz D, Reim D, Engels R, Linnemann A, Schmeisser MJ, Bockmann J, Kühl M, Boeckers TM, Kühl SJ. An Epha4/Sipa1l3/Wnt pathway regulates eye development and lens maturation. Development 2016; 144:321-333. [DOI: 10.1242/dev.147462] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 01/21/2023]
Abstract
The signal-induced proliferation associated family of proteins comprises four members, SIPA1 and SIPA1L1-1L3. Mutations of the human SIPA1L3 gene result in congenital cataracts. In Xenopus, loss of Sipa1l3 function led to a severe eye phenotype that was distinguished by smaller eyes and lenses including lens fiber cell maturation defects. We found a direct interaction between Sipa1l3 and Epha4, building a functional platform for proper ocular development. Epha4 deficiency phenocopied loss of Sipa1l3 and rescue experiments demonstrated that Epha4 acts up-stream of Sipa1l3 during eye development. Both, Sipa1l3 and Epha4 are required for early eye specification. The ocular phenotype, upon loss of either Epha4 or Sipa1l3, was partially mediated by rax. We demonstrated that canonical Wnt signaling is inhibited downstream of Epha4/Sipa1l3 during normal eye development. Depletion of either Sipa1l3 or Epha4 resulted in an up-regulation of axin2 expression, a direct Wnt/β-catenin target gene. In line with this, Sipa1l3 or Epha4 depletion could be rescued by blocking Wnt/β-catenin or activating non-canonical Wnt signaling. We therefore conclude that this pathomechanism prevents proper eye development and maturation of lens fiber cells resulting in congenital cataracts.
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Affiliation(s)
- Melanie Rothe
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Noreen Kanwal
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Petra Dietmann
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Franziska Seigfried
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Annemarie Hempel
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Desiree Schütz
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Dominik Reim
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Rebecca Engels
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Alexander Linnemann
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Michael J. Schmeisser
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
- Department of Neurology, Ulm University, 89081 Ulm, Germany
| | - Juergen Bockmann
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Tobias M. Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
| | - Susanne J. Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
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Zhang Y, Fan J, Ho JWK, Hu T, Kneeland SC, Fan X, Xi Q, Sellarole MA, de Vries WN, Lu W, Lachke SA, Lang RA, John SWM, Maas RL. Crim1 regulates integrin signaling in murine lens development. Development 2015; 143:356-66. [PMID: 26681494 PMCID: PMC4725338 DOI: 10.1242/dev.125591] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 12/07/2015] [Indexed: 12/19/2022]
Abstract
The developing lens is a powerful system for investigating the molecular basis of inductive tissue interactions and for studying cataract, the leading cause of blindness. The formation of tightly controlled cell-cell adhesions and cell-matrix junctions between lens epithelial (LE) cells, between lens fiber (LF) cells, and between these two cell populations enables the vertebrate lens to adopt a highly ordered structure and acquire optical transparency. Adhesion molecules are thought to maintain this ordered structure, but little is known about their identity or interactions. Cysteine-rich motor neuron 1 (Crim1), a type I transmembrane protein, is strongly expressed in the developing lens and its mutation causes ocular disease in both mice and humans. How Crim1 regulates lens morphogenesis is not understood. We identified a novel ENU-induced hypomorphic allele of Crim1, Crim1glcr11, which in the homozygous state causes cataract and microphthalmia. Using this and two other mutant alleles, Crim1null and Crim1cko, we show that the lens defects in Crim1 mouse mutants originate from defective LE cell polarity, proliferation and cell adhesion. Crim1 adhesive function is likely to be required for interactions both between LE cells and between LE and LF cells. We show that Crim1 acts in LE cells, where it colocalizes with and regulates the levels of active β1 integrin and of phosphorylated FAK and ERK. The RGD and transmembrane motifs of Crim1 are required for regulating FAK phosphorylation. These results identify an important function for Crim1 in the regulation of integrin- and FAK-mediated LE cell adhesion during lens development. Summary: Crim1, a type I transmembrane protein, acts in lens epithelial cells where it colocalizes with and regulates the levels of active β1 integrin to control cell adhesion during mouse lens morphogenesis.
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Affiliation(s)
- Ying Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jieqing Fan
- Department of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joshua W K Ho
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA Victor Chang Cardiac Research Institute, and The University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Tommy Hu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C Kneeland
- Howard Hughes Medical Institute and The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Xueping Fan
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Qiongchao Xi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Sellarole
- Victor Chang Cardiac Research Institute, and The University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Wilhelmine N de Vries
- Victor Chang Cardiac Research Institute, and The University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Salil A Lachke
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Richard A Lang
- Department of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Simon W M John
- Victor Chang Cardiac Research Institute, and The University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Richard L Maas
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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57
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Audette DS, Anand D, So T, Rubenstein TB, Lachke SA, Lovicu FJ, Duncan MK. Prox1 and fibroblast growth factor receptors form a novel regulatory loop controlling lens fiber differentiation and gene expression. Development 2015; 143:318-28. [PMID: 26657765 DOI: 10.1242/dev.127860] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/26/2015] [Indexed: 01/19/2023]
Abstract
Lens epithelial cells differentiate into lens fibers (LFs) in response to a fibroblast growth factor (FGF) gradient. This cell fate decision requires the transcription factor Prox1, which has been hypothesized to promote cell cycle exit in differentiating LF cells. However, we find that conditional deletion of Prox1 from mouse lenses results in a failure in LF differentiation despite maintenance of normal cell cycle exit. Instead, RNA-seq demonstrated that Prox1 functions as a global regulator of LF cell gene expression. Intriguingly, Prox1 also controls the expression of fibroblast growth factor receptors (FGFRs) and can bind to their promoters, correlating with decreased downstream signaling through MAPK and AKT in Prox1 mutant lenses. Further, culturing rat lens explants in FGF increased their expression of Prox1, and this was attenuated by the addition of inhibitors of MAPK. Together, these results describe a novel feedback loop required for lens differentiation and morphogenesis, whereby Prox1 and FGFR signaling interact to mediate LF differentiation in response to FGF.
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Affiliation(s)
- Dylan S Audette
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Tammy So
- Discipline of Anatomy & Histology, Bosch Institute & Save Sight Institute, University of Sydney, Sydney, New South Wales 2000, Australia
| | - Troy B Rubenstein
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Frank J Lovicu
- Discipline of Anatomy & Histology, Bosch Institute & Save Sight Institute, University of Sydney, Sydney, New South Wales 2000, Australia
| | - Melinda K Duncan
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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Boone PM, Yuan B, Gu S, Ma Z, Gambin T, Gonzaga-Jauregui C, Jain M, Murdock TJ, White JJ, Jhangiani SN, Walker K, Wang Q, Muzny DM, Gibbs RA, Hejtmancik JF, Lupski JR, Posey JE, Lewis RA. Hutterite-type cataract maps to chromosome 6p21.32-p21.31, cosegregates with a homozygous mutation in LEMD2, and is associated with sudden cardiac death. Mol Genet Genomic Med 2015; 4:77-94. [PMID: 26788539 PMCID: PMC4707028 DOI: 10.1002/mgg3.181] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Juvenile-onset cataracts are known among the Hutterites of North America. Despite being identified over 30 years ago, this autosomal recessive condition has not been mapped, and the disease gene is unknown. METHODS We performed whole exome sequencing of three Hutterite-type cataract trios and follow-up genotyping and mapping in four extended kindreds. RESULTS Trio exomes enabled genome-wide autozygosity mapping, which localized the disease gene to a 9.5-Mb region on chromosome 6p. This region contained two candidate variants, LEMD2 c.T38G and MUC21 c.665delC. Extended pedigrees recruited for variant genotyping revealed multiple additional relatives with juvenile-onset cataract, as well as six deceased relatives with both cataracts and sudden cardiac death. The candidate variants were genotyped in 84 family members, including 17 with cataracts; only the variant in LEMD2 cosegregated with cataracts (LOD = 9.62). SNP-based fine mapping within the 9.5 Mb linked region supported this finding by refining the cataract locus to a 0.5- to 2.9-Mb subregion (6p21.32-p21.31) containing LEMD2 but not MUC21. LEMD2 is expressed in mouse and human lenses and encodes a LEM domain-containing protein; the c.T38G missense mutation is predicted to mutate a highly conserved residue within this domain (p.Leu13Arg). CONCLUSION We performed a genetic and genomic study of Hutterite-type cataract and found evidence for an association of this phenotype with sudden cardiac death. Using combined genetic and genomic approaches, we mapped cataracts to a small portion of chromosome 6 and propose that they result from a homozygous missense mutation in LEMD2.
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Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Bo Yuan
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Shen Gu
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch National Eye Institute Rockville Maryland
| | - Tomasz Gambin
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Mahim Jain
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Janson J White
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Kimberly Walker
- Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Qiaoyan Wang
- Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Donna M Muzny
- Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Richard A Gibbs
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Human Genome Sequencing CenterBaylor College of MedicineHoustonTexas
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch National Eye Institute Rockville Maryland
| | - James R Lupski
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Human Genome Sequencing CenterBaylor College of MedicineHoustonTexas; Department of PediatricsBaylor College of MedicineHoustonTexas; Texas Children's HospitalHoustonTexas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Richard A Lewis
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Department of PediatricsBaylor College of MedicineHoustonTexas; Texas Children's HospitalHoustonTexas; Department of OphthalmologyBaylor College of MedicineHoustonTexas; Department of MedicineBaylor College of MedicineHoustonTexas
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59
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Khan SY, Hackett SF, Lee MCW, Pourmand N, Talbot CC, Riazuddin SA. Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing. Invest Ophthalmol Vis Sci 2015. [PMID: 26225632 DOI: 10.1167/iovs.14-16253] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Transcriptome is the entire repertoire of transcripts present in a cell at any particular time. We undertook a next-generation whole transcriptome sequencing approach to gain insight into the transcriptional landscape of the developing mouse lens. METHODS We ascertained mouse lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The ocular tissue at each time point was maintained as two distinct pools serving as biological replicates for each developmental stage. The mRNA and small RNA libraries were paired-end sequenced on Illumina HiSeq 2000 and subsequently analyzed using bioinformatics tools. RESULTS Mapping of mRNA and small RNA libraries generated 187.56 and 154.22 million paired-end reads, respectively. We detected a total of 14,465 genes in the mouse ocular lens at the above-mentioned six developmental stages. Of these, 46 genes exhibited a 40-fold differential (higher or lower) expression at one the five developmental stages (E18, P0, P3, P6, and P9) compared with their expression level at E15. Likewise, small RNA profiling identified 379 microRNAs (miRNAs) expressed in mouse lens at six developmental time points. Of these, 49 miRNAs manifested an 8-fold differential (higher or lower) expression at one the five developmental stages, as mentioned above compared with their expression level at E15. CONCLUSIONS We report a comprehensive profile of developing murine lens transcriptome including both mRNA and miRNA through next-generation RNA sequencing. A complete repository of the lens transcriptome of six developmental time points will be monumental in elucidating processes essential for the development of the ocular lens and maintenance of its transparency.
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Affiliation(s)
- Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Sean F Hackett
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Mei-Chong W Lee
- Departpart of Biomolecular Engineering, University of California, Santa Cruz, California, United States
| | - Nader Pourmand
- Departpart of Biomolecular Engineering, University of California, Santa Cruz, California, United States
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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Anand D, Agrawal S, Siddam A, Motohashi H, Yamamoto M, Lachke SA. An integrative approach to analyze microarray datasets for prioritization of genes relevant to lens biology and disease. GENOMICS DATA 2015; 5:223-227. [PMID: 26185746 PMCID: PMC4500531 DOI: 10.1016/j.gdata.2015.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Microarray-based profiling represents an effective method to analyze cellular or tissue-specific gene expression on the genome-level. However, in comparative analyses between control and mutant samples, microarrays often identify a large number of differentially expressed genes, in turn making it challenging to isolate the select “high-priority candidates” that are most relevant to an observed mutant phenotype. Here, we describe an integrative approach for mouse mutant lens microarray gene expression analysis using publically accessible systems-level information such as wild-type mouse lens expression data in iSyTE (integrated Systems Tool for Eye gene discovery), protein–protein interaction data in public databases, gene ontology enrichment data, and transcription factor binding profile data. This strategy, when applied to small Maf Mafg −/−:Mafk +/− mouse lens microarray datasets (deposited in NCBI Gene Expression Omnibus database with accession number GSE65500) in Agrawal et al. 2015 [1], led to the effective prioritization of candidate genes linked to lens defects in these mutants. Indeed, from the original list of genes that are differentially expressed at ± 1.5-fold and p < 0.05 in Mafg −/−:Mafk +/− mutant lenses, this analysis led to the identification of thirty-six high-priority candidates, in turn reducing the number of genes for further study by approximately 1/3 of the total. Moreover, eight of these genes are linked to mammalian cataract in the published literature, validating the efficacy of this approach. Additionally, these high-priority candidates contribute valuable information for the assembly of a gene regulatory network in the lens. In sum, the pipeline outlined in this report represents an effective approach for initial as well as downstream microarray expression data analysis to identify genes important for lens biology and cataracts. We anticipate that this integrative strategy can be extended to prioritize phenotypically relevant candidate genes from microarray data in other cells and tissues.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Smriti Agrawal
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Archana Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA ; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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Sun J, Rockowitz S, Chauss D, Wang P, Kantorow M, Zheng D, Cvekl A. Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators. Mol Vis 2015; 21:955-73. [PMID: 26330747 PMCID: PMC4551281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/26/2015] [Indexed: 10/26/2022] Open
Abstract
PURPOSE Gene expression correlates with local chromatin structure. Our studies have mapped histone post-translational modifications, RNA polymerase II (pol II), and transcription factor Pax6 in lens chromatin. These data represent the first genome-wide insights into the relationship between lens chromatin structure and lens transcriptomes and serve as an excellent source for additional data analysis and refinement. The principal lens proteins, the crystallins, are encoded by predominantly expressed mRNAs; however, the regulatory mechanisms underlying their high expression in the lens remain poorly understood. METHODS The formaldehyde-assisted identification of regulatory regions (FAIRE-Seq) was employed to analyze newborn lens chromatin. ChIP-seq and RNA-seq data published earlier (GSE66961) have been used to assist in FAIRE-seq data interpretation. RNA transcriptomes from murine lens epithelium, lens fibers, erythrocytes, forebrain, liver, neurons, and pancreas were compared to establish the gene expression levels of the most abundant mRNAs versus median gene expression across other differentiated cells. RESULTS Normalized RNA expression data from multiple tissues show that crystallins rank among the most highly expressed genes in mammalian cells. These findings correlate with the extremely high abundance of pol II all across the crystallin loci, including crystallin genes clustered on chromosomes 1 and 5, as well as within regions of "open" chromatin, as identified by FAIRE-seq. The expression levels of mRNAs encoding DNA-binding transcription factors (e.g., Foxe3, Hsf4, Maf, Pax6, Prox1, Sox1, and Tfap2a) revealed that their transcripts form "clusters" of abundant mRNAs in either lens fibers or lens epithelium. The expression of three autophagy regulatory mRNAs, encoding Tfeb, FoxO1, and Hif1α, was found within a group of lens preferentially expressed transcription factors compared to the E12.5 forebrain. CONCLUSIONS This study reveals novel features of lens chromatin, including the remarkably high abundance of pol II at the crystallin loci that exhibit features of "open" chromatin. Hsf4 ranks among the most abundant fiber cell-preferred DNA-binding transcription factors. Notable transcripts, including Atf4, Ctcf, E2F4, Hey1, Hmgb1, Mycn, RXRβ, Smad4, Sp1, and Taf1 (transcription factors) and Ctsd, Gabarapl1, and Park7 (autophagy regulators) have been identified with high levels of expression in lens fibers, which suggests specific roles in lens fiber cell terminal differentiation.
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Affiliation(s)
- Jian Sun
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
| | - Shira Rockowitz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
| | - Daniel Chauss
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL
| | - Ping Wang
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY
| | - Marc Kantorow
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY,Department of Neurology, Albert Einstein College of Medicine, Bronx, NY,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY
| | - Ales Cvekl
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
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Dash S, Dang CA, Beebe DC, Lachke SA. Deficiency of the RNA binding protein caprin2 causes lens defects and features of Peters anomaly. Dev Dyn 2015; 244:1313-27. [PMID: 26177727 DOI: 10.1002/dvdy.24303] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/18/2015] [Accepted: 07/02/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND It was recently demonstrated that deficiency of a conserved RNA binding protein (RBP) and RNA granule (RG) component Tdrd7 causes ocular defects including cataracts in human, mouse and chicken, indicating the importance of posttranscriptional regulation in eye development. Here we investigated the function of a second conserved RBP/RG component Caprin2 that is identified by the eye gene discovery tool iSyTE. RESULTS In situ hybridization, Western blotting and immunostaining confirmed highly enriched expression of Caprin2 mRNA and protein in mouse embryonic and postnatal lens. To gain insight into its function, lens-specific Caprin2 conditional knockout (cKO) mouse mutants were generated using a lens-Cre deleter line Pax6GFPCre. Phenotypic analysis of Caprin2(cKO/cKO) mutants revealed distinct eye defects at variable penetrance. Wheat germ agglutinin staining and scanning electron microscopy demonstrated that Caprin2(cKO/cKO) mutants have an abnormally compact lens nucleus, which is the core of the lens comprised of centrally located terminally differentiated fiber cells. Additionally, Caprin2(cKO/cKO) mutants also exhibited at 8% penetrance a developmental defect that resembles a human condition called Peters anomaly, wherein the lens and the cornea remain attached by a persistent stalk. CONCLUSIONS These data suggest that a conserved RBP Caprin2 functions in distinct morphological events in mammalian eye development.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, Delaware
| | - Christine A Dang
- Department of Biological Sciences, University of Delaware, Newark, Delaware
| | - David C Beebe
- Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, Missouri
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, Delaware.,Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware
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Greenlees R, Mihelec M, Yousoof S, Speidel D, Wu SK, Rinkwitz S, Prokudin I, Perveen R, Cheng A, Ma A, Nash B, Gillespie R, Loebel DA, Clayton-Smith J, Lloyd IC, Grigg JR, Tam PP, Yap AS, Becker TS, Black GC, Semina E, Jamieson RV. Mutations inSIPA1L3cause eye defects through disruption of cell polarity and cytoskeleton organization. Hum Mol Genet 2015; 24:5789-804. [DOI: 10.1093/hmg/ddv298] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/21/2015] [Indexed: 01/27/2023] Open
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Compound mouse mutants of bZIP transcription factors Mafg and Mafk reveal a regulatory network of non-crystallin genes associated with cataract. Hum Genet 2015; 134:717-35. [PMID: 25896808 DOI: 10.1007/s00439-015-1554-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022]
Abstract
Although majority of the genes linked to early-onset cataract exhibit lens fiber cell-enriched expression, our understanding of gene regulation in these cells is limited to function of just eight transcription factors and largely in the context of crystallins. We report on small Maf transcription factors Mafg and Mafk as regulators of several non-crystallin human cataract-associated genes in fiber cells and establish their significance to this disease. We applied a bioinformatics tool for cataract gene discovery iSyTE to identify Mafg and its co-regulators in the lens, and generated various null-allelic combinations of Mafg:Mafk mouse mutants for phenotypic and molecular analysis. By age 4 months, Mafg-/-:Mafk+/- mutants exhibit lens defects that progressively develop into cataract. High-resolution phenotypic characterization of Mafg-/-:Mafk+/- mouse lens reveals severely disorganized fiber cells, while microarray-based expression profiling identifies 97 differentially regulated genes (DRGs). Integrative analysis of Mafg-/-:Mafk+/- lens-DRGs with (1) binding motifs and genomic targets of small Mafs and their regulatory partners, (2) iSyTE lens expression data, and (3) interactions between DRGs in the String database, unravel a detailed small Maf regulatory network in the lens, several nodes of which are linked to cataract. This approach identifies 36 high-priority candidates from the original 97 DRGs. Significantly, 8/36 (22%) DRGs are associated with cataracts in human (GSTO1, MGST1, SC4MOL, UCHL1) or mouse (Aldh3a1, Crygf, Hspb1, Pcbd1), suggesting a multifactorial etiology that includes oxidative stress and misregulation of sterol synthesis. These data identify Mafg and Mafk as new cataract-associated candidates and define their function in regulating largely non-crystallin genes linked to human cataract.
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SIPA1L3 identified by linkage analysis and whole-exome sequencing as a novel gene for autosomal recessive congenital cataract. Eur J Hum Genet 2015; 23:1627-33. [PMID: 25804400 DOI: 10.1038/ejhg.2015.46] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/25/2022] Open
Abstract
Congenital cataract (CC) is one of the most important causes for blindness or visual impairment in infancy. A substantial proportion of isolated CCs has monogenic causes. The disease is genetically heterogeneous, and all Mendelian modes of inheritance have been reported. We mapped a locus for isolated CC on 19p13.1-q13.2 in a distantly consanguineous German family with two sisters affected by dense white cataracts. Whole-exome sequencing identified a homozygous nonsense variant c.4489C>T (p.(R1497*)) in SIPA1L3 (signal-induced proliferation-associated 1 like 3) in both affected children. SIPA1L3 encodes a GTPase-activating protein (GAP), which interacts with small GTPases of the Rap family via its Rap-GAP-domain. The suggested role of Rap GTPases in cell growth, differentiation and organization of the cytoskeleton in the human lens, and lens-enriched expression of the murine ortholog gene Sipa1l3 in embryonic mice indicates that this gene is crucial for early lens development. Our results provide evidence that sequence variants in human SIPA1L3 cause autosomal recessive isolated CC and give new insight into the molecular pathogenesis underlying human cataracts.
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66
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Decoding the complex genetic causes of heart diseases using systems biology. Biophys Rev 2015; 7:141-159. [PMID: 28509974 DOI: 10.1007/s12551-014-0145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022] Open
Abstract
The pace of disease gene discovery is still much slower than expected, even with the use of cost-effective DNA sequencing and genotyping technologies. It is increasingly clear that many inherited heart diseases have a more complex polygenic aetiology than previously thought. Understanding the role of gene-gene interactions, epigenetics, and non-coding regulatory regions is becoming increasingly critical in predicting the functional consequences of genetic mutations identified by genome-wide association studies and whole-genome or exome sequencing. A systems biology approach is now being widely employed to systematically discover genes that are involved in heart diseases in humans or relevant animal models through bioinformatics. The overarching premise is that the integration of high-quality causal gene regulatory networks (GRNs), genomics, epigenomics, transcriptomics and other genome-wide data will greatly accelerate the discovery of the complex genetic causes of congenital and complex heart diseases. This review summarises state-of-the-art genomic and bioinformatics techniques that are used in accelerating the pace of disease gene discovery in heart diseases. Accompanying this review, we provide an interactive web-resource for systems biology analysis of mammalian heart development and diseases, CardiacCode ( http://CardiacCode.victorchang.edu.au/ ). CardiacCode features a dataset of over 700 pieces of manually curated genetic or molecular perturbation data, which enables the inference of a cardiac-specific GRN of 280 regulatory relationships between 33 regulator genes and 129 target genes. We believe this growing resource will fill an urgent unmet need to fully realise the true potential of predictive and personalised genomic medicine in tackling human heart disease.
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Altered ubiquitin causes perturbed calcium homeostasis, hyperactivation of calpain, dysregulated differentiation, and cataract. Proc Natl Acad Sci U S A 2015; 112:1071-6. [PMID: 25583491 DOI: 10.1073/pnas.1404059112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Although the ocular lens shares many features with other tissues, it is unique in that it retains its cells throughout life, making it ideal for studies of differentiation/development. Precipitation of proteins results in lens opacification, or cataract, the major blinding disease. Lysines on ubiquitin (Ub) determine fates of Ub-protein substrates. Information regarding ubiquitin proteasome systems (UPSs), specifically of K6 in ubiquitin, is undeveloped. We expressed in the lens a mutant Ub containing a K6W substitution (K6W-Ub). Protein profiles of lenses that express wild-type ubiquitin (WT-Ub) or K6W-Ub differ by only ∼2%. Despite these quantitatively minor differences, in K6W-Ub lenses and multiple model systems we observed a fourfold Ca(2+) elevation and hyperactivation of calpain in the core of the lens, as well as calpain-associated fragmentation of critical lens proteins including Filensin, Fodrin, Vimentin, β-Crystallin, Caprin family member 2, and tudor domain containing 7. Truncations can be cataractogenic. Additionally, we observed accumulation of gap junction Connexin43, and diminished Connexin46 levels in vivo and in vitro. These findings suggest that mutation of Ub K6 alters UPS function, perturbs gap junction function, resulting in Ca(2+) elevation, hyperactivation of calpain, and associated cleavage of substrates, culminating in developmental defects and a cataractous lens. The data show previously unidentified connections between UPS and calpain-based degradative systems and advance our understanding of roles for Ub K6 in eye development. They also inform about new approaches to delay cataract and other protein precipitation diseases.
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68
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Lens Development and Crystallin Gene Expression. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 134:129-67. [DOI: 10.1016/bs.pmbts.2015.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Terrell AM, Anand D, Smith SF, Dang CA, Waters SM, Pathania M, Beebe DC, Lachke SA. Molecular characterization of mouse lens epithelial cell lines and their suitability to study RNA granules and cataract associated genes. Exp Eye Res 2014; 131:42-55. [PMID: 25530357 DOI: 10.1016/j.exer.2014.12.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/02/2014] [Accepted: 12/18/2014] [Indexed: 01/10/2023]
Abstract
The discovery of cytosolic RNA granule (RG) component proteins associated with human cataract has initiated investigations on post-transcriptional mechanisms of gene expression control in the lens. Application of established mouse lens epithelial cell lines (LECs) can provide rapid insights on RG function in lens cells, especially because mouse mutants in several RG components are not available. However, although these LECs represent potential reagents for such analyses, they are uncharacterized for lens gene expression or RG formation. Therefore, a detailed molecular and cellular characterization of three permanent mouse LECs 17EM15, 21EM15 and αTN4 is performed in this study. Comparative analysis between microarray gene expression datasets on LEC 21EM15 and iSyTE lens tissue demonstrates that 30% of top 200 iSyTE identified lens-enriched genes are expressed in these cells. Majority of these candidates are independently validated to either have lens expression, function or linkage to cataract. Moreover, analysis of microarray data with genes described in Cat-Map, an online database of cataract associated genes and loci, demonstrates that 131 genes linked to cataract loci are expressed in 21EM15 cells. Furthermore, gene expression in LECs is compared to isolated lens epithelium or fiber cells by qRT-PCR and by comparative analyses with publically available epithelium or fiber-specific microarray and RNA-seq (sequencing) datasets. Expression of select candidate genes was validated by regular and real-time quantitative RT-PCR. Expression of lens epithelium-enriched genes Foxe3, Pax6, Anxa4 and Mcm4 is up-regulated in LEC lines, compared to isolated lens fiber cells. Moreover, similar to isolated lens epithelium, all three LECs exhibit down-regulation of fiber cell-expressed genes Crybb1, Mip and Prox1 when compared to fiber cells. These data indicate that the LEC lines exhibit greater similarity to lens epithelium than to fiber cells. Compared to non-lens cell line NIH3T3, LECs exhibit significantly enriched expression of transcription factors with important function in the lens, namely Pax6, Foxe3 and Prox1. In addition to these genes, all three LECs also express key lens- and cataract-associated genes, namely Dkk3, Epha2, Hsf4, Jag1, Mab21l1, Meis1, Pknox1, Pou2f1, Sfrp1, Sparc, Tdrd7 and Trpm3. Additionally, 21EM15 microarrays indicate expression of Chmp4b, Cryab and Tcfap2a among others important genes. Immunostaining with makers for Processing bodies (P-bodies) and Stress granules (SGs) demonstrates that these classes of RGs are robustly expressed in all three LECs. Moreover, under conditions of stress, 17EM15 and αTN4 exhibit significantly higher numbers of P-bodies and SGs compared to NIH3T3 cells. In sum, these data indicate that mouse LECs 21EM15, 17EM15 and αTN4 express key lens or cataract genes, are similar to lens epithelium than fiber cells, and exhibit high levels of P-bodies and SGs, indicating their suitability for investigating gene expression control and RG function in lens-derived cells.
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Affiliation(s)
- Anne M Terrell
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Sylvie F Smith
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Christine A Dang
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Stephanie M Waters
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Mallika Pathania
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - David C Beebe
- Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, MO, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, USA.
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Anchan RM, Lachke SA, Gerami-Naini B, Lindsey J, Ng N, Naber C, Nickerson M, Cavallesco R, Rowan S, Eaton JL, Xi Q, Maas RL. Pax6- and Six3-mediated induction of lens cell fate in mouse and human ES cells. PLoS One 2014; 9:e115106. [PMID: 25517354 PMCID: PMC4269389 DOI: 10.1371/journal.pone.0115106] [Citation(s) in RCA: 11] [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: 07/01/2014] [Accepted: 11/18/2014] [Indexed: 11/19/2022] Open
Abstract
Embryonic stem (ES) cells provide a potentially useful in vitro model for the study of in vivo tissue differentiation. We used mouse and human ES cells to investigate whether the lens regulatory genes Pax6 and Six3 could induce lens cell fate in vitro. To help assess the onset of lens differentiation, we derived a new mES cell line (Pax6-GFP mES) that expresses a GFP reporter under the control of the Pax6 P0 promoter and lens ectoderm enhancer. Pax6 or Six3 expression vectors were introduced into mES or hES cells by transfection or lentiviral infection and the differentiating ES cells analyzed for lens marker expression. Transfection of mES cells with Pax6 or Six3 but not with other genes induced the expression of lens cell markers and up-regulated GFP reporter expression in Pax6-GFP mES cells by 3 days post-transfection. By 7 days post-transfection, mES cell cultures exhibited a>10-fold increase over controls in the number of colonies expressing γA-crystallin, a lens fiber cell differentiation marker. RT-PCR and immunostaining revealed induction of additional lens epithelial or fiber cell differentiation markers including Foxe3, Prox1, α- and β-crystallins, and Tdrd7. Moreover, γA-crystallin- or Prox1-expressing lentoid bodies formed by 30 days in culture. In hES cells, Pax6 or Six3 lentiviral vectors also induced lens marker expression. mES cells that express lens markers reside close to but are distinct from the Pax6 or Six3 transduced cells, suggesting that the latter induce nearby undifferentiated ES cells to adopt a lens fate by non-cell autonomous mechanisms. In sum, we describe a novel mES cell GFP reporter line that is useful for monitoring induction of lens fate, and demonstrate that Pax6 or Six3 is sufficient to induce ES cells to adopt a lens fate, potentially via non-cell autonomous mechanisms. These findings should facilitate investigations of lens development.
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Affiliation(s)
- Raymond M. Anchan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology and Reproductive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Salil A. Lachke
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
- Department of Biological Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, 9716, United States of America
| | - Behzad Gerami-Naini
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology and Reproductive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Jennifer Lindsey
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology and Reproductive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Nicholas Ng
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology and Reproductive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Catherine Naber
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Michael Nickerson
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology and Reproductive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Resy Cavallesco
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Sheldon Rowan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Jennifer L. Eaton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Qiongchao Xi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Richard L. Maas
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
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Manthey AL, Terrell AM, Lachke SA, Polson SW, Duncan MK. Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis. GENOMICS DATA 2014; 2:369-374. [PMID: 25478318 PMCID: PMC4248573 DOI: 10.1016/j.gdata.2014.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Next-generation sequencing of the transcriptome (RNA-Seq) is a powerful method that allows for the quantitative determination of absolute gene expression, and can be used to investigate how these levels change in response to an experimental manipulation or disease condition. The sensitivity of this method allows one to analyze transcript levels of all expressed genes, including low abundance transcripts that encode important regulatory molecules, providing valuable insights into the global effects of experimental manipulations. However, this increased sensitivity can also make it challenging to ascertain which expression changes are biologically significant. Here, we describe a novel set of filtering criteria - based on biological insights and computational approaches - that were applied to prioritize genes for further study from an extensive number of differentially expressed transcripts in lenses lacking Smad interacting protein 1 (Sip1) obtained via RNA-Seq by Manthey and colleagues in Mechanisms of Development (Manthey et al., 2014). Notably, this workflow allowed an original list of over 7,100 statistically significant differentially expressed genes (DEGs) to be winnowed down to 190 DEGs that likely play a biologically significant role in Sip1 function during lens development. Focusing on genes whose expression was upregulated or downregulated in a manner opposite to what normally occurs during lens development, we identified 78 genes that appear to be strongly dependent on Sip1 function. From these data (GEO accession number GSE49949), it appears that Sip1 regulates multiple genes in the lens that are generally distinct from those regulated by Sip1 in other cellular contexts, including genes whose expression is prominent in the early head ectoderm, from which the lens differentiates. Further, the analysis criteria outlined here represent a filtering scheme that can be used to prioritize genes in future RNA-Seq investigations performed at this stage of ocular lens development.
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Affiliation(s)
- Abby L. Manthey
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Anne M. Terrell
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Melinda K. Duncan
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
- Corresponding author at: Melinda K. Duncan, Professor, Department of Biological Sciences, University of Delaware, Newark DE 19716.
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72
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Cvekl A, Ashery-Padan R. The cellular and molecular mechanisms of vertebrate lens development. Development 2014; 141:4432-47. [PMID: 25406393 PMCID: PMC4302924 DOI: 10.1242/dev.107953] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ocular lens is a model system for understanding important aspects of embryonic development, such as cell specification and the spatiotemporally controlled formation of a three-dimensional structure. The lens, which is characterized by transparency, refraction and elasticity, is composed of a bulk mass of fiber cells attached to a sheet of lens epithelium. Although lens induction has been studied for over 100 years, recent findings have revealed a myriad of extracellular signaling pathways and gene regulatory networks, integrated and executed by the transcription factor Pax6, that are required for lens formation in vertebrates. This Review summarizes recent progress in the field, emphasizing the interplay between the diverse regulatory mechanisms employed to form lens progenitor and precursor cells and highlighting novel opportunities to fill gaps in our understanding of lens tissue morphogenesis.
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Affiliation(s)
- Aleš Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine and Sagol School of Neuroscience, Tel-Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
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Mackay DS, Bennett TM, Culican SM, Shiels A. Exome sequencing identifies novel and recurrent mutations in GJA8 and CRYGD associated with inherited cataract. Hum Genomics 2014; 8:19. [PMID: 25403472 PMCID: PMC4240822 DOI: 10.1186/s40246-014-0019-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inherited cataract is a clinically important and genetically heterogeneous cause of visual impairment. Typically, it presents at an early age with or without other ocular/systemic signs and lacks clear phenotype-genotype correlation rendering both clinical classification and molecular diagnosis challenging. Here we have utilized trio-based whole exome sequencing to discover mutations in candidate genes underlying autosomal dominant cataract segregating in three nuclear families. RESULTS In family A, we identified a recurrent heterozygous mutation in exon-2 of the gene encoding γD-crystallin (CRYGD; c.70C > A, p.Pro24Thr) that co-segregated with 'coralliform' lens opacities. Families B and C were found to harbor different novel variants in exon-2 of the gene coding for gap-junction protein α8 (GJA8; c.20T > C, p.Leu7Pro and c.293A > C, p.His98Pro). Each novel variant co-segregated with disease and was predicted in silico to have damaging effects on protein function. CONCLUSIONS Exome sequencing facilitates concurrent mutation-profiling of the burgeoning list of candidate genes for inherited cataract, and the results can provide enhanced clinical diagnosis and genetic counseling for affected families.
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Affiliation(s)
- Donna S Mackay
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, 660 S. Euclid Ave., Box 8096, St. Louis, Missouri, 63110, USA.
| | - Thomas M Bennett
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, 660 S. Euclid Ave., Box 8096, St. Louis, Missouri, 63110, USA.
| | - Susan M Culican
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, 660 S. Euclid Ave., Box 8096, St. Louis, Missouri, 63110, USA.
| | - Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, 660 S. Euclid Ave., Box 8096, St. Louis, Missouri, 63110, USA.
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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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75
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Chograni M, Alkuraya FS, Ourteni I, Maazoul F, Lariani I, Chaabouni HB. Autosomal recessive congenital cataract, intellectual disability phenotype linked to STX3 in a consanguineous Tunisian family. Clin Genet 2014; 88:283-7. [PMID: 25358429 DOI: 10.1111/cge.12489] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/08/2014] [Accepted: 08/18/2014] [Indexed: 11/27/2022]
Abstract
The aim of this study is to investigate the genetic basis of autosomal recessive congenital cataract and intellectual disability phenotype in a consanguineous Tunisian family. The whole genome scan of the studied family was performed with single nucleotide polymorphisms (SNPs). The resulted runs of homozygosity (ROH) were analyzed through the integrated Systems Tool for Eye gene discovery (iSyTE) in order to prioritize candidate genes associated with congenital cataract. Selected genes were amplified and sequenced. Bioinformatic analysis was conducted to predict the function of the mutant gene. We identified a new specific lens gene named syntaxin 3 linked to the studied phenotype. The direct sequencing of this gene revealed a novel missense mutation c.122A>G which results in p.E41G. Bioinformatic analysis suggested a deleterious effect of this mutation on protein structure and function. Here, we report for the first time a missense mutation of a novel lens specific gene STX3 in a phenotype associating autosomal recessive congenital cataract and intellectual disability.
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Affiliation(s)
- M Chograni
- Laboratory of Human Genetics, Faculty of Medicine of Tunis, University Tunis ElManar, Tunis, Tunisia
| | - F S Alkuraya
- Developmental Genetics Unit, King Faisal Specialist Hospital and Research Center, Riyad, Saudi Arabia
| | - I Ourteni
- Congenital and Hereditary Disorders Department, Charles Nicolle hospital, Tunis, Tunisia
| | - F Maazoul
- Congenital and Hereditary Disorders Department, Charles Nicolle hospital, Tunis, Tunisia
| | - I Lariani
- Laboratory of Human Genetics, Faculty of Medicine of Tunis, University Tunis ElManar, Tunis, Tunisia
| | - H B Chaabouni
- Laboratory of Human Genetics, Faculty of Medicine of Tunis, University Tunis ElManar, Tunis, Tunisia.,Congenital and Hereditary Disorders Department, Charles Nicolle hospital, Tunis, Tunisia
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76
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Patel N, Khan AO, Mansour A, Mohamed JY, Al-Assiri A, Haddad R, Jia X, Xiong Y, Mégarbané A, Traboulsi EI, Alkuraya FS. Mutations in ASPH cause facial dysmorphism, lens dislocation, anterior-segment abnormalities, and spontaneous filtering blebs, or Traboulsi syndrome. Am J Hum Genet 2014; 94:755-9. [PMID: 24768550 DOI: 10.1016/j.ajhg.2014.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/02/2014] [Indexed: 11/15/2022] Open
Abstract
We have previously described a syndrome characterized by facial dysmorphism, lens dislocation, anterior-segment abnormalities, and spontaneous filtering blebs (FDLAB, or Traboulsi syndrome). In view of the consanguineous nature of the affected families and the likely autosomal-recessive inheritance pattern of this syndrome, we undertook autozygosity mapping and whole-exome sequencing to identify ASPH as the disease locus, in which we identified two homozygous mutations. ASPH encodes aspartyl/asparaginyl β-hydroxylase (ASPH), which has been found to hydroxylate aspartic acid and asparagine residues on epidermal growth factor (EGF)-domain-containing proteins. The truncating and missense mutations we identified are predicted to severely impair the enzymatic function of ASPH, which suggests a possible link to other forms of ectopia lentis given that many of the genes implicated in this phenotype encode proteins that harbor EGF domains. Developmental analysis of Asph revealed an expression pattern consistent with the proposed link to the human syndrome. Indeed, Asph-knockout mice had a foreshortened snout, which corresponds to the facial abnormalities in individuals with Traboulsi syndrome. These data support a genetic basis for a syndromic form of ectopia lentis and the role of aspartyl hydroxylation in human development.
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Affiliation(s)
- Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Arif O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia; Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital, Riyadh 11462, Saudi Arabia
| | - Ahmad Mansour
- Department of Ophthalmology, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Jawahir Y Mohamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Abdullah Al-Assiri
- Division of Anterior Segment, King Khaled Eye Specialist Hospital, Riyadh 11462, Saudi Arabia
| | - Randa Haddad
- Department of Ophthalmology, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Xiaofei Jia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - André Mégarbané
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut 1104-2020, Lebanon
| | - Elias I Traboulsi
- Center for Genetic Eye Diseases, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
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77
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Manthey AL, Lachke SA, FitzGerald PG, Mason RW, Scheiblin DA, McDonald JH, Duncan MK. Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development. Mech Dev 2013; 131:86-110. [PMID: 24161570 DOI: 10.1016/j.mod.2013.09.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 09/04/2013] [Accepted: 09/11/2013] [Indexed: 12/17/2022]
Abstract
SIP1 encodes a DNA-binding transcription factor that regulates multiple developmental processes, as highlighted by the pleiotropic defects observed in Mowat-Wilson syndrome, which results from mutations in this gene. Further, in adults, dysregulated SIP1 expression has been implicated in both cancer and fibrotic diseases, where it functionally links TGFβ signaling to the loss of epithelial cell characteristics and gene expression. In the ocular lens, an epithelial tissue important for vision, Sip1 is co-expressed with epithelial markers, such as E-cadherin, and is required for the complete separation of the lens vesicle from the head ectoderm during early ocular morphogenesis. However, the function of Sip1 after early lens morphogenesis is still unknown. Here, we conditionally deleted Sip1 from the developing mouse lens shortly after lens vesicle closure, leading to defects in coordinated fiber cell tip migration, defective suture formation, and cataract. Interestingly, RNA-Sequencing analysis on Sip1 knockout lenses identified 190 differentially expressed genes, all of which are distinct from previously described Sip1 target genes. Furthermore, 34% of the genes with increased expression in the Sip1 knockout lenses are normally downregulated as the lens transitions from the lens vesicle to early lens, while 49% of the genes with decreased expression in the Sip1 knockout lenses are normally upregulated during early lens development. Overall, these data imply that Sip1 plays a major role in reprogramming the lens vesicle away from a surface ectoderm cell fate towards that necessary for the development of a transparent lens and demonstrate that Sip1 regulates distinctly different sets of genes in different cellular contexts.
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Affiliation(s)
- Abby L Manthey
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Paul G FitzGerald
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, CA 95616, USA
| | - Robert W Mason
- Department of Biomedical Research, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - David A Scheiblin
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - John H McDonald
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Melinda K Duncan
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
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78
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Wolf L, Harrison W, Huang J, Xie Q, Xiao N, Sun J, Kong L, Lachke SA, Kuracha MR, Govindarajan V, Brindle PK, Ashery-Padan R, Beebe DC, Overbeek PA, Cvekl A. Histone posttranslational modifications and cell fate determination: lens induction requires the lysine acetyltransferases CBP and p300. Nucleic Acids Res 2013; 41:10199-214. [PMID: 24038357 PMCID: PMC3905850 DOI: 10.1093/nar/gkt824] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lens induction is a classical embryologic model to study cell fate determination. It has been proposed earlier that specific changes in core histone modifications accompany the process of cell fate specification and determination. The lysine acetyltransferases CBP and p300 function as principal enzymes that modify core histones to facilitate specific gene expression. Herein, we performed conditional inactivation of both CBP and p300 in the ectodermal cells that give rise to the lens placode. Inactivation of both CBP and p300 resulted in the dramatic discontinuation of all aspects of lens specification and organogenesis, resulting in aphakia. The CBP/p300−/− ectodermal cells are viable and not prone to apoptosis. These cells showed reduced expression of Six3 and Sox2, while expression of Pax6 was not upregulated, indicating discontinuation of lens induction. Consequently, expression of αB- and αA-crystallins was not initiated. Mutant ectoderm exhibited markedly reduced levels of histone H3 K18 and K27 acetylation, subtly increased H3 K27me3 and unaltered overall levels of H3 K9ac and H3 K4me3. Our data demonstrate that CBP and p300 are required to establish lens cell-type identity during lens induction, and suggest that posttranslational histone modifications are integral to normal cell fate determination in the mammalian lens.
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Affiliation(s)
- Louise Wolf
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY10461, USA, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY10461, USA, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA, Departments of Ophthalmology and Visual Sciences, Washington University Saint Louis, Saint Louis, MO 63110, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA, Department of Surgery, Creighton University, Omaha, NE 68178, USA, Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, TN 38105, USA and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine and Sagol School of Neuroscience, Tel Aviv University, Israel 69978
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Aldahmesh MA, Alshammari MJ, Khan AO, Mohamed JY, Alhabib FA, Alkuraya FS. The syndrome of microcornea, myopic chorioretinal atrophy, and telecanthus (MMCAT) is caused by mutations in ADAMTS18. Hum Mutat 2013; 34:1195-9. [PMID: 23818446 DOI: 10.1002/humu.22374] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 06/13/2013] [Indexed: 11/09/2022]
Abstract
One of us recently described an apparently novel ocular syndrome characterized by microcornea, myopic chorioretinal atrophy, and telecanthus (MMCAT) in a number of Saudi families. Consistent with the presumed pseudodominant inheritance in one of the original families, we show that MMCAT maps to a single autozygous locus on chr16q23.1 in which exome sequencing revealed a homozygous missense change in ADAMTS18. Direct sequencing of this gene in four additional probands with the same phenotype revealed three additional homozygous changes in ADAMTS18 including two nonsense mutations. Reassuringly, the autozygomes of all probands overlap on the same chr16q23.1 locus, further supporting the positional mapping of MMCAT to ADAMTS18. ADAMTS18 encodes a member of a family of metalloproteinases that are known for their role in extracellular matrix remodeling, and previous work has shown a strong expression of Adamts18 in the developing eye. Our data suggest that ADAMTS18 plays an essential role in early eye development and that mutations therein cause a distinct eye phenotype that is mainly characterized by microcornea and myopia.
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Affiliation(s)
- Mohammed A Aldahmesh
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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80
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Schilter KF, Reis LM, Schneider A, Bardakjian TM, Abdul-Rahman O, Kozel BA, Zimmerman HH, Broeckel U, Semina EV. Whole-genome copy number variation analysis in anophthalmia and microphthalmia. Clin Genet 2013; 84:473-81. [PMID: 23701296 DOI: 10.1111/cge.12202] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 05/17/2013] [Accepted: 05/17/2013] [Indexed: 01/19/2023]
Abstract
Anophthalmia/microphthalmia (A/M) represent severe developmental ocular malformations. Currently, mutations in known genes explain less than 40% of A/M cases. We performed whole-genome copy number variation analysis in 60 patients affected with isolated or syndromic A/M. Pathogenic deletions of 3q26 (SOX2) were identified in four independent patients with syndromic microphthalmia. Other variants of interest included regions with a known role in human disease (likely pathogenic) as well as novel rearrangements (uncertain significance). A 2.2-Mb duplication of 3q29 in a patient with non-syndromic anophthalmia and an 877-kb duplication of 11p13 (PAX6) and a 1.4-Mb deletion of 17q11.2 (NF1) in two independent probands with syndromic microphthalmia and other ocular defects were identified; while ocular anomalies have been previously associated with 3q29 duplications, PAX6 duplications, and NF1 mutations in some cases, the ocular phenotypes observed here are more severe than previously reported. Three novel regions of possible interest included a 2q14.2 duplication which cosegregated with microphthalmia/microcornea and congenital cataracts in one family, and 2q21 and 15q26 duplications in two additional cases; each of these regions contains genes that are active during vertebrate ocular development. Overall, this study identified causative copy number mutations and regions with a possible role in ocular disease in 17% of A/M cases.
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Affiliation(s)
- K F Schilter
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
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81
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Ho JWK. Application of a systems approach to study developmental gene regulation. Biophys Rev 2012; 4:245-253. [PMID: 28510076 DOI: 10.1007/s12551-012-0092-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/21/2012] [Indexed: 12/20/2022] Open
Abstract
All cells in a multicellular organism contain the same genome, yet different cell types express different sets of genes. Recent advances in high throughput genomic technologies have opened up new opportunities to understand the gene regulatory network in diverse cell types in a genome-wide manner. Here, I discuss recent advances in experimental and computational approaches for the study of gene regulation in embryonic development from a systems perspective. This review is written for computational biologists who have an interest in studying developmental gene regulation through integrative analysis of gene expression, chromatin landscape, and signaling pathways. I highlight the utility of publicly available data and tools, as well as some common analysis approaches.
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Affiliation(s)
- Joshua W K Ho
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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82
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Aldahmesh MA, Khan AO, Mohamed JY, Hijazi H, Al-Owain M, Alswaid A, Alkuraya FS. Genomic analysis of pediatric cataract in Saudi Arabia reveals novel candidate disease genes. Genet Med 2012; 14:955-62. [PMID: 22935719 DOI: 10.1038/gim.2012.86] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Pediatric cataract is an important preventable blinding disease. Previous studies have estimated 10-25% of cases to be genetic in etiology. METHODS In an effort to characterize the genetics of cataract in our population, we have conducted a comprehensive clinical and genomic analysis (including autozygome and exome analysis) on a series of 38 index patients. RESULTS Pediatric cataract is genetic in at least 79% of the study families. Although crystallins accounted for most of the mutant alleles, mutations in other genes were encountered, including recessive mutations in genes that usually cause the disease in a dominant manner. In addition, several novel candidate genes (MFSD6L, AKR1E2, RNLS, and CYP51A1) were identified. CONCLUSION Pediatric cataract is typically a genetic disease, usually autosomal recessive, in Saudi Arabia. Although defining a specific cataract phenotype can sometimes predict the genetic cause, genomic analysis is often required to unravel the causative mutation given the marked genetic heterogeneity. The identified novel candidate genes require independent confirmation in future studies.
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Affiliation(s)
- Mohammed A Aldahmesh
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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