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Trejo-Reveles V, Owen N, Ching Chan BH, Toms M, Schoenebeck JJ, Moosajee M, Rainger J. Identification of Novel Coloboma Candidate Genes through Conserved Gene Expression Analyses across Four Vertebrate Species. Biomolecules 2023; 13:293. [PMID: 36830662 PMCID: PMC9953556 DOI: 10.3390/biom13020293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/08/2023] Open
Abstract
Ocular coloboma (OC) is a failure of complete optic fissure closure during embryonic development and presents as a tissue defect along the proximal-distal axis of the ventral eye. It is classed as part of the clinical spectrum of structural eye malformations with microphthalmia and anophthalmia, collectively abbreviated to MAC. Despite deliberate attempts to identify causative variants in MAC, many patients remain without a genetic diagnosis. To reveal potential candidate genes, we utilised transcriptomes experimentally generated from embryonic eye tissues derived from humans, mice, zebrafish, and chicken at stages coincident with optic fissure closure. Our in-silico analyses found 10 genes with optic fissure-specific enriched expression: ALDH1A3, BMPR1B, EMX2, EPHB3, NID1, NTN1, PAX2, SMOC1, TENM3, and VAX1. In situ hybridization revealed that all 10 genes were broadly expressed ventrally in the developing eye but that only PAX2 and NTN1 were expressed in cells at the edges of the optic fissure margin. Of these conserved optic fissure genes, EMX2, NID1, and EPHB3 have not previously been associated with human MAC cases. Targeted genetic manipulation in zebrafish embryos using CRISPR/Cas9 caused the developmental MAC phenotype for emx2 and ephb3. We analysed available whole genome sequencing datasets from MAC patients and identified a range of variants with plausible causality. In combination, our data suggest that expression of genes involved in ventral eye development is conserved across a range of vertebrate species and that EMX2, NID1, and EPHB3 are candidate loci that warrant further functional analysis in the context of MAC and should be considered for sequencing in cohorts of patients with structural eye malformations.
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Affiliation(s)
- Violeta Trejo-Reveles
- Roslin Institute, R(D)SVS, Easter Bush Campus, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Nicholas Owen
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1A, UK
| | - Brian Ho Ching Chan
- Roslin Institute, R(D)SVS, Easter Bush Campus, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Maria Toms
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1A, UK
| | - Jeffrey J. Schoenebeck
- Roslin Institute, R(D)SVS, Easter Bush Campus, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1A, UK
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Joe Rainger
- Roslin Institute, R(D)SVS, Easter Bush Campus, University of Edinburgh, Edinburgh EH25 9RG, UK
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2
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Hanot M, Raby L, Völkel P, Le Bourhis X, Angrand PO. The Contribution of the Zebrafish Model to the Understanding of Polycomb Repression in Vertebrates. Int J Mol Sci 2023; 24:ijms24032322. [PMID: 36768643 PMCID: PMC9916924 DOI: 10.3390/ijms24032322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
Polycomb group (PcG) proteins are highly conserved proteins assembled into two major types of complexes, PRC1 and PRC2, involved in the epigenetic silencing of a wide range of gene expression programs regulating cell fate and tissue development. The crucial role of PRC1 and PRC2 in the fundamental cellular processes and their involvement in human pathologies such as cancer attracted intense attention over the last few decades. Here, we review recent advancements regarding PRC1 and PRC2 function using the zebrafish model. We point out that the unique characteristics of the zebrafish model provide an exceptional opportunity to increase our knowledge of the role of the PRC1 and PRC2 complexes in tissue development, in the maintenance of organ integrity and in pathology.
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Affiliation(s)
- Mariette Hanot
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Ludivine Raby
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Pamela Völkel
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Xuefen Le Bourhis
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Pierre-Olivier Angrand
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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3
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Almohaisen FLJ, Heidary S, Sobah ML, Ward AC, Liongue C. B cell lymphoma 6A regulates immune development and function in zebrafish. Front Cell Infect Microbiol 2022; 12:887278. [PMID: 36389136 PMCID: PMC9650189 DOI: 10.3389/fcimb.2022.887278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 10/03/2022] [Indexed: 11/25/2022] Open
Abstract
BCL6A is a transcriptional repressor implicated in the development and survival of B and T lymphoctyes, which is also highly expressed in many non-Hodgkin’s lymphomas, such as diffuse large B cell lymphoma and follicular lymphoma. Roles in other cell types, including macrophages and non-hematopoietic cells, have also been suggested but require further investigation. This study sought to identify and characterize zebrafish BCL6A and investigate its role in immune cell development and function, with a focus on early macrophages. Bioinformatics analysis identified a homologue for BCL6A (bcl6aa), as well as an additional fish-specific duplicate (bcl6ab) and a homologue for the closely-related BCL6B (bcl6b). The human BCL6A and zebrafish Bcl6aa proteins were highly conserved across the constituent BTB/POZ, PEST and zinc finger domains. Expression of bcl6aa during early zebrafish embryogenesis was observed in the lateral plate mesoderm, a site of early myeloid cell development, with later expression seen in the brain, eye and thymus. Homozygous bcl6aa mutants developed normally until around 14 days post fertilization (dpf), after which their subsequent growth and maturation was severely impacted along with their relative survival, with heterozygous bcl6aa mutants showing an intermediate phenotype. Analysis of immune cell development revealed significantly decreased lymphoid and macrophage cells in both homozygous and heterozygous bcl6aa mutants, being exacerbated in homozygous mutants. In contrast, the number of neutrophils was unaffected. Only the homozygous bcl6aa mutants showed decreased macrophage mobility in response to wounding and reduced ability to contain bacterial infection. Collectively, this suggests strong conservation of BCL6A across evolution, including a role in macrophage biology.
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Affiliation(s)
- Farooq L. J. Almohaisen
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Department of Medical Laboratory Technology, Southern Technical University, Basra, Iraq
| | | | | | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- *Correspondence: Clifford Liongue,
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4
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Zhong X, Gu J, Zhang S, Chen X, Zhang J, Miao J, Ding Z, Xu J, Cheng H. Dynamic transcriptome analysis of the muscles in high-fat diet-induced obese zebrafish (Danio rerio) under 5-HT treatment. Gene 2022; 819:146265. [PMID: 35121026 DOI: 10.1016/j.gene.2022.146265] [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: 11/16/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 11/04/2022]
Abstract
Peripheral 5-hydroxytryptamine (5-HT, also called serotonin) is reportedly a potential therapeutic target in obesity-related metabolic diseases due to its regulatory role in energy homeostasis in mammals. However, information on the detailed effect of peripheral 5-HT on the energy metabolism in fishes, especially the lipid metabolism, and the underlying mechanism remains elusive. In this study, a diet-induced obesity model was developed in the zebrafish (Danio rerio), a prototypical animal model for metabolic disorders. The zebrafish were fed a high-fat diet for 8 weeks and were simultaneously injected with PBS, 0.1 mM and 10 mM 5-HT, intraperitoneally. The body weight was significantly lower in the zebrafish injected with 0.1 mM 5-HT (P < 0.05), however, there was no change in body length (P > 0.05) at the end of the 8-week treatment. The muscle tissues from the zebrafish treated with PBS and 5-HT were collected for transcriptomic analysis and the RNA-seq revealed 1134, 3713, and 2535 genes were screened out compared to the muscular DEGs among three groups. The enrichment analysis revealed DEGs to be significantly associated with multiple metabolic pathways, including ribosome, oxidative phosphorylation, proteasome, PPAR signaling pathway, and ferroptosis. Additionally, the qRT-PCR validated 12 DEGs out of which 10 genes exhibited consistent trends. Taken together, this data provided useful information on the transcriptional characteristics of the muscle tissue in the obese zebrafish exposed to 5-HT, offering important insights into the regulatory effect of peripheral 5-HT in teleosts, as well as novel approaches for preventing and treating obesity-related metabolic dysfunction.
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Affiliation(s)
- Xiangqi Zhong
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Key Laboratory of Cultivation and High-value Utilization of Marine Organisms, Fisheries Research Institute of Fujian, Xiamen 361000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jiaze Gu
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Siying Zhang
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiangning Chen
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Key Laboratory of Cultivation and High-value Utilization of Marine Organisms, Fisheries Research Institute of Fujian, Xiamen 361000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Jingjing Zhang
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jintao Miao
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhujin Ding
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jianhe Xu
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hanliang Cheng
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
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5
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Fox SC, Widen SA, Asai-Coakwell M, Havrylov S, Benson M, Prichard LB, Baddam P, Graf D, Lehmann OJ, Waskiewicz AJ. BMP3 is a novel locus involved in the causality of ocular coloboma. Hum Genet 2022; 141:1385-1407. [PMID: 35089417 DOI: 10.1007/s00439-022-02430-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022]
Abstract
Coloboma, a congenital disorder characterized by gaps in ocular tissues, is caused when the choroid fissure fails to close during embryonic development. Several loci have been associated with coloboma, but these represent less than 40% of those that are involved with this disease. Here, we describe a novel coloboma-causing locus, BMP3. Whole exome sequencing and Sanger sequencing of patients with coloboma identified three variants in BMP3, two of which are predicted to be disease causing. Consistent with this, bmp3 mutant zebrafish have aberrant fissure closure. bmp3 is expressed in the ventral head mesenchyme and regulates phosphorylated Smad3 in a population of cells adjacent to the choroid fissure. Furthermore, mutations in bmp3 sensitize embryos to Smad3 inhibitor treatment resulting in open choroid fissures. Micro CT scans and Alcian blue staining of zebrafish demonstrate that mutations in bmp3 cause midface hypoplasia, suggesting that bmp3 regulates cranial neural crest cells. Consistent with this, we see active Smad3 in a population of periocular neural crest cells, and bmp3 mutant zebrafish have reduced neural crest cells in the choroid fissure. Taken together, these data suggest that Bmp3 controls Smad3 phosphorylation in neural crest cells to regulate early craniofacial and ocular development.
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Affiliation(s)
- Sabrina C Fox
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada.,Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Sonya A Widen
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada.,Vienna BioCenter, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.,Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Mika Asai-Coakwell
- Department of Animal and Poultry and Animal Science, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Ophthalmology, University of Alberta, Edmonton, AB, Canada
| | - Serhiy Havrylov
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.,Department of Ophthalmology, University of Alberta, Edmonton, AB, Canada
| | - Matthew Benson
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.,Department of Ophthalmology, University of Alberta, Edmonton, AB, Canada
| | - Lisa B Prichard
- Department of Biological Sciences, MacEwan University, Edmonton, AB, Canada
| | - Pranidhi Baddam
- Department of Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Daniel Graf
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.,Department of Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ordan J Lehmann
- Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.,Department of Ophthalmology, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Waskiewicz
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada. .,Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada.
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6
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Ke X, Zhang R, Yao Q, Duan S, Hong W, Cao M, Zhou Q, Zhong X, Zhao H. Alternative splicing of medaka bcl6aa and its repression by Prdm1a and Prdm1b. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1229-1242. [PMID: 34218391 DOI: 10.1007/s10695-021-00980-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Bcl6 and Prdm1 (Blimp1) are a pair of transcriptional factors that repressing each other in mammals. Prdm1 represses the expression of bcl6 by binding a cis-element of the bcl6 gene in mammals. The homologs of Bcl6 and Prdm1 have been identified in teleost fish. However, whether these two factors regulate each other in the same way in fish like that in mammals is not clear. In this study, the regulation of bcl6aa by Prdm1 was investigated in medaka. The mRNA of bcl6aa has three variants (bcl6aaX1-X3) at the 5'-end by alternative splicing detected by RT-PCR. The three variants can be detected in adult tissues and developing embryos of medaka. Prdm1a and prdm1b are expressed in the tissues and embryos where and when bcl6aa is expressed. The expression of prdm1a was high while the expression of bcl6aa was low, and vice versa, detected in the spleen after stimulation with LPS or polyI:C. In vitro reporter assay indicated that bcl6aa could be directly repressed by both Prdm1a and Prdm1b in a dosage-dependent manner. After mutation of the key base, G, of all predicted binding sites in the core promoter region of bcl6aa, the repression by Prdm1a and/or Prdm1b disappeared. The binding site of Prdm1 in the bcl6aa gene is GAAAA(T/G). These results indicate that both Prdm1a and Prdm1b directly repress the expression of bcl6aa by binding their binding sites where the 5'-G is critical in medaka fish.
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Affiliation(s)
- Xiaomei Ke
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Runshuai Zhang
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Qiting Yao
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Shi Duan
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Wentao Hong
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Mengxi Cao
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Qingchun Zhou
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Xueping Zhong
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Haobin Zhao
- Hubei Key Laboratory of Gene Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China.
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7
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BCOR gene alterations in hematological diseases. Blood 2021; 138:2455-2468. [PMID: 33945606 DOI: 10.1182/blood.2021010958] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
The BCL6 co-repressor (BCOR) is a transcription factor involved in the control of embryogenesis, mesenchymal stem cells function, hematopoiesis and lymphoid development. Recurrent somatic clonal mutations of the BCOR gene and its homologue BCORL1 have been detected in several hematological malignancies and aplastic anemia. They are scattered across the whole gene length and mostly represent frameshifts (deletions, insertions), nonsense and missence mutations. These disruptive events lead to the loss of full-length BCOR protein and to the lack or low expression of a truncated form of the protein, both consistent with the tumor suppressor role of BCOR. BCOR and BCORL1 mutations are similar to those causing two rare X-linked diseases: the oculo-facio-cardio-dental (OFCD) and the Shukla-Vernon syndromes, respectively. Here, we focus on the structure and function of normal BCOR and BCORL1 in normal hematopoietic and lymphoid tissues and review the frequency and clinical significance of the mutations of these genes in malignant and non-malignant hematological diseases. Moreover, we discuss the importance of mouse models to better understand the role of Bcor loss, alone and combined with alterations of other genes (e.g. Dnmt3a and Tet2), in promoting hematological malignancies and in providing a useful platform for the development of new targeted therapies.
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8
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Chan BHC, Moosajee M, Rainger J. Closing the Gap: Mechanisms of Epithelial Fusion During Optic Fissure Closure. Front Cell Dev Biol 2021; 8:620774. [PMID: 33505973 PMCID: PMC7829581 DOI: 10.3389/fcell.2020.620774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
A key embryonic process that occurs early in ocular development is optic fissure closure (OFC). This fusion process closes the ventral optic fissure and completes the circumferential continuity of the 3-dimensional eye. It is defined by the coming together and fusion of opposing neuroepithelia along the entire proximal-distal axis of the ventral optic cup, involving future neural retina, retinal pigment epithelium (RPE), optic nerve, ciliary body, and iris. Once these have occurred, cells within the fused seam differentiate into components of the functioning visual system. Correct development and progression of OFC, and the continued integrity of the fused margin along this axis, are important for the overall structure of the eye. Failure of OFC results in ocular coloboma-a significant cause of childhood visual impairment that can be associated with several complex ocular phenotypes including microphthalmia and anterior segment dysgenesis. Despite a large number of genes identified, the exact pathways that definitively mediate fusion have not yet been found, reflecting both the biological complexity and genetic heterogeneity of the process. This review will highlight how recent developmental studies have become focused specifically on the epithelial fusion aspects of OFC, applying a range of model organisms (spanning fish, avian, and mammalian species) and utilizing emerging high-resolution live-imaging technologies, transgenic fluorescent models, and unbiased transcriptomic analyses of segmentally-dissected fissure tissue. Key aspects of the fusion process are discussed, including basement membrane dynamics, unique cell behaviors, and the identities and fates of the cells that mediate fusion. These will be set in the context of what is now known, and how these point the way to new avenues of research.
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Affiliation(s)
- Brian Ho Ching Chan
- The Division of Functional Genetics and Development, The Royal Dick School of Veterinary Sciences, The Roslin Institute, The University of Edinburgh, Scotland, United Kingdom
| | - Mariya Moosajee
- University College London Institute of Ophthalmology, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom.,Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Joe Rainger
- The Division of Functional Genetics and Development, The Royal Dick School of Veterinary Sciences, The Roslin Institute, The University of Edinburgh, Scotland, United Kingdom
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9
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Patel A, Anderson G, Galea GL, Balys M, Sowden JC. A molecular and cellular analysis of human embryonic optic fissure closure related to the eye malformation coloboma. Development 2020; 147:dev193649. [PMID: 33158926 DOI: 10.1242/dev.193649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Ocular coloboma is a congenital eye malformation, resulting from a failure in optic fissure closure (OFC) and causing visual impairment. There has been little study of the epithelial fusion process underlying closure in the human embryo and coloboma aetiology remains poorly understood. We performed RNAseq of cell populations isolated using laser capture microdissection to identify novel human OFC signature genes and probe the expression profile of known coloboma genes, along with a comparative murine analysis. Gene set enrichment patterns showed conservation between species. Expression of genes involved in epithelial-to-mesenchymal transition was transiently enriched in the human fissure margins during OFC at days 41-44. Electron microscopy and histological analyses showed that cells transiently delaminate at the point of closure, and produce cytoplasmic protrusions, before rearranging to form two continuous epithelial layers. Apoptosis was not observed in the human fissure margins. These analyses support a model of human OFC in which epithelial cells at the fissure margins undergo a transient epithelial-to-mesenchymal-like transition, facilitating cell rearrangement to form a complete optic cup.
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Affiliation(s)
- Aara Patel
- UCL Great Ormond Street Institute of Child Health, and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Glenn Anderson
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Gabriel L Galea
- UCL Great Ormond Street Institute of Child Health, and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Monika Balys
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health, and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
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10
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Sun WR, Ramirez S, Spiller KE, Zhao Y, Fuhrmann S. Nf2 fine-tunes proliferation and tissue alignment during closure of the optic fissure in the embryonic mouse eye. Hum Mol Genet 2020; 29:3373-3387. [PMID: 33075808 DOI: 10.1093/hmg/ddaa228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/29/2020] [Accepted: 10/12/2020] [Indexed: 11/14/2022] Open
Abstract
Uveal coloboma represents one of the most common congenital ocular malformations accounting for up to 10% of childhood blindness (~1 in 5000 live birth). Coloboma originates from defective fusion of the optic fissure (OF), a transient gap that forms during eye morphogenesis by asymmetric, ventral invagination. Genetic heterogeneity combined with the activity of developmentally regulated genes suggests multiple mechanisms regulating OF closure. The tumor suppressor and FERM domain protein Neurofibromin 2 (NF2) controls diverse processes in cancer, development and regeneration, via Hippo pathway and cytoskeleton regulation. In humans, NF2 mutations can cause ocular abnormalities, including coloboma, however, its actual role in OF closure is unknown. Using conditional inactivation in the embryonic mouse eye, our data indicate that loss of Nf2 function results in a novel underlying cause for coloboma. In particular, mutant eyes show substantially increased retinal pigmented epithelium (RPE) proliferation in the fissure region with concomitant acquisition of RPE cell fate. Cells lining the OF margin can maintain RPE fate ectopically and fail to transition from neuroepithelial to cuboidal shape. In the dorsal RPE of the optic cup, Nf2 inactivation leads to a robust increase in cell number, with local disorganization of the cytoskeleton components F-actin and pMLC2. We propose that RPE hyperproliferation is the primary cause for the observed defects causing insufficient alignment of the OF margins in Nf2 mutants and failure to fuse properly, resulting in persistent coloboma. Our findings indicate that limiting proliferation particularly in the RPE layer is a critical mechanism during OF closure.
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Affiliation(s)
- Wesley R Sun
- Department of Ophthalmology and Visual Sciences, VEI, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sara Ramirez
- Department of Ophthalmology and Visual Sciences, VEI, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Kelly E Spiller
- Department of Ophthalmology and Visual Sciences, VEI, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yan Zhao
- Department of Ophthalmology and Visual Sciences, VEI, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sabine Fuhrmann
- Department of Ophthalmology and Visual Sciences, VEI, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
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11
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Gath N, Gross JM. Zebrafish mab21l2 mutants possess severe defects in optic cup morphogenesis, lens and cornea development. Dev Dyn 2019; 248:514-529. [PMID: 31037784 DOI: 10.1002/dvdy.44] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/09/2019] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Mutations in MAB21L2 result in severe ocular defects including microphthalmia, anophthalmia, coloboma, microcornea, and cataracts. The molecular and cellular underpinnings of these defects are unknown, as is the normal cellular function of MAB21L2. Zebrafish mab21l2 au10 mutants possess ocular defects resembling those in humans with MAB21L2 mutations, providing an excellent model to characterize mab21l2 functions during eye development. RESULTS mab21l2 -/- mutants possessed a host of ocular defects including microphthalmia and colobomas as well as small, disorganized lenses and cornea dysgenesis. Decreased proliferation, increased cell death, and defects in marker gene expression were detected in the lens. Cell death in the optic stalk was elevated in mab21l2 -/- mutants and the basement membrane between the edges of the choroid fissure failed to break down. Neuronal differentiation in the retina was normal, however. mab21l2 -/- mutant corneas were disorganized, possessed an increased number of cells, some of which proliferated ectopically, and failed to differentiate the corneal stroma. CONCLUSIONS mab21l2 function is required for morphogenesis and cell survival in the lens and optic cup, and basement membrane breakdown in the choroid fissure. mab21l2 function also regulates proliferation in the lens and cornea; in its absence, the lens is small and mispatterned, and corneal morphogenesis and patterning are also disrupted.
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Affiliation(s)
- Natalie Gath
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jeffrey M Gross
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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12
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An update on the genetics of ocular coloboma. Hum Genet 2019; 138:865-880. [PMID: 31073883 DOI: 10.1007/s00439-019-02019-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/19/2019] [Indexed: 01/04/2023]
Abstract
Ocular coloboma is an uncommon, but often severe, sight-threatening condition that can be identified from birth. This congenital anomaly is thought to be caused by maldevelopment of optic fissure closure during early eye morphogenesis. It has been causally linked to both inherited (genetic) and environmental influences. In particular, as a consequence of work to identify genetic causes of coloboma, new molecular pathways that control optic fissure closure have now been identified. Many more regulatory mechanisms still await better understanding to inform on the development of potential therapies for patients with this malformation. This review provides an update of known coloboma genes, the pathways they influence and how best to manage the condition. In the age of precision medicine, determining the underlying genetic cause in any given patient is of high importance.
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13
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Zhang R, Wu K, Ke X, Zhang X, Xu G, Shen H, Nibona E, Al Hafiz A, Liang X, Wang Z, Qi C, Zhou Q, Zhong X, Zhao H. Bcl6aa and bcl6ab are ubiquitously expressed and are inducible by lipopolysaccharide and polyI:C in adult tissues of medaka Oryzias latipes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:17-25. [PMID: 30680935 DOI: 10.1002/jez.b.22843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/17/2019] [Indexed: 11/10/2022]
Abstract
B-cell lymphoma-6 (Bcl6) is a transcriptional repressor that plays important roles in various physiological activities such as innate and adaptive immune response, lymphocyte differentiation, and cell cycle regulation in mammals. Two homologs of Bcl6a, namely Bcl6aa and Bcl6ab, are identified in teleost fish including medaka Oryzias latipes. The expression profiles of bcl6aa and bcl6ab in medaka were studied using reverse-transcription polymerase chain reaction and in situ hybridization. The transcripts of bcl6aa and bcl6ab were detected from very early embryos such as the four-cell stage until hatching. Bcl6aa and bcl6ab were clearly detected in the embryonic body from 5 days postfertilization onward by in situ hybridization. Bcl6aa was specifically expressed in the retina, whereas bcl6ab was expressed in entire embryonic body. The results referred to that both bcl6aa and bcl6ab originate maternally in the zygotes and may play major roles in embryogenesis of medaka. The transcripts of bcl6aa and bcl6ab were detected in all examined adult tissues, including immune organs such as the gill, spleen, kidney, liver, and intestine. The expression of bcl6aa and bcl6ab in the liver, spleen, head-kidney, and intestine could be upregulated or downregulated by lipopolysaccharide and polyriboinosinic-polyribocytidylic acid. These results indicate that both bcl6aa and bcl6ab may be involved in immune response in medaka.
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Affiliation(s)
- Runshuai Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Kongyue Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xiaomei Ke
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xueyan Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Gongyu Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Hao Shen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Emile Nibona
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Abdullah Al Hafiz
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xiaoting Liang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zequn Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Chao Qi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qingchun Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xueping Zhong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Haobin Zhao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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14
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Ragge N, Isidor B, Bitoun P, Odent S, Giurgea I, Cogné B, Deb W, Vincent M, Le Gall J, Morton J, Lim D, Le Meur G, Zazo Seco C, Zafeiropoulou D, Bax D, Zwijnenburg P, Arteche A, Swafiri ST, Cleaver R, McEntagart M, Kini U, Newman W, Ayuso C, Corton M, Herenger Y, Jeanne M, Calvas P, Chassaing N. Expanding the phenotype of the X-linked BCOR microphthalmia syndromes. Hum Genet 2018; 138:1051-1069. [PMID: 29974297 DOI: 10.1007/s00439-018-1896-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/07/2018] [Indexed: 10/28/2022]
Abstract
Two distinct syndromes arise from pathogenic variants in the X-linked gene BCOR (BCL-6 corepressor): oculofaciocardiodental (OFCD) syndrome, which affects females, and a severe microphthalmia ('Lenz'-type) syndrome affecting males. OFCD is an X-linked dominant syndrome caused by a variety of BCOR null mutations. As it manifests only in females, it is presumed to be lethal in males. The severe male X-linked recessive microphthalmia syndrome ('Lenz') usually includes developmental delay in addition to the eye findings and is caused by hypomorphic BCOR variants, mainly by a specific missense variant c.254C > T, p.(Pro85Leu). Here, we detail 16 new cases (11 females with 4 additional, genetically confirmed, affected female relatives; 5 male cases each with unaffected carrier mothers). We describe new variants and broaden the phenotypic description for OFCD to include neuropathy, muscle hypotonia, pituitary underdevelopment, brain atrophy, lipoma and the first description of childhood lymphoma in an OFCD case. Our male X-linked recessive cases show significant new phenotypes: developmental delay (without eye anomalies) in two affected half-brothers with a novel BCOR variant, and one male with high myopia, megalophthalmos, posterior embryotoxon, developmental delay, and heart and bony anomalies with a previously undescribed BCOR splice site variant. Our female OFCD cases and their affected female relatives showed variable features, but consistently had early onset cataracts. We show that a mosaic carrier mother manifested early cataract and dental anomalies. All female carriers of the male X-linked recessive cases for whom genetic confirmation was available showed skewed X-inactivation and were unaffected. In view of the extended phenotype, we suggest a new term of X-linked BCOR-related syndrome.
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Affiliation(s)
- Nicola Ragge
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK. .,West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK.
| | - Bertrand Isidor
- Service de génétique médicale, Hôtel-Dieu, CHU de Nantes, Nantes, France
| | - Pierre Bitoun
- SIDVA 91, Ophthalmic Genetics, 1 rue de la Cour de, 91260, Juvisy s/orge, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence CLAD-Ouest, Université Rennes 1, UMR 6290 CNRS IGDR, CHU Rennes, Rennes, France
| | - Irina Giurgea
- U.F. de Génétique moléculaire, Hôpital Armand Trousseau, Assistance Publique, Hôpitaux de Paris, 75012, Paris, France.,Faculté de médecine, INSERM UMR S933, Sorbonne Université, 75012, Paris, France
| | - Benjamin Cogné
- Service de génétique médicale, Hôtel-Dieu, CHU de Nantes, Nantes, France
| | - Wallid Deb
- Service de génétique médicale, Hôtel-Dieu, CHU de Nantes, Nantes, France
| | - Marie Vincent
- Service de génétique médicale, Hôtel-Dieu, CHU de Nantes, Nantes, France
| | - Jessica Le Gall
- Service de génétique médicale, Hôtel-Dieu, CHU de Nantes, Nantes, France
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Derek Lim
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | | | - Guylène Le Meur
- Service d'ophtalmologie, Hôtel Dieu, CHU de Nantes, Nantes, France
| | - Celia Zazo Seco
- UDEAR, UMR 1056 Inserm, Université de Toulouse, Toulouse, France
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Dorine Bax
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Petra Zwijnenburg
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Anara Arteche
- Department of Genetics, Health Research Institute-Jiménez Díaz Foundation, University Hospital (IIS-FJD-UAM), Madrid, Spain
| | - Saoud Tahsin Swafiri
- Department of Genetics, Health Research Institute-Jiménez Díaz Foundation, University Hospital (IIS-FJD-UAM), Madrid, Spain
| | - Ruth Cleaver
- South West Thames Regional Genetics Service, St. George's Healthcare NHS Trust, London, UK
| | - Meriel McEntagart
- South West Thames Regional Genetics Service, St. George's Healthcare NHS Trust, London, UK
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford, UK
| | | | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Jiménez Díaz Foundation, University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Marta Corton
- Department of Genetics, Health Research Institute-Jiménez Díaz Foundation, University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Yvan Herenger
- Service de Génétique Médicale, CHU de Tours, Tours, France
| | - Médéric Jeanne
- Service de Génétique Médicale, CHU de Tours, Tours, France
| | - Patrick Calvas
- UDEAR, UMR 1056 Inserm, Université de Toulouse, Toulouse, France.,Department of Medical Genetics, CHU Toulouse, Purpan Hospital, 31059, Toulouse, France
| | - Nicolas Chassaing
- UDEAR, UMR 1056 Inserm, Université de Toulouse, Toulouse, France.,Department of Medical Genetics, CHU Toulouse, Purpan Hospital, 31059, Toulouse, France
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15
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Bernstein CS, Anderson MT, Gohel C, Slater K, Gross JM, Agarwala S. The cellular bases of choroid fissure formation and closure. Dev Biol 2018; 440:137-151. [PMID: 29803644 DOI: 10.1016/j.ydbio.2018.05.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/30/2018] [Accepted: 05/14/2018] [Indexed: 01/11/2023]
Abstract
Defects in choroid fissure (CF) formation and closure lead to coloboma, a major cause of childhood blindness. Despite genetic advances, the cellular defects underlying coloboma remain poorly elucidated due to our limited understanding of normal CF morphogenesis. We address this deficit by conducting high-resolution spatio-temporal analyses of CF formation and closure in the chick, mouse and fish. We show that a small ventral midline invagination initiates CF formation in the medial-proximal optic cup, subsequently extending it dorsally toward the lens, and proximally into the optic stalk. Unlike previously supposed, the optic disc does not form solely as a result of this invagination. Morphogenetic events that alter the shape of the proximal optic cup also direct clusters of outer layer and optic stalk cells to form dorsal optic disc. A cross-species comparison suggests that CF closure can be accomplished by breaking down basement membranes (BM) along the CF margins, and by establishing BM continuity along the dorsal and ventral surfaces of the CF. CF closure is subsequently accomplished via two distinct mechanisms: tissue fusion or the intercalation of various tissues into the inter-CF space. We identify several novel cell behaviors that underlie CF fusion, many of which involve remodeling of the retinal epithelium. In addition to BM disruption, these include NCAD downregulation along the SOX2+ retinal CF margin, and the protrusion or movement of partially polarized retinal cells into the inter-CF space to mediate fusion. Proximally, the inter-CF space does not fuse or narrow and is instead loosely packed with migrating SOX2+/PAX2+/Vimentin+ astrocytes until it is closed by the outgoing optic nerve. Taken together, our results highlight distinct proximal-distal differences in CF morphogenesis and closure and establish detailed cellular models that can be utilized for understanding the genetic bases of coloboma.
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Affiliation(s)
- Cassidy S Bernstein
- Molecular Biosciences Department, University of Texas at Austin, Austin, TX 78712, USA
| | - Mitchell T Anderson
- Molecular Biosciences Department, University of Texas at Austin, Austin, TX 78712, USA
| | - Chintan Gohel
- Molecular Biosciences Department, University of Texas at Austin, Austin, TX 78712, USA
| | - Kayleigh Slater
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jeffrey M Gross
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Seema Agarwala
- Molecular Biosciences Department, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cell and Molecular Biology, University of Texas at Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA.
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16
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Identification of novel prognosis-related genes associated with cancer using integrative network analysis. Sci Rep 2018; 8:3233. [PMID: 29459674 PMCID: PMC5818516 DOI: 10.1038/s41598-018-21691-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/08/2018] [Indexed: 12/28/2022] Open
Abstract
Prognosis identifies the seriousness and the chances of survival of a cancer patient. However, it remains a challenge to identify the key cancer genes in prognostic studies. In this study, we collected 2064 genes that were related to prognostic studies by using gene expression measurements curated from published literatures. Among them, 1820 genes were associated with copy number variations (CNVs). The further functional enrichment on 889 genes with frequent copy number gains (CNGs) revealed that these genes were significantly associated with cancer pathways including regulation of cell cycle, cell differentiation and mitogen-activated protein kinase (MAPK) cascade. We further conducted integrative analyses of CNV and their target genes expression using the data from matched tumour samples of The Cancer Genome Atlas (TCGA). Ultimately, 95 key prognosis-related genes were extracted, with concordant CNG events and increased up-regulation in at least 300 tumour samples. These genes, and the number of samples in which they were found, included: ACTL6A (399), ATP6V1C1 (425), EBAG9 (412), FADD (308), MTDH (377), and SENP5 (304). This study provides the first observation of CNV in prognosis-related genes across pan-cancer. The systematic concordance between CNG and up-regulation of gene expression in these novel prognosis-related genes may indicate their prognostic significance.
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17
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Genes and pathways in optic fissure closure. Semin Cell Dev Biol 2017; 91:55-65. [PMID: 29198497 DOI: 10.1016/j.semcdb.2017.10.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/29/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
Embryonic development of the vertebrate eye begins with the formation of an optic vesicle which folds inwards to form a double-layered optic cup with a fissure on the ventral surface, known as the optic fissure. Closure of the optic fissure is essential for subsequent growth and development of the eye. A defect in this process can leave a gap in the iris, retina or optic nerve, known as a coloboma, which can lead to severe visual impairment. This review brings together current information about genes and pathways regulating fissure closure from human coloboma patients and animal models. It focuses especially on current understanding of the morphological changes and processes of epithelial remodelling occurring at the fissure margins.
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18
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Zhou Y, Wojcik A, Sanders VR, Rahmani B, Kurup SP. Ocular findings in a patient with oculofaciocardiodental (OFCD) syndrome and a novel BCOR pathogenic variant. Int Ophthalmol 2017; 38:2677-2682. [PMID: 29058245 DOI: 10.1007/s10792-017-0754-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/16/2017] [Indexed: 01/19/2023]
Abstract
PURPOSE To report a case of OFCD associated with a de novo BCOR pathogenic variant and highlight the ocular findings and possible mechanisms. METHODS A retrospective chart review of the patient's ocular and systemic findings was performed. The patient underwent diagnostic whole exome sequencing (WES). RESULTS The patient had a comprehensive eye exam in infancy demonstrating bilateral congenital cataracts consisting of posterior lenticonus with a posterior cortical opacity. She also had blepharoptosis with a hooded appearance and retinal pigment hypertrophy of the inferior retina bilaterally. Systemic findings include atrial septal defect, patent ductus arteriosus, congenital clubfoot, syndactyly, tethered cord, and laryngeal cleft. WES identified a de novo heterozygous R1136X pathogenic variant in the BCOR gene. CONCLUSION The typical ocular manifestation of OFCD syndrome is congenital cataracts, which can have a significant impact on visual development and so should be considered in patients with multiple medical issues that may fit the diagnosis. A comprehensive eye exam in these patients is thus warranted.
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Affiliation(s)
- Yujia Zhou
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Box 70, Chicago, IL, 60611, USA.,Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Antonina Wojcik
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Box 70, Chicago, IL, 60611, USA.,Division of Genetics Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Victoria R Sanders
- Division of Genetics Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Bahram Rahmani
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Box 70, Chicago, IL, 60611, USA.,Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sudhi P Kurup
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Box 70, Chicago, IL, 60611, USA. .,Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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19
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Blanco-Sánchez B, Clément A, Phillips JB, Westerfield M. Zebrafish models of human eye and inner ear diseases. Methods Cell Biol 2016; 138:415-467. [PMID: 28129854 DOI: 10.1016/bs.mcb.2016.10.006] [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] [Indexed: 12/27/2022]
Abstract
Eye and inner ear diseases are the most common sensory impairments that greatly impact quality of life. Zebrafish have been intensively employed to understand the fundamental mechanisms underlying eye and inner ear development. The zebrafish visual and vestibulo-acoustic systems are very similar to these in humans, and although not yet mature, they are functional by 5days post-fertilization (dpf). In this chapter, we show how the zebrafish has significantly contributed to the field of biomedical research and how researchers, by establishing disease models and meticulously characterizing their phenotypes, have taken the first steps toward therapies. We review here models for (1) eye diseases, (2) ear diseases, and (3) syndromes affecting eye and/or ear. The use of new genome editing technologies and high-throughput screening systems should increase considerably the speed at which knowledge from zebrafish disease models is acquired, opening avenues for better diagnostics, treatments, and therapies.
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Affiliation(s)
| | - A Clément
- University of Oregon, Eugene, OR, United States
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20
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Noh H, Lee H, Park E, Park S. Proper closure of the optic fissure requires ephrin A5-EphB2-JNK signaling. Development 2016; 143:461-72. [PMID: 26839344 DOI: 10.1242/dev.129478] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The development of complex organs such as the eye requires a delicate and coordinated balance of cell division and cell death. Although apoptosis is prevalent in the proximoventral optic cup, the precise role it plays in eye development needs to be investigated further. In this study, we show that reduced apoptosis in the proximoventral optic cup prevents closure of the optic fissure. We also show that expression of ephrin A5 (Efna5) partially overlaps with Eph receptor B2 (Ephb2) expression in the proximoventral optic cup and that binding of EphB2 to ephrin A5 induces a sustained activation of JNK. This prolonged JNK signal promotes apoptosis and prevents cell proliferation. Thus, we propose that the unique cross-subclass interaction of EphB2 with ephrin A5 has evolved to function upstream of JNK signaling for the purpose of maintaining an adequate pool of progenitor cells to ensure proper closure of the optic fissure.
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Affiliation(s)
- Hyuna Noh
- Department of Biological Science, Sookmyung Women's University, Chungpa-ro 47gil 100, Yongsan-gu, Seoul 140-742, Korea
| | - Haeryung Lee
- Department of Biological Science, Sookmyung Women's University, Chungpa-ro 47gil 100, Yongsan-gu, Seoul 140-742, Korea
| | - Eunjeong Park
- Department of Biological Science, Sookmyung Women's University, Chungpa-ro 47gil 100, Yongsan-gu, Seoul 140-742, Korea
| | - Soochul Park
- Department of Biological Science, Sookmyung Women's University, Chungpa-ro 47gil 100, Yongsan-gu, Seoul 140-742, Korea
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21
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Andreeva K, Soliman MM, Cooper NGF. Regulatory networks in retinal ischemia-reperfusion injury. BMC Genet 2015; 16:43. [PMID: 25902940 PMCID: PMC4424502 DOI: 10.1186/s12863-015-0201-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/14/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Retinal function is ordered by interactions between transcriptional and posttranscriptional regulators at the molecular level. These regulators include transcription factors (TFs) and posttranscriptional factors such as microRNAs (miRs). Some studies propose that miRs predominantly target the TFs rather than other types of protein coding genes and such studies suggest a possible interconnection of these two regulators in co-regulatory networks. RESULTS Our lab has generated mRNA and miRNA microarray expression data to investigate time-dependent changes in gene expression, following induction of ischemia-reperfusion (IR) injury in the rat retina. Data from different reperfusion time points following retinal IR-injury were analyzed. Paired expression data for miRNA-target gene (TG), TF-TG, miRNA-TF were used to identify regulatory loop motifs whose expressions were altered by the IR injury paradigm. These loops were subsequently integrated into larger regulatory networks and biological functions were assayed. Systematic analyses of the networks have provided new insights into retinal gene regulation in the early and late periods of IR. We found both overlapping and unique patterns of molecular expression at the two time points. These patterns can be defined by their characteristic molecular motifs as well as their associated biological processes. We highlighted the regulatory elements of miRs and TFs associated with biological processes in the early and late phases of ischemia-reperfusion injury. CONCLUSIONS The etiology of retinal ischemia-reperfusion injury is orchestrated by complex and still not well understood gene networks. This work represents the first large network analysis to integrate miRNA and mRNA expression profiles in context of retinal ischemia. It is likely that an appreciation of such regulatory networks will have prognostic potential. In addition, the computational framework described in this study can be used to construct miRNA-TF interactive systems networks for various diseases/disorders of the retina and other tissues.
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Affiliation(s)
- Kalina Andreeva
- Department of Anatomical Science and Neurobiology, University of Louisville, School of Medicine, 500 S. Preston Street, Louisville, KY, 40292, USA.
| | - Maha M Soliman
- Department of Anatomical Science and Neurobiology, University of Louisville, School of Medicine, 500 S. Preston Street, Louisville, KY, 40292, USA.
| | - Nigel G F Cooper
- Department of Anatomical Science and Neurobiology, University of Louisville, School of Medicine, 500 S. Preston Street, Louisville, KY, 40292, USA.
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22
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Bankhead EJ, Colasanto MP, Dyorich KM, Jamrich M, Murtaugh LC, Fuhrmann S. Multiple requirements of the focal dermal hypoplasia gene porcupine during ocular morphogenesis. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 185:197-213. [PMID: 25451153 DOI: 10.1016/j.ajpath.2014.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/25/2014] [Accepted: 09/02/2014] [Indexed: 12/13/2022]
Abstract
Wnt glycoproteins control key processes during development and disease by activating various downstream pathways. Wnt secretion requires post-translational modification mediated by the O-acyltransferase encoded by the Drosophila porcupine homolog gene (PORCN). In humans, PORCN mutations cause focal dermal hypoplasia (FDH, or Goltz syndrome), an X-linked dominant multisystem birth defect that is frequently accompanied by ocular abnormalities such as coloboma, microphthalmia, or even anophthalmia. Although genetic ablation of Porcn in mouse has provided insight into the etiology of defects caused by ectomesodermal dysplasia in FDH, the requirement for Porcn and the actual Wnt ligands during eye development have been unknown. In this study, Porcn hemizygosity occasionally caused ocular defects reminiscent of FDH. Conditional inactivation of Porcn in periocular mesenchyme led to defects in mid- and hindbrain and in craniofacial development, but was insufficient to cause ocular abnormalities. However, a combination of conditional Porcn depletion in optic vesicle neuroectoderm, lens, and neural crest-derived periocular mesenchyme induced severe eye abnormalities with high penetrance. In particular, we observed coloboma, transdifferentiation of the dorsal and ventral retinal pigment epithelium, defective optic cup periphery, and closure defects of the eyelid, as well as defective corneal morphogenesis. Thus, Porcn is required in both extraocular and neuroectodermal tissues to regulate distinct Wnt-dependent processes during morphogenesis of the posterior and anterior segments of the eye.
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Affiliation(s)
- Elizabeth J Bankhead
- Departments of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah
| | - Mary P Colasanto
- Departments of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah
| | - Kayla M Dyorich
- Departments of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah
| | - Milan Jamrich
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Sabine Fuhrmann
- Departments of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah.
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23
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McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O’Quin KE, Rétaux S, Rohner N, Searle SMJ, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC. The cavefish genome reveals candidate genes for eye loss. Nat Commun 2014; 5:5307. [PMID: 25329095 PMCID: PMC4218959 DOI: 10.1038/ncomms6307] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/17/2014] [Indexed: 11/10/2022] Open
Abstract
Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.
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Affiliation(s)
- Suzanne E. McGaugh
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
| | - Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maryline Blin
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - Richard Borowsky
- Department of Biology, New York University, New York, New York 10003-6688, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d’Italie, Lyon F-69364, France
| | - Hélène Hinaux
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - William R. Jeffery
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Alex Keene
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Li Ma
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Patrick Minx
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
| | - Daniel Murphy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kelly E. O’Quin
- Department of Biology, Centre College, 600 West Walnut St, Danville, Kentucky 40422, USA
| | - Sylvie Rétaux
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - Nicolas Rohner
- Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA
| | - Steve M. J. Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Bethany A. Stahl
- Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA
| | - Cliff Tabin
- Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d’Italie, Lyon F-69364, France
| | - Masato Yoshizawa
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Wesley C. Warren
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
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24
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Danda S, van Rahden VA, John D, Paul P, Raju R, Koshy S, Kutsche K. Evidence of Germline Mosaicism for a Novel BCOR Mutation in Two Indian Sisters with Oculo-Facio-Cardio-Dental Syndrome. Mol Syndromol 2014; 5:251-6. [PMID: 25337074 DOI: 10.1159/000365768] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 02/04/2023] Open
Abstract
In this study, we report on 2 sisters from India with oculo-facio-cardio-dental (OFCD) syndrome caused by a novel heterozygous mutation c.3490C>T (p.R1164*) in the BCOR gene. OFCD syndrome is an X-linked inherited disorder which is lethal in males. Interestingly, both parents of the sisters were phenotypically normal, and DNA analysis from blood and buccal or saliva cells failed to detect the BCOR mutation found in their 2 daughters. To the best of our knowledge, for the first time, we provide indirect evidence of germline mosaicism for the BCOR mutation in one of the parents of the 2 sisters affected by OFCD syndrome. Although this condition is lethal in males, gonadal mosaicism could also be present in the father. The relevance of clinical diagnosis and mutation analysis required for genetic counseling is described in this family.
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Affiliation(s)
- Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Vanessa A van Rahden
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Deepa John
- Department of Ophthalmology, Christian Medical College and Hospital, Vellore, India
| | - Padma Paul
- Department of Ophthalmology, Christian Medical College and Hospital, Vellore, India
| | - Renu Raju
- Department of Ophthalmology, Christian Medical College and Hospital, Vellore, India
| | - Santosh Koshy
- Department of Dental Surgery, Christian Medical College and Hospital, Vellore, India
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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25
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Kelberman D, Islam L, Lakowski J, Bacchelli C, Chanudet E, Lescai F, Patel A, Stupka E, Buck A, Wolf S, Beales PL, Jacques TS, Bitner-Glindzicz M, Liasis A, Lehmann OJ, Kohlhase J, Nischal KK, Sowden JC. Mutation of SALL2 causes recessive ocular coloboma in humans and mice. Hum Mol Genet 2014; 23:2511-26. [PMID: 24412933 PMCID: PMC3990155 DOI: 10.1093/hmg/ddt643] [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] [Indexed: 01/25/2023] Open
Abstract
Ocular coloboma is a congenital defect resulting from failure of normal closure of the optic fissure during embryonic eye development. This birth defect causes childhood blindness worldwide, yet the genetic etiology is poorly understood. Here, we identified a novel homozygous mutation in the SALL2 gene in members of a consanguineous family affected with non-syndromic ocular coloboma variably affecting the iris and retina. This mutation, c.85G>T, introduces a premature termination codon (p.Glu29*) predicted to truncate the SALL2 protein so that it lacks three clusters of zinc-finger motifs that are essential for DNA-binding activity. This discovery identifies SALL2 as the third member of the Drosophila homeotic Spalt-like family of developmental transcription factor genes implicated in human disease. SALL2 is expressed in the developing human retina at the time of, and subsequent to, optic fissure closure. Analysis of Sall2-deficient mouse embryos revealed delayed apposition of the optic fissure margins and the persistence of an anterior retinal coloboma phenotype after birth. Sall2-deficient embryos displayed correct posterior closure toward the optic nerve head, and upon contact of the fissure margins, dissolution of the basal lamina occurred and PAX2, known to be critical for this process, was expressed normally. Anterior closure was disrupted with the fissure margins failing to meet, or in some cases misaligning leading to a retinal lesion. These observations demonstrate, for the first time, a role for SALL2 in eye morphogenesis and that loss of function of the gene causes ocular coloboma in humans and mice.
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