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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Dynamic enhancer landscapes in human craniofacial development. Nat Commun 2024; 15:2030. [PMID: 38448444 PMCID: PMC10917818 DOI: 10.1038/s41467-024-46396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Laura E Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Cailyn H Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, 3010, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Lucile Packard Children's Hospital, Stanford University, Stanford, CA, 94304, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA, 94110, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Octant Inc., Emeryville, CA, 94608, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, CA, USA.
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2
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Coronel J, Yu J, Pilli N, Kane MA, Amengual J. The conversion of β-carotene to vitamin A in adipocytes drives the anti-obesogenic effects of β-carotene in mice. Mol Metab 2022; 66:101640. [PMID: 36400405 PMCID: PMC9707038 DOI: 10.1016/j.molmet.2022.101640] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/30/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE The β-carotene oxygenase 1 (BCO1) is the enzyme responsible for the cleavage of β-carotene to retinal, the first intermediate in vitamin A formation. Preclinical studies suggest that BCO1 expression is required for dietary β-carotene to affect lipid metabolism. The goal of this study was to generate a gene therapy strategy that over-expresses BCO1 in the adipose tissue and utilizes the β-carotene stored in adipocytes to produce vitamin A and reduce obesity. METHODS We generated a novel adipose-tissue-specific, adeno-associated vector to over-express BCO1 (AT-AAV-BCO1) in murine adipocytes. We tested this vector using a unique model to achieve β-carotene accumulation in the adipose tissue, in which Bco1-/- mice were fed β-carotene. An AT-AAV over-expressing green fluorescent protein was utilized as control. We evaluated the adequate delivery route and optimized cellular and organ specificity, dosage, and exposure of our vectors. We also employed morphometric analyses to evaluate the effect of BCO1 expression in adiposity, as well as HPLC and mass spectrometry to quantify β-carotene and retinoids in tissues, including retinoic acid. RESULTS AT-AAV-BCO1 infusions in the adipose tissue of the mice resulted in the production of retinoic acid, a vitamin A metabolite with strong effects on gene regulation. AT-AAV-BCO1 treatment also reduced adipose tissue size and adipocyte area by 35% and 30%, respectively. These effects were sex-specific, highlighting the complexity of vitamin A metabolism in mammals. CONCLUSIONS The over-expression of BCO1 through delivery of an AT-AAV-BCO1 leads to the conversion of β-carotene to vitamin A in adipocytes, which subsequently results in reduction of adiposity. These studies highlight for the first time the potential of adipose tissue β-carotene as a target for BCO1 over-expression in the reduction of obesity.
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Affiliation(s)
- Johana Coronel
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jianshi Yu
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Nageswara Pilli
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Jaume Amengual
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Corresponding author. Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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3
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Duester G. Towards a Better Vision of Retinoic Acid Signaling during Eye Development. Cells 2022; 11:cells11030322. [PMID: 35159132 PMCID: PMC8834304 DOI: 10.3390/cells11030322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Retinoic acid (RA) functions as an essential signal for development of the vertebrate eye by controlling the transcriptional regulatory activity of RA receptors (RARs). During eye development, the optic vesicles and later the retina generate RA as a metabolite of vitamin A (retinol). Retinol is first converted to retinaldehyde by retinol dehydrogenase 10 (RDH10) and then to RA by all three retinaldehyde dehydrogenases (ALDH1A1, ALDH1A2, and ALDH1A3). In early mouse embryos, RA diffuses to tissues throughout the optic placode, optic vesicle, and adjacent mesenchyme to stimulate folding of the optic vesicle to form the optic cup. RA later generated by the retina is needed for further morphogenesis of the optic cup and surrounding perioptic mesenchyme; loss of RA at this stage leads to microphthalmia and cornea plus eyelid defects. RA functions by binding to nuclear RARs at RA response elements (RAREs) that either activate or repress transcription of key genes. Binding of RA to RARs regulates recruitment of transcriptional coregulators such as nuclear receptor coactivator (NCOA) or nuclear receptor corepressor (NCOR), which in turn control binding of the generic coactivator p300 or the generic corepressor PRC2. No genes have been identified as direct targets of RA signaling during eye development, so future studies need to focus on identifying such genes and their RAREs. Studies designed to learn how RA normally controls eye development in vivo will provide basic knowledge valuable for determining how developmental eye defects occur and for improving strategies to treat eye defects.
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Affiliation(s)
- Gregg Duester
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
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4
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Sirbu IO, Chiş AR, Moise AR. Role of carotenoids and retinoids during heart development. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158636. [PMID: 31978553 DOI: 10.1016/j.bbalip.2020.158636] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 02/08/2023]
Abstract
The nutritional requirements of the developing embryo are complex. In the case of dietary vitamin A (retinol, retinyl esters and provitamin A carotenoids), maternal derived nutrients serve as precursors to signaling molecules such as retinoic acid, which is required for embryonic patterning and organogenesis. Despite variations in the composition and levels of maternal vitamin A, embryonic tissues need to generate a precise amount of retinoic acid to avoid congenital malformations. Here, we summarize recent findings regarding the role and metabolism of vitamin A during heart development and we survey the association of genes known to affect retinoid metabolism or signaling with various inherited disorders. A better understanding of the roles of vitamin A in the heart and of the factors that affect retinoid metabolism and signaling can help design strategies to meet nutritional needs and to prevent birth defects and disorders associated with altered retinoid metabolism. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
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Affiliation(s)
- Ioan Ovidiu Sirbu
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, 300041 Timisoara, Romania; Timisoara Institute of Complex Systems, V. Lucaciu 18, 300044 Timisoara, Romania.
| | - Aimée Rodica Chiş
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Alexander Radu Moise
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON P3E 2C6, Canada; Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada.
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5
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Pequerul R, Vera J, Giménez-Dejoz J, Crespo I, Coines J, Porté S, Rovira C, Parés X, Farrés J. Structural and kinetic features of aldehyde dehydrogenase 1A (ALDH1A) subfamily members, cancer stem cell markers active in retinoic acid biosynthesis. Arch Biochem Biophys 2020; 681:108256. [PMID: 31923393 DOI: 10.1016/j.abb.2020.108256] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/01/2020] [Accepted: 01/02/2020] [Indexed: 11/30/2022]
Abstract
Aldehyde dehydrogenases catalyze the NAD(P)+-dependent oxidation of aldehydes to their corresponding carboxylic acids. The three-dimensional structures of the human ALDH1A enzymes were recently obtained, while a complete kinetic characterization of them, under the same experimental conditions, is lacking. We show that the three enzymes, ALDH1A1, ALDH1A2 and ALDH1A3, have similar topologies, although with decreasing volumes in their substrate-binding pockets. The activity with aliphatic and retinoid aldehydes was characterized side-by-side, using an improved HPLC-based method for retinaldehyde. Hexanal was the most efficient substrate. ALDH1A1 displayed lower Km values with hexanal, trans-2-hexenal and citral, compared to ALDH1A2 and ALDH1A3. ALDH1A2 was the best enzyme for the lipid peroxidation product, 4-hydroxy-2-nonenal, in terms of kcat/Km. The catalytic efficiency towards all-trans and 9-cis-retinaldehyde was in general lower than for alkanals and alkenals. ALDH1A2 and ALDH1A3 showed higher catalytic efficiency for all-trans-retinaldehyde. The lower specificity of ALDH1A3 for 9-cis-retinaldehyde against the all-trans- isomer might be related to the smaller volume of its substrate-binding pocket. Magnesium inhibited ALDH1A1 and ALDH1A2, while it activated ALDH1A3, which is consistent with cofactor dissociation being the rate-limiting step for ALDH1A1 and ALDH1A2, and deacylation for ALDH1A3, with hexanal as a substrate. We mutated both ALDH1A1 (L114P) and ALDH1A2 (N475G, A476V, L477V, N478S) to mimic their counterpart substrate-binding pockets. ALDH1A1 specificity for citral was traced to residue 114 and to residues 458 to 461. Regarding retinaldehyde, the mutants did not show significant differences with their respective wild-type forms, suggesting that the mutated residues are not critical for retinoid specificity.
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Affiliation(s)
- Raquel Pequerul
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Javier Vera
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Joan Giménez-Dejoz
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Joan Coines
- Department of Inorganic and Organic Chemistry, Universitat de Barcelona, E-08028, Barcelona, Spain
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry, Universitat de Barcelona, E-08028, Barcelona, Spain
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain.
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6
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Thompson B, Katsanis N, Apostolopoulos N, Thompson DC, Nebert DW, Vasiliou V. Genetics and functions of the retinoic acid pathway, with special emphasis on the eye. Hum Genomics 2019; 13:61. [PMID: 31796115 PMCID: PMC6892198 DOI: 10.1186/s40246-019-0248-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/12/2019] [Indexed: 02/07/2023] Open
Abstract
Retinoic acid (RA) is a potent morphogen required for embryonic development. RA is formed in a multistep process from vitamin A (retinol); RA acts in a paracrine fashion to shape the developing eye and is essential for normal optic vesicle and anterior segment formation. Perturbation in RA-signaling can result in severe ocular developmental diseases—including microphthalmia, anophthalmia, and coloboma. RA-signaling is also essential for embryonic development and life, as indicated by the significant consequences of mutations in genes involved in RA-signaling. The requirement of RA-signaling for normal development is further supported by the manifestation of severe pathologies in animal models of RA deficiency—such as ventral lens rotation, failure of optic cup formation, and embryonic and postnatal lethality. In this review, we summarize RA-signaling, recent advances in our understanding of this pathway in eye development, and the requirement of RA-signaling for embryonic development (e.g., organogenesis and limb bud development) and life.
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Affiliation(s)
- Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College St, New Haven, CT, 06520, USA
| | - Nicholas Katsanis
- Stanley Manne Research Institute, Lurie Children's Hospital, Chicago, IL, 60611, USA.,Departments of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Nicholas Apostolopoulos
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College St, New Haven, CT, 06520, USA
| | - David C Thompson
- Department of Clinical Pharmacy, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Daniel W Nebert
- Department of Environmental Health and Center for Environmental Genetics, University Cincinnati Medical Center, Cincinnati, OH, 45267-0056, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College St, New Haven, CT, 06520, USA.
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7
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Nedelec B, Rozet JM, Fares Taie L. Genetic architecture of retinoic-acid signaling-associated ocular developmental defects. Hum Genet 2019; 138:937-955. [DOI: 10.1007/s00439-019-02052-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022]
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8
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Genetics of anophthalmia and microphthalmia. Part 1: Non-syndromic anophthalmia/microphthalmia. Hum Genet 2019; 138:799-830. [PMID: 30762128 DOI: 10.1007/s00439-019-01977-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
Eye formation is the result of coordinated induction and differentiation processes during embryogenesis. Disruption of any one of these events has the potential to cause ocular growth and structural defects, such as anophthalmia and microphthalmia (A/M). A/M can be isolated or occur with systemic anomalies, when they may form part of a recognizable syndrome. Their etiology includes genetic and environmental factors; several hundred genes involved in ocular development have been identified in humans or animal models. In humans, around 30 genes have been repeatedly implicated in A/M families, although many other genes have been described in single cases or families, and some genetic syndromes include eye anomalies occasionally as part of a wider phenotype. As a result of this broad genetic heterogeneity, with one or two notable exceptions, each gene explains only a small percentage of cases. Given the overlapping phenotypes, these genes can be most efficiently tested on panels or by whole exome/genome sequencing for the purposes of molecular diagnosis. However, despite whole exome/genome testing more than half of patients currently remain without a molecular diagnosis. The proportion of undiagnosed cases is even higher in those individuals with unilateral or milder phenotypes. Furthermore, even when a strong gene candidate is available for a patient, issues of incomplete penetrance and germinal mosaicism make diagnosis and genetic counseling challenging. In this review, we present the main genes implicated in non-syndromic human A/M phenotypes and, for practical purposes, classify them according to the most frequent or predominant phenotype each is associated with. Our intention is that this will allow clinicians to rank and prioritize their molecular analyses and interpretations according to the phenotypes of their patients.
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9
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Lin S, Harlalka GV, Hameed A, Reham HM, Yasin M, Muhammad N, Khan S, Baple EL, Crosby AH, Saleha S. Novel mutations in ALDH1A3 associated with autosomal recessive anophthalmia/microphthalmia, and review of the literature. BMC MEDICAL GENETICS 2018; 19:160. [PMID: 30200890 PMCID: PMC6131798 DOI: 10.1186/s12881-018-0678-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/02/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Autosomal recessive anophthalmia and microphthalmia are rare developmental eye defects occurring during early fetal development. Syndromic and non-syndromic forms of anophthalmia and microphthalmia demonstrate extensive genetic and allelic heterogeneity. To date, disease mutations have been identified in 29 causative genes associated with anophthalmia and microphthalmia, with autosomal dominant, autosomal recessive and X-linked inheritance patterns described. Biallelic ALDH1A3 gene variants are the leading genetic causes of autosomal recessive anophthalmia and microphthalmia in countries with frequent parental consanguinity. METHODS This study describes genetic investigations in two consanguineous Pakistani families with a total of seven affected individuals with bilateral non-syndromic clinical anophthalmia. RESULTS Using whole exome and Sanger sequencing, we identified two novel homozygous ALDH1A3 sequence variants as likely responsible for the condition in each family; missense mutation [NM_000693.3:c.1240G > C, p.Gly414Arg; Chr15:101447332G > C (GRCh37)] in exon 11 (family 1), and, a frameshift mutation [NM_000693.3:c.172dup, p.Glu58Glyfs*5; Chr15:101425544dup (GRCh37)] in exon 2 predicted to result in protein truncation (family 2). CONCLUSIONS This study expands the molecular spectrum of pathogenic ALDH1A3 variants associated with anophthalmia and microphthalmia, and provides further insight of the key role of the ALDH1A3 in human eye development.
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Affiliation(s)
- Siying Lin
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Gaurav V Harlalka
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Abdul Hameed
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, 44000, Pakistan
| | - Hadia Moattar Reham
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Emma L Baple
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew H Crosby
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Khyber Pakhtunkhwa, 26000, Pakistan.
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10
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Dehghani M, Dehghan Tezerjani M, Metanat Z, Vahidi Mehrjardi MY. A Novel Missense Mutation in the ALDH13 Gene Causes Anophthalmia in Two Unrelated Iranian Consanguineous Families. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2017; 6:131-134. [PMID: 28890889 PMCID: PMC5581554 DOI: 10.22088/acadpub.bums.6.2.7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/18/2017] [Indexed: 11/05/2022]
Abstract
Anophthalmia or microphthalmia (A/M) is a rare group of congenital/developmental ocular malformations, characterized by absent or small eye within the orbit affecting one or both eyes. It has complex etiology with chromosomal, monogenic with high heterogeneity, and environmental causes. We performed genome SNP-array analysis followed by autozygosity mapping and sequencing in the members of two families in which three individuals are suffering from severe bilateral anophthalmia. The genetic analysis revealed a novel missense c.709G>A mutation in exon 7 of ALDH1A3 (aldehyde dehydrogenase 1 family member A3), causing a substitution of glycine (Gly) to arginine (Arg) at residue 237. This study consolidates the importance of ALDH1A3 gene screening in autosomal recessive anophthalmia. This variation may also be suggestive of a founder effect in the southeastern area of Iran.
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Affiliation(s)
- Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Masoud Dehghan Tezerjani
- Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Zahra Metanat
- Provincial Clinical Genetic Counseling Center, Zahedan University of Medical Sciences Zahedan, Iran
| | - Mohammad Yahya Vahidi Mehrjardi
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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11
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Liu Y, Lu Y, Liu S, Liao S. Novel compound heterozygous mutations of ALDH1A3 contribute to anophthalmia in a non-consanguineous Chinese family. Genet Mol Biol 2017; 40:430-435. [PMID: 28590501 PMCID: PMC5488456 DOI: 10.1590/1678-4685-gmb-2016-0120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/31/2016] [Indexed: 02/05/2023] Open
Abstract
Anophthalmia is a rare eye development anomaly resulting in absent ocular globes or
tissue in the orbit since birth. Here, we investigated a newborn with bilateral
anophthalmia in a Chinese family. Exome sequencing revealed that compound
heterozygous mutations c.287G > A (p.(Arg96His)) and c.709G > A (p.(Gly237Arg))
of the ALDH1A3 gene were present in the affected newborn. Both
mutations were absent in all of the searched databases, including 10,000 in-house
Chinese exome sequences, and these mutations were confirmed as having been
transmitted from the parents. Comparative amino acid sequence analysis across
distantly related species revealed that the residues at positions 96 and 234 were
evolutionarily highly conserved. In silico analysis predicted these
changes to be damaging, and in vitro expression analysis revealed
that the mutated alleles were associated with decreased protein production and
impaired tetrameric protein formation. This study firstly reported that compound
heterozygous mutations of the ALDH1A3 gene can result in
anophthalmia in humans, thus highlighting those heterozygous mutations in
ALDH1A3 should be considered for molecular screening in
anophthalmia, particularly in cases from families without consanguineous
relationships.
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Affiliation(s)
- Yunqiang Liu
- Department of Medical Genetics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yongjie Lu
- Department of Medical Genetics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Shasha Liu
- Diabetes Center & Institute of Transplantation, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shunyao Liao
- Diabetes Center & Institute of Transplantation, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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12
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Olivares AM, Moreno-Ramos OA, Haider NB. Role of Nuclear Receptors in Central Nervous System Development and Associated Diseases. J Exp Neurosci 2016; 9:93-121. [PMID: 27168725 PMCID: PMC4859451 DOI: 10.4137/jen.s25480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/13/2022] Open
Abstract
The nuclear hormone receptor (NHR) superfamily is composed of a wide range of receptors involved in a myriad of important biological processes, including development, growth, metabolism, and maintenance. Regulation of such wide variety of functions requires a complex system of gene regulation that includes interaction with transcription factors, chromatin-modifying complex, and the proper recognition of ligands. NHRs are able to coordinate the expression of genes in numerous pathways simultaneously. This review focuses on the role of nuclear receptors in the central nervous system and, in particular, their role in regulating the proper development and function of the brain and the eye. In addition, the review highlights the impact of mutations in NHRs on a spectrum of human diseases from autism to retinal degeneration.
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Affiliation(s)
- Ana Maria Olivares
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Oscar Andrés Moreno-Ramos
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Neena B Haider
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
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13
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Genetic analysis of consanguineous families presenting with congenital ocular defects. Exp Eye Res 2016; 146:163-171. [DOI: 10.1016/j.exer.2016.03.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/11/2016] [Accepted: 03/14/2016] [Indexed: 01/08/2023]
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14
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Genetic Testing for Eye Diseases: A Comprehensive Guide and Review of Ocular Genetic Manifestations from Anterior Segment Malformation to Retinal Dystrophy. CURRENT GENETIC MEDICINE REPORTS 2016. [DOI: 10.1007/s40142-016-0087-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Incomplete penetrance of biallelic ALDH1A3 mutations. Eur J Med Genet 2016; 59:215-8. [PMID: 26873617 DOI: 10.1016/j.ejmg.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 01/31/2016] [Accepted: 02/06/2016] [Indexed: 12/24/2022]
Abstract
The formation of a properly shaped eye is a complex developmental event that requires the coordination of many induction processes and differentiation pathways. Microphthalmia and anophthalmia (MA) represent the most severe defects that can affect the ocular globe during embryonic development. When genetic, these ocular disorders exhibit large genetic heterogeneity and extreme variable expressivity. Around 20 monogenic diseases are known to be associated with MA as main phenotype and the penetrance of mutations is usually full in the patients. Some of these genes encode proteins involved in the vitamin A pathway, tightly regulated during eye development. One of those retinoic acid synthesis genes is ALDH1A3 and biallelic mutations in that gene have been recently found to lead to MA phenotype in patients. Interestingly, we report here the lack of ocular defect in a girl carrying the same homozygous mutation in the ALDH1A3 gene than the affected members of her family. Thus, this report brings new information for the phenotype-genotype correlation of ALDH1A3 mutations and raises important questions, especially in terms of genetic counselling given to the patients and their families. Furthermore, these data contribute to the more general understanding that we have for the complex genetic inheritance of these MA phenotypes.
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16
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Moreno-Ramos OA, Olivares AM, Haider NB, de Autismo LC, Lattig MC. Whole-Exome Sequencing in a South American Cohort Links ALDH1A3, FOXN1 and Retinoic Acid Regulation Pathways to Autism Spectrum Disorders. PLoS One 2015; 10:e0135927. [PMID: 26352270 PMCID: PMC4564166 DOI: 10.1371/journal.pone.0135927] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 07/28/2015] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a range of complex neurodevelopmental conditions principally characterized by dysfunctions linked to mental development. Previous studies have shown that there are more than 1000 genes likely involved in ASD, expressed mainly in brain and highly interconnected among them. We applied whole exome sequencing in Colombian—South American trios. Two missense novel SNVs were found in the same child: ALDH1A3 (RefSeq NM_000693: c.1514T>C (p.I505T)) and FOXN1 (RefSeq NM_003593: c.146C>T (p.S49L)). Gene expression studies reveal that Aldh1a3 and Foxn1 are expressed in ~E13.5 mouse embryonic brain, as well as in adult piriform cortex (PC; ~P30). Conserved Retinoic Acid Response Elements (RAREs) upstream of human ALDH1A3 and FOXN1 and in mouse Aldh1a3 and Foxn1 genes were revealed using bioinformatic approximation. Chromatin immunoprecipitation (ChIP) assay using Retinoid Acid Receptor B (Rarb) as the immunoprecipitation target suggests RA regulation of Aldh1a3 and Foxn1 in mice. Our results frame a possible link of RA regulation in brain to ASD etiology, and a feasible non-additive effect of two apparently unrelated variants in ALDH1A3 and FOXN1 recognizing that every result given by next generation sequencing should be cautiously analyzed, as it might be an incidental finding.
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Affiliation(s)
- Oscar A. Moreno-Ramos
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá D.C., Colombia
| | - Ana María Olivares
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - Neena B. Haider
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | | | - María Claudia Lattig
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá D.C., Colombia
- * E-mail:
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17
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Abouzeid H, Favez T, Schmid A, Agosti C, Youssef M, Marzouk I, El Shakankiry N, Bayoumi N, Munier FL, Schorderet DF. Mutations inALDH1A3Represent a Frequent Cause of Microphthalmia/Anophthalmia in Consanguineous Families. Hum Mutat 2014; 35:949-53. [DOI: 10.1002/humu.22580] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Hana Abouzeid
- IRO - Institute for Research in Ophthalmology; Sion Switzerland
- Jules-Gonin Eye Hospital; Fondation Asile des Aveugles; University of Lausanne; Lausanne (UNIL); Switzerland
| | - Tatiana Favez
- IRO - Institute for Research in Ophthalmology; Sion Switzerland
| | | | - Céline Agosti
- IRO - Institute for Research in Ophthalmology; Sion Switzerland
| | - Mohammed Youssef
- Department of Pediatrics; University of Alexandria; Alexandria Egypt
| | - Iman Marzouk
- Department of Pediatrics; University of Alexandria; Alexandria Egypt
| | | | - Nader Bayoumi
- Department of Ophthalmology; University of Alexandria; Alexandria Egypt
| | - Francis L. Munier
- IRO - Institute for Research in Ophthalmology; Sion Switzerland
- Jules-Gonin Eye Hospital; Fondation Asile des Aveugles; University of Lausanne; Lausanne (UNIL); Switzerland
| | - Daniel F. Schorderet
- IRO - Institute for Research in Ophthalmology; Sion Switzerland
- Jules-Gonin Eye Hospital; Fondation Asile des Aveugles; University of Lausanne; Lausanne (UNIL); Switzerland
- Faculty of Life Sciences; Ecole polytechnique fédérale de Lausanne (EPFL); Lausanne Switzerland
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18
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Williamson KA, FitzPatrick DR. The genetic architecture of microphthalmia, anophthalmia and coloboma. Eur J Med Genet 2014; 57:369-80. [PMID: 24859618 DOI: 10.1016/j.ejmg.2014.05.002] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/14/2014] [Indexed: 10/25/2022]
Abstract
Microphthalmia, anophthalmia and coloboma (MAC) are distinct phenotypes that represent a continuum of structural developmental eye defects. In severe bilateral cases (anophthalmia or severe microphthalmia) the genetic cause is now identifiable in approximately 80 percent of cases, with de novo heterozygous loss-of-function mutations in SOX2 or OTX2 being the most common. The genetic cause of other forms of MAC, in particular isolated coloboma, remains unknown in the majority of cases. This review will focus on MAC phenotypes that are associated with mutation of the genes SOX2, OTX2, PAX6, STRA6, ALDH1A3, RARB, VSX2, RAX, FOXE3, BMP4, BMP7, GDF3, GDF6, ABCB6, ATOH7, C12orf57, TENM3 (ODZ3), and VAX1. Recently reported mutation of the SALL2 and YAP1 genes are discussed in brief. Clinical and genetic features were reviewed in a total of 283 unrelated MAC cases or families that were mutation-positive from these 20 genes. Both the relative frequency of mutations in MAC cohort screens and the level of confidence in the assignment of disease-causing status were evaluated for each gene.
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Affiliation(s)
- Kathleen A Williamson
- Medical Research Council Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - David R FitzPatrick
- Medical Research Council Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
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