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Silveira KC, Fonseca IC, Oborn C, Wengryn P, Ghafoor S, Beke A, Dreseris ES, Wong C, Iacovone A, Soltys CL, Babul-Hirji R, Artigalas O, Antolini-Tavares A, Gingras AC, Campos E, Cavalcanti DP, Kannu P. CYP26B1-related disorder: expanding the ends of the spectrum through clinical and molecular evidence. Hum Genet 2023; 142:1571-1586. [PMID: 37755482 PMCID: PMC10602971 DOI: 10.1007/s00439-023-02598-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
CYP26B1 metabolizes retinoic acid in the developing embryo to regulate its levels. A limited number of individuals with pathogenic variants in CYP26B1 have been documented with a varied phenotypic spectrum, spanning from a severe manifestation involving skull anomalies, craniosynostosis, encephalocele, radio-humeral fusion, oligodactyly, and a narrow thorax, to a milder presentation characterized by craniosynostosis, restricted radio-humeral joint mobility, hearing loss, and intellectual disability. Here, we report two families with CYP26B1-related phenotypes and describe the data obtained from functional studies of the variants. Exome and Sanger sequencing were used for variant identification in family 1 and family 2, respectively. Family 1 reflects a mild phenotype, which includes craniofacial dysmorphism with brachycephaly (without craniosynostosis), arachnodactyly, reduced radioulnar joint movement, conductive hearing loss, learning disability-and compound heterozygous CYP26B1 variants: (p.[(Pro118Leu)];[(Arg234Gln)]) were found. In family 2, a stillborn fetus presented a lethal phenotype with spina bifida occulta, hydrocephalus, poor skeletal mineralization, synostosis, limb defects, and a synonymous homozygous variant in CYP26B1: c.1083C > A. A minigene assay revealed that the synonymous variant created a new splice site, removing part of exon 5 (p.Val361_Asp382del). Enzymatic activity was assessed using a luciferase assay, demonstrating a notable reduction in exogenous retinoic acid metabolism for the variant p.Val361_Asp382del. (~ 3.5 × decrease compared to wild-type); comparatively, the variants p.(Pro118Leu) and p.(Arg234Gln) demonstrated a partial loss of metabolism (1.7× and 2.3× reduction, respectively). A proximity-dependent biotin identification assay reaffirmed previously reported ER-resident protein interactions. Additional work into these interactions is critical to determine if CYP26B1 is involved with other biological events on the ER. Immunofluorescence assay suggests that mutant CYP26B1 is still localized in the endoplasmic reticulum. These results indicate that novel pathogenic variants in CYP26B1 result in varying levels of enzymatic activity that impact retinoic acid metabolism and relate to the distinct phenotypes observed.
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Affiliation(s)
- Karina C Silveira
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Inara Chacon Fonseca
- Clinical Genetics, Durham Region Cancer Centre, Lakeridge Health Oshawa, Oshawa, ON, L1G 2B9, Canada
| | - Connor Oborn
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Parker Wengryn
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Saima Ghafoor
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Alexander Beke
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Ema S Dreseris
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Aline Iacovone
- Skeletal Dysplasia Group, Medical Genetics Area, Translational Medicine Department, FCM, University of Campinas (UNICAMP), R. Tessália V de Camargo, 126, Campinas, SP, 13083-887, Brazil
| | - Carrie-Lynn Soltys
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Riyana Babul-Hirji
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Osvaldo Artigalas
- Clinical Genetics Unit, Children's Hospital, Grupo Hospitalar Conceicao, Porto Alegre, Brazil
| | | | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Eric Campos
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Denise P Cavalcanti
- Skeletal Dysplasia Group, Medical Genetics Area, Translational Medicine Department, FCM, University of Campinas (UNICAMP), R. Tessália V de Camargo, 126, Campinas, SP, 13083-887, Brazil.
| | - Peter Kannu
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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Yang J, Wang C, Zhang Y, Cheng S, Xu Y, Wang Y. A Novel pyroptosis-related signature for predicting prognosis and evaluating tumor immune microenvironment in ovarian cancer. J Ovarian Res 2023; 16:196. [PMID: 37730669 PMCID: PMC10512632 DOI: 10.1186/s13048-023-01275-2] [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: 08/15/2022] [Accepted: 09/03/2023] [Indexed: 09/22/2023] Open
Abstract
Ovarian cancer (OV) is the most fatal gynecological malignant tumor worldwide, with high recurrence rates and great heterogeneity. Pyroptosis is a newly-acknowledged inflammatory form of cell death with an essential role in cancer progression, though studies focusing on prognostic patterns of pyroptosis in OV are still lacking. Our research filtered 106 potential pyroptosis-related genes (PRGs) among the 6406 differentially expressed genes (DEGs) between the 376 TCGA-OV samples and 180 normal controls. Through the LASSO-Cox analysis, the 6-gene prognostic signature, namely CITED2, EXOC6B, MIA2, NRAS, SETBP1, and TRPV46, was finally distinguished. Then, the K-M survival analysis and time-dependent ROC curves demonstrated the promising prognostic value of the 6-gene signature (p-value < 0.0001). Furthermore, based on the signature and corresponding clinical features, we constructed and validated a nomogram model for 1-year, 2-year, and 3-year OV survival, with reliable prognostic values in TCGA-OV (p-value < 0.001) and ICGC-OV cohort (p-value = 0.040). Pathway analysis enriched several critical pathways in cancer, refer to the pyroptosis-related signature, while the m6A analysis indicated greater m6A level in high-risk group. We assessed tumor immune microenvironment through the CIBERSORT algorithm, which demonstrated the upregulation of M1 Macrophages and activated DCs and high expression of key immune checkpoint molecules (CTLA4, PDCD1LG2, and HAVCR2) in high-risk group. Interestingly, the high-risk group exhibited poor sensitivity towards immunotherapy and better sensitivity towards chemotherapies, including Vinblastine, Docetaxel, and Sorafenib. Briefly, the pyroptosis-related signature was a promising tool to predict prognosis and evaluate immune responses, in order to assist decision-making for OV patients in the realm of precision medicine.
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Affiliation(s)
- Jiani Yang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Chao Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yue Zhang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Shanshan Cheng
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yanna Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yu Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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Halim DO, Munson M, Gao FB. The exocyst complex in neurological disorders. Hum Genet 2023; 142:1263-1270. [PMID: 37085629 PMCID: PMC10449956 DOI: 10.1007/s00439-023-02558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Exocytosis is the process by which secretory vesicles fuse with the plasma membrane to deliver materials to the cell surface or to release cargoes to the extracellular space. The exocyst-an evolutionarily conserved octameric protein complex-mediates spatiotemporal control of SNARE complex assembly for vesicle fusion and tethering the secretory vesicles to the plasma membrane. The exocyst participates in diverse cellular functions, including protein trafficking to the plasma membrane, membrane extension, cell polarity, neurite outgrowth, ciliogenesis, cytokinesis, cell migration, autophagy, host defense, and tumorigenesis. Exocyst subunits are essential for cell viability; and mutations or variants in several exocyst subunits have been implicated in human diseases, mostly neurodevelopmental disorders and ciliopathies. These conditions often share common features such as developmental delay, intellectual disability, and brain abnormalities. In this review, we summarize the mutations and variants in exocyst subunits that have been linked to disease and discuss the implications of exocyst dysfunction in other disorders.
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Affiliation(s)
- Dilara O Halim
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Mary Munson
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Lira M, Zamorano P, Cerpa W. Exo70 intracellular redistribution after repeated mild traumatic brain injury. Biol Res 2021; 54:5. [PMID: 33593425 PMCID: PMC7885507 DOI: 10.1186/s40659-021-00329-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/03/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Exo70 is a subunit of the greater exocyst complex, a collection of proteins that oversees cellular membrane addition and polarized exocytosis by acting as a tethering intermediate between the plasma membrane and newly synthesized secretory vesicles. Although Exo70 function has been implicated in several developmental events including cytokinesis and the establishment of cell polarity, its role in neuropathologies is poorly understood. On the other hand, traumatic brain injury is the result of mechanical external force including contusion, fast acceleration, and expansive waves that produce temporal or permanent cognitive damage and triggers physical and psychosocial alterations including headache, memory problems, attention deficits, difficulty thinking, mood swings, and frustration. Traumatic brain injury is a critical health problem on a global scale, constituting a major cause of deaths and disability among young adults. Trauma-related cellular damage includes redistribution of N-methyl-D-aspartate receptors outside of the synaptic compartment triggering detrimental effects to neurons. The exocyst has been related to glutamate receptor constitutive trafficking/delivery towards synapse as well. This work examines whether the exocyst complex subunit Exo70 participates in traumatic brain injury and if it is redistributed among subcellular compartments RESULTS: Our analysis shows that Exo70 expression is not altered upon injury induction. By using subcellular fractionation, we determined that Exo70 is redistributed from microsomes fraction into the synaptic compartment after brain trauma. In the synaptic compartment, we also show that the exocyst complex assembly and its interaction with GluN2B are increased. Finally, we show that the Exo70 pool that is redistributed comes from the plasma membrane. CONCLUSIONS The present findings position Exo70 in the group of proteins that could modulate GluN2B synaptic availability in acute neuropathology like a traumatic brain injury. By acting as a nucleator factor, Exo70 is capable of redirecting the ensembled complex into the synapse. We suggest that this redistribution is part of a compensatory mechanism by which Exo70 is able to maintain GluN2B partially on synapses. Hence, reducing the detrimental effects associated with TBI pathophysiology.
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Affiliation(s)
- Matías Lira
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Pedro Zamorano
- Departamento Biomédico, Universidad de Antofagasta, Antofagasta, Chile.,Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Waldo Cerpa
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O´Higgins 340, Santiago, Chile. .,Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Universidad de Magallanes, Punta Arenas, Chile.
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5
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Snyder JM, Zhong G, Hogarth C, Huang W, Topping T, LaFrance J, Palau L, Czuba LC, Griswold M, Ghiaur G, Isoherranen N. Knockout of Cyp26a1 and Cyp26b1 during postnatal life causes reduced lifespan, dermatitis, splenomegaly, and systemic inflammation in mice. FASEB J 2020; 34:15788-15804. [PMID: 33105029 DOI: 10.1096/fj.202001734r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 01/08/2023]
Abstract
All-trans-retinoic acid (atRA), the active metabolite of vitamin A, is an essential signaling molecule in all chordates. Global knockouts of the atRA clearing enzymes Cyp26a1 or Cyp26b1 are embryonic lethal. In adult rodents, inhibition of Cyp26a1 and Cyp26b1 increases atRA concentrations and signaling. However, postnatal knockout of Cyp26a1 does not cause a severe phenotype. We hypothesized that Cyp26b1 is the main atRA clearing Cyp in postnatal mammals. This hypothesis was tested by generating tamoxifen-inducible knockout mouse models of Cyp26b1 alone or with Cyp26a1. Both mouse models showed dermatitis, blepharitis, and splenomegaly. Histology showed infiltration of inflammatory cells including neutrophils and T lymphocytes into the skin and hyperkeratosis/hyperplasia of the nonglandular stomach. The mice lacking both Cyp26a1 and Cyp26b1 also had a reduced lifespan, failed to gain weight, and showed fat atrophy. There were significant changes in vitamin A homeostasis. Postnatal knockout of Cyp26b1 resulted in increased atRA concentrations in the skin while the postnatal knockout of both Cyp26a1 and Cyp26b1 resulted in increased atRA concentrations in the liver, serum, skin, spleen, and intestines. This study demonstrates the paramount role of Cyp26b1 in regulating retinoid homeostasis in postnatal life.
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Affiliation(s)
- Jessica M Snyder
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Guo Zhong
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Cathryn Hogarth
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA.,Department of Pharmacy and Biomedical Science, School of Molecular Science, La Trobe University, Wodonga, VIC, Australia
| | - Weize Huang
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Traci Topping
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jeffrey LaFrance
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Laura Palau
- School of Medicine, The Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay C Czuba
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Michael Griswold
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Gabriel Ghiaur
- School of Medicine, The Johns Hopkins University, Baltimore, MD, USA
| | - Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
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Fitak RR, Mohandesan E, Corander J, Yadamsuren A, Chuluunbat B, Abdelhadi O, Raziq A, Nagy P, Walzer C, Faye B, Burger PA. Genomic signatures of domestication in Old World camels. Commun Biol 2020; 3:316. [PMID: 32561887 PMCID: PMC7305198 DOI: 10.1038/s42003-020-1039-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 05/28/2020] [Indexed: 12/30/2022] Open
Abstract
Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack secondary bottlenecks associated with breed development. By re-sequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, here we show that positive selection for candidate genes underlying traits collectively referred to as 'domestication syndrome' is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Comparing our results with other domestic species, we postulate that the core set of domestication genes is considerably smaller than the pan-domestication set - and overlapping genes are likely a result of chance and redundancy. These results, along with the extensive genomic resources provided, are an important contribution to understanding the evolutionary history of camels and the genomic features of their domestication.
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Affiliation(s)
- Robert Rodgers Fitak
- Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, 32816, USA.
| | - Elmira Mohandesan
- Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Department of Evolutionary Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Jukka Corander
- Wellcome Sanger Institute, Hinxton, UK
- Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, FIN-00014, Helsinki, Finland
- Department of Biostatistics, University of Oslo, N-0317, Oslo, Norway
| | - Adiya Yadamsuren
- Institute of Remote Sensing and Digital Earth, Chinese Academy of Sciences, Jia No.20 North, DaTun road, ChaoYang District, Beijing, China
- Wild Camel Protection Foundation Mongolia. Jukov avenue, Bayanzurh District, Ulaanbaatar, 13343, Mongolia
| | - Battsetseg Chuluunbat
- Laboratory of Genetics, Institute of General and Experimental Biology, Mongolian Academy of Sciences, Peace avenue-54b, Bayarzurh District, Ulaanbaatar, 210351, Mongolia
| | - Omer Abdelhadi
- University of Khartoum, Department for Meat Sciences, Khartoum, Sudan
| | - Abdul Raziq
- Camelait, Alain Farms for Livestock Production, Alain Dubai Road, Alain, United Arab Emirates
| | - Peter Nagy
- Farm and Veterinary Department, Emirates Industry for Camel Milk and Products, PO Box 294236, Dubai, Umm Nahad, United Arab Emirates
| | - Chris Walzer
- Wildlife Conservation Society, Wildlife Health Program, Bronx, NY, USA
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria
| | - Bernard Faye
- CIRAD-ES, UMR 112, Campus International de Baillarguet, TA C/112A, 34398, Montpellier, France
| | - Pamela Anna Burger
- Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.
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7
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Roberts C. Regulating Retinoic Acid Availability during Development and Regeneration: The Role of the CYP26 Enzymes. J Dev Biol 2020; 8:jdb8010006. [PMID: 32151018 PMCID: PMC7151129 DOI: 10.3390/jdb8010006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
This review focuses on the role of the Cytochrome p450 subfamily 26 (CYP26) retinoic acid (RA) degrading enzymes during development and regeneration. Cyp26 enzymes, along with retinoic acid synthesising enzymes, are absolutely required for RA homeostasis in these processes by regulating availability of RA for receptor binding and signalling. Cyp26 enzymes are necessary to generate RA gradients and to protect specific tissues from RA signalling. Disruption of RA homeostasis leads to a wide variety of embryonic defects affecting many tissues. Here, the function of CYP26 enzymes is discussed in the context of the RA signalling pathway, enzymatic structure and biochemistry, human genetic disease, and function in development and regeneration as elucidated from animal model studies.
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Affiliation(s)
- Catherine Roberts
- Developmental Biology of Birth Defects, UCL-GOS Institute of Child Health, 30 Guilford St, London WC1N 1EH, UK;
- Institute of Medical and Biomedical Education St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
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8
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Isoherranen N, Zhong G. Biochemical and physiological importance of the CYP26 retinoic acid hydroxylases. Pharmacol Ther 2019; 204:107400. [PMID: 31419517 PMCID: PMC6881548 DOI: 10.1016/j.pharmthera.2019.107400] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022]
Abstract
The Cytochrome P450 (CYP) family 26 enzymes contribute to retinoic acid (RA) metabolism and homeostasis in humans, mammals and other chordates. The three CYP26 family enzymes, CYP26A1, CYP26B1 and CYP26C1 have all been shown to metabolize all-trans-retinoic acid (atRA) it's 9-cisRA and 13-cisRA isomers and primary metabolites 4-OH-RA and 4-oxo-RA with high efficiency. While no crystal structures of CYP26 enzymes are available, the binding of various ligands has been extensively explored via homology modeling. All three CYP26 enzymes are inducible by treatment with atRA in various prenatal and postnatal tissues and cell types. However, current literature shows that in addition to regulation by atRA, CYP26 enzyme expression is also regulated by other endogenous processes and inflammatory cytokines. In humans and in animal models the expression patterns of CYP26 enzymes have been shown to be tissue and cell type specific, and the expression of the CYP26 enzymes is believed to regulate the formation of critical atRA concentration gradients in various tissue types. Yet, very little data exists on direct disease associations of altered CYP26 expression or activity. Nevertheless, data is emerging describing a variety of human genetic variations in the CYP26 enzymes that are associated with different pathologies. Interestingly, some of these genetic variants result in increased activity of the CYP26 enzymes potentially leading to complex gene-environment interactions due to variability in dietary intake of retinoids. This review highlights the current knowledge of structure-function of CYP26 enzymes and focuses on their role in human retinoid metabolism in different tissues.
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Affiliation(s)
- Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA.
| | - Guo Zhong
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
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9
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Lopes F, Torres F, Soares G, Barbosa M, Silva J, Duque F, Rocha M, Sá J, Oliveira G, Sá MJ, Temudo T, Sousa S, Marques C, Lopes S, Gomes C, Barros G, Jorge A, Rocha F, Martins C, Mesquita S, Loureiro S, Cardoso EM, Cálix MJ, Dias A, Martins C, Mota CR, Antunes D, Dupont J, Figueiredo S, Figueiroa S, Gama-de-Sousa S, Cruz S, Sampaio A, Eijk P, Weiss MM, Ylstra B, Rendeiro P, Tavares P, Reis-Lima M, Pinto-Basto J, Fortuna AM, Maciel P. Genomic imbalances defining novel intellectual disability associated loci. Orphanet J Rare Dis 2019; 14:164. [PMID: 31277718 PMCID: PMC6612161 DOI: 10.1186/s13023-019-1135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/12/2019] [Indexed: 11/29/2022] Open
Abstract
Background High resolution genome-wide copy number analysis, routinely used in clinical diagnosis for several years, retrieves new and extremely rare copy number variations (CNVs) that provide novel candidate genes contributing to disease etiology. The aim of this work was to identify novel genetic causes of neurodevelopmental disease, inferred from CNVs detected by array comparative hybridization (aCGH), in a cohort of 325 Portuguese patients with intellectual disability (ID). Results We have detected CNVs in 30.1% of the patients, of which 5.2% corresponded to novel likely pathogenic CNVs. For these 11 rare CNVs (which encompass novel ID candidate genes), we identified those most likely to be relevant, and established genotype-phenotype correlations based on detailed clinical assessment. In the case of duplications, we performed expression analysis to assess the impact of the rearrangement. Interestingly, these novel candidate genes belong to known ID-related pathways. Within the 8% of patients with CNVs in known pathogenic loci, the majority had a clinical presentation fitting the phenotype(s) described in the literature, with a few interesting exceptions that are discussed. Conclusions Identification of such rare CNVs (some of which reported for the first time in ID patients/families) contributes to our understanding of the etiology of ID and for the ever-improving diagnosis of this group of patients. Electronic supplementary material The online version of this article (10.1186/s13023-019-1135-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fátima Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Fátima Torres
- CGC Genetics, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Gabriela Soares
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Mafalda Barbosa
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,The Mindich Child Health & Development Institute and the Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - João Silva
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Frederico Duque
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Rocha
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Medical Genetics Unit, Hospital de Braga, Braga, Portugal
| | - Joaquim Sá
- CGC Genetics, Porto, Portugal.,Department of Medical Genetics, Hospital de Faro, Faro, Portugal
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Maria João Sá
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Teresa Temudo
- Pediatric Neurology Department, Centro Materno-Infantil Centro Hospitalar do Porto, Porto, Portugal
| | - Susana Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Carla Marques
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal
| | - Sofia Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Catarina Gomes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gisela Barros
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Arminda Jorge
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal.,CICS - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Felisbela Rocha
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Cecília Martins
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sandra Mesquita
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal
| | - Susana Loureiro
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Elisa Maria Cardoso
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Maria José Cálix
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Andreia Dias
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Cristina Martins
- Neuropaediatric Unit - Garcia de Orta Hospital, Almada, Portugal
| | - Céu R Mota
- Pediatric and Neonatal Intensive Care, Department of Pediatrics, Porto Hospital Center, Porto, Portugal
| | - Diana Antunes
- Department of Genetics, Hospital D. Estefânia, Lisboa-Norte Hospital Center, Lisbon, Portugal
| | - Juliette Dupont
- Genetics Service, Paediatric Department, University Hospital Santa Maria, Lisbon, Portugal
| | - Sara Figueiredo
- Department of Pediatrics, Médio Ave Hospital Center, Santo Tirso, Portugal
| | - Sónia Figueiroa
- Division of Pediatric Neurology, Department of Child and Adolescent, Centro Hospitalar do Porto e Hospital de Santo António, Porto, Portugal
| | - Susana Gama-de-Sousa
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sara Cruz
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Adriana Sampaio
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Paul Eijk
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | | | | | - Margarida Reis-Lima
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,GDPN- SYNLAB, Porto, Portugal
| | | | - Ana Maria Fortuna
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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10
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Zhong G, Hogarth C, Snyder JM, Palau L, Topping T, Huang W, Czuba LC, LaFrance J, Ghiaur G, Isoherranen N. The retinoic acid hydroxylase Cyp26a1 has minor effects on postnatal vitamin A homeostasis, but is required for exogenous atRA clearance. J Biol Chem 2019; 294:11166-11179. [PMID: 31167781 DOI: 10.1074/jbc.ra119.009023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/01/2019] [Indexed: 12/20/2022] Open
Abstract
The all-trans-retinoic acid (atRA) hydroxylase Cyp26a1 is essential for embryonic development and may play a key role in regulating atRA clearance also in adults. We hypothesized that loss of Cyp26a1 activity via inducible knockout in juvenile or adult mice would result in decreased atRA clearance and increased tissue atRA concentrations and atRA-related adverse effects. To test these hypotheses, Cyp26a1 was knocked out in juvenile and adult male and female Cyp26a1 floxed mice using standard Cre-Lox technology and tamoxifen injections. Biochemical and histological methods were used to study the effects of global Cyp26a1 knockout. The Cyp26a1 knockout did not result in consistent histopathological changes in any major organs. Cyp26a1 -/- mice gained weight normally and exhibited no adverse phenotypes for up to 1 year after loss of Cyp26a1 expression. Similarly, atRA concentrations were not increased in the liver, testes, spleen, or serum of these mice, and the Cyp26a1 knockout did not cause compensatory induction of lecithin:retinol acetyltransferase (Lrat) or retinol dehydrogenase 11 (Rdh11) mRNA or a decrease in aldehyde dehydrogenase 1a1 (Aldh1a1) mRNA in the liver compared with tamoxifen-treated controls. However, the Cyp26a1 -/- mice showed increased bone marrow cellularity and decreased frequency of erythroid progenitor cells in the bone marrow consistent with a retinoid-induced myeloid skewing of hematopoiesis. In addition, the Cyp26a1 knockout decreased clearance of exogenous atRA by 70% and increased atRA half-life 6-fold. These findings demonstrate that despite lacking a major impact on endogenous atRA signaling, Cyp26a1 critically contributes as a barrier for exogenous atRA exposure.
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Affiliation(s)
- Guo Zhong
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington 98195
| | - Cathryn Hogarth
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164
| | - Jessica M Snyder
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, Washington 98195
| | - Laura Palau
- School of Medicine, The Johns Hopkins University, Baltimore, Maryland 21231
| | - Traci Topping
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164
| | - Weize Huang
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington 98195
| | - Lindsay C Czuba
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington 98195
| | - Jeffrey LaFrance
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington 98195
| | - Gabriel Ghiaur
- School of Medicine, The Johns Hopkins University, Baltimore, Maryland 21231
| | - Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington 98195
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11
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Barbalho SM, Goulart RDA, Batista GLDSA. Vitamin A and inflammatory bowel diseases: from cellular studies and animal models to human disease. Expert Rev Gastroenterol Hepatol 2019; 13:25-35. [PMID: 30791845 DOI: 10.1080/17474124.2019.1543588] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Vitamin A (VA) and metabolites such as Retinoic Acid (RA) and all-trans-RA (at-RA) are crucial in the modulation of the immune system and may be determinative in the balance of the immune responses. Inflammatory bowel diseases (IBD) consist of chronic relapsing and heterogeneous disorders with not well-known etiology. Due to its role in inflammatory processes, VA may be helpful in the treatment of IBD. Area covered: As VA plays a significant role in the inflammatory processes, this review aims to show the potential role of this vitamin in IBD, searching for cellular studies, animal models, and studies with humans. Expert commentary: Many studies have described the importance of alternative therapeutic approaches for IBD. Due to its role in the immune system, VA may also exert an indispensable role in the IBD. Nevertheless, some authors have shown that these compounds could stimulate the release of pro-inflammatory cytokines. For these reasons, more studies should be performed to establish the precise mechanisms of VA and its metabolites in systemic and intestinal inflammation.
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Affiliation(s)
- Sandra Maria Barbalho
- a School of Medicine , University of Marília (UNIMAR) , São Paulo , Brazil.,b Department of Biochemistry and Nutrition , Faculty of Food Technology of Marília (FATEC) , São Paulo , Brazil
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12
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Lobo GP, Fulmer D, Guo L, Zuo X, Dang Y, Kim SH, Su Y, George K, Obert E, Fogelgren B, Nihalani D, Norris RA, Rohrer B, Lipschutz JH. The exocyst is required for photoreceptor ciliogenesis and retinal development. J Biol Chem 2017; 292:14814-14826. [PMID: 28729419 DOI: 10.1074/jbc.m117.795674] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/10/2017] [Indexed: 11/06/2022] Open
Abstract
We previously have shown that the highly conserved eight-protein exocyst trafficking complex is required for ciliogenesis in kidney tubule cells. We hypothesized here that ciliogenic programs are conserved across organs and species. To determine whether renal primary ciliogenic programs are conserved in the eye, and to characterize the function and mechanisms by which the exocyst regulates eye development in zebrafish, we focused on exoc5, a central component of the exocyst complex, by analyzing both exoc5 zebrafish mutants, and photoreceptor-specific Exoc5 knock-out mice. Two separate exoc5 mutant zebrafish lines phenocopied exoc5 morphants and, strikingly, exhibited a virtual absence of photoreceptors, along with abnormal retinal development and cell death. Because the zebrafish mutant was a global knockout, we also observed defects in several ciliated organs, including the brain (hydrocephalus), heart (cardiac edema), and kidney (disordered and shorter cilia). exoc5 knockout increased phosphorylation of the regulatory protein Mob1, consistent with Hippo pathway activation. exoc5 mutant zebrafish rescue with human EXOC5 mRNA completely reversed the mutant phenotype. We accomplished photoreceptor-specific knockout of Exoc5 with our Exoc5 fl/fl mouse line crossed with a rhodopsin-Cre driver line. In Exoc5 photoreceptor-specific knock-out mice, the photoreceptor outer segment structure was severely impaired at 4 weeks of age, although a full-field electroretinogram indicated a visual response was still present. However, by 6 weeks, visual responses were eliminated. In summary, we show that ciliogenesis programs are conserved in the kidneys and eyes of zebrafish and mice and that the exocyst is necessary for photoreceptor ciliogenesis and retinal development, most likely by trafficking cilia and outer-segment proteins.
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Affiliation(s)
- Glenn P Lobo
- From the Departments of Medicine.,Ophthalmology, and
| | - Diana Fulmer
- From the Departments of Medicine.,Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Lilong Guo
- From the Departments of Medicine.,Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | | | | | | | | | | | | | - Ben Fogelgren
- the Department of Anatomy, Biochemistry, and Physiology, University of Hawaii at Manoa, Honolulu, Hawaii 96813
| | | | - Russell A Norris
- Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Bärbel Rohrer
- Ophthalmology, and.,the Division of Research, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina 29401, and
| | - Joshua H Lipschutz
- From the Departments of Medicine, .,the Department of Medicine, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina 29425
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13
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Qiao Y, Badduke C, Tang F, Cowieson D, Martell S, Lewis SME, Peñaherrera MS, Robinson WP, Volchuk A, Rajcan-Separovic E. Whole exome sequencing of families with 1q21.1 microdeletion or microduplication. Am J Med Genet A 2017; 173:1782-1791. [DOI: 10.1002/ajmg.a.38247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/16/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Ying Qiao
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
| | - Chansonette Badduke
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
| | - Flamingo Tang
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
| | - David Cowieson
- Division of Advanced Diagnostics-Metabolism Toronto General Research Institute; University Health Network; Toronto Ontario Canada
| | - Sally Martell
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
| | | | - Maria S. Peñaherrera
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
- Department of Medical Genetics; UBC; Vancouver British Columbia Canada
| | - Wendy P. Robinson
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
- Department of Medical Genetics; UBC; Vancouver British Columbia Canada
| | - Allen Volchuk
- Keenan Research Centre for Biomedical Science; St. Michael's Hospital; Toronto Ontario Canada
| | - Evica Rajcan-Separovic
- Department of Pathology; University of British Columbia (UBC); Vancouver British Columbia Canada
- BC Children's Hospital Research Institute; Vancouver British Columbia Canada
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14
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Zhang X, Chu Q, Guo G, Dong G, Li X, Zhang Q, Zhang S, Zhang Z, Wang Y. Genome-wide association studies identified multiple genetic loci for body size at four growth stages in Chinese Holstein cattle. PLoS One 2017; 12:e0175971. [PMID: 28426785 PMCID: PMC5398616 DOI: 10.1371/journal.pone.0175971] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022] Open
Abstract
The growth and maturity of cattle body size affect not only feed efficiency, but also productivity and longevity. Dissecting the genetic architecture of body size is critical for cattle breeding to improve both efficiency and productivity. The volume and weight of body size are indicated by several measurements. Among them, Heart Girth (HG) and Hip Height (HH) are the most important traits. They are widely used as predictors of body weight (BW). Few association studies have been conducted for HG and HH in cattle focusing on single growth stage. In this study, we extended the Genome-wide association studies to a full spectrum of four growth stages (6-, 12-, 18-, and 24-months after birth) in Chinese Holstein heifers. The whole genomic single nucleotide polymorphisms (SNPs) were obtained from the Illumina BovineSNP50 v2 BeadChip genotyped on 3,325 individuals. Estimated breeding values (EBVs) were derived for both HG and HH at the four different ages and analyzed separately for GWAS by using the Fixed and random model Circuitous Probability Unification (FarmCPU) method. In total, 27 SNPs were identified to be significantly associated with HG and HH at different growth stages. We found 66 candidate genes located nearby the associated SNPs, including nine genes that were known as highly related to development and skeletal and muscular growth. In addition, biological function analysis was performed by Ingenuity Pathway Analysis and an interaction network related to development was obtained, which contained 16 genes out of the 66 candidates. The set of putative genes provided valuable resources and can help elucidate the genomic architecture and mechanisms underlying growth traits in dairy cattle.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P.R. China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Ganghui Dong
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Xizhi Li
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Qin Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Shengli Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail: (YW); (ZZ)
| | - Yachun Wang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
- * E-mail: (YW); (ZZ)
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15
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Nilsson O, Isoherranen N, Guo MH, Lui JC, Jee YH, Guttmann-Bauman I, Acerini C, Lee W, Allikmets R, Yanovski JA, Dauber A, Baron J. Accelerated Skeletal Maturation in Disorders of Retinoic Acid Metabolism: A Case Report and Focused Review of the Literature. Horm Metab Res 2016; 48:737-744. [PMID: 27589347 PMCID: PMC5534175 DOI: 10.1055/s-0042-114038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nutritional excess of vitamin A, a precursor for retinoic acid (RA), causes premature epiphyseal fusion, craniosynostosis, and light-dependent retinopathy. Similarly, homozygous loss-of-function mutations in CYP26B1, one of the major RA-metabolizing enzymes, cause advanced bone age, premature epiphyseal fusion, and craniosynostosis. In this paper, a patient with markedly accelerated skeletal and dental development, retinal scarring, and autism-spectrum disease is presented and the role of retinoic acid in longitudinal bone growth and skeletal maturation is reviewed. Genetic studies were carried out using SNP array and exome sequencing. RA isomers were measured in the patient, family members, and in 18 age-matched healthy children using high-performance liquid chromatography coupled to tandem mass spectrometry. A genomic SNP array identified a novel 8.3 megabase microdeletion on chromosome 10q23.2-23.33. The 79 deleted genes included CYP26A1 and C1, both major RA-metabolizing enzymes. Exome sequencing did not detect any variants that were predicted to be deleterious in the remaining alleles of these genes or other known retinoic acid-metabolizing enzymes. The patient exhibited elevated plasma total RA (16.5 vs. 12.6±1.5 nM, mean±SD, subject vs. controls) and 13-cisRA (10.7 nM vs. 6.1±1.1). The findings support the hypothesis that elevated RA concentrations accelerate bone and dental maturation in humans. CYP26A1 and C1 haploinsufficiency may contribute to the elevated retinoic acid concentrations and clinical findings of the patient, although this phenotype has not been reported in other patients with similar deletions, suggesting that other unknown genetic or environmental factors may also contribute.
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Affiliation(s)
- Ola Nilsson
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Center for Molecular Medicine and Pediatric Endocrinology Unit, Department of Women’s and Children’s Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Nina Isoherranen
- Department of Pharmaceutics School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Michael H. Guo
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Julian C. Lui
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Youn Hee Jee
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ines Guttmann-Bauman
- Harold Schnitzer Diabetes Health Center, Oregon Health and Science University, Portland, OR, USA
| | - Carlo Acerini
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jack A. Yanovski
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Dauber
- Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jeffrey Baron
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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16
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Girisha KM, Kortüm F, Shah H, Alawi M, Dalal A, Bhavani GS, Kutsche K. A novel multiple joint dislocation syndrome associated with a homozygous nonsense variant in the EXOC6B gene. Eur J Hum Genet 2016; 24:1206-10. [PMID: 26669664 PMCID: PMC4970677 DOI: 10.1038/ejhg.2015.261] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/04/2015] [Accepted: 11/15/2015] [Indexed: 01/12/2023] Open
Abstract
We report two brothers from a consanguineous couple with spondyloepimetaphyseal dysplasia (SEMD), multiple joint dislocations at birth, severe joint laxity, scoliosis, gracile metacarpals and metatarsals, delayed bone age and poorly ossified carpal and tarsal bones, probably representing a yet uncharacterized SEMD with laxity and dislocations. This condition has clinical overlap with autosomal dominantly inherited SEMD with joint laxity, leptodactylic type caused by recurrent missense variants in the kinesin family member 22 gene (KIF22). Single-nucleotide polymorphism array analysis and whole-exome sequencing in the two affected siblings revealed a shared homozygous nonsense variant [c.906T>A/p.(Tyr302*)] in EXOC6B as the most likely cause. EXOC6B encodes a component of the exocyst complex required for tethering secretory vesicles to the plasma membrane. As transport of vesicles from the golgi apparatus to the plasma membrane occurs through kinesin motor proteins along microtubule tracks, the function of EXOC6B is linked to KIF22 suggesting a common pathogenic mechanism in skeletal dysplasias with joint laxity and dislocations.
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Affiliation(s)
- Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hitesh Shah
- Division of Pediatric Orthopedics, Department of Orthopedics, Kasturba Medical College, Manipal University, Manipal, India
| | - Malik Alawi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Service Facility, Hamburg, Germany
- Center for Bioinformatics, University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz-Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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17
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Peng Y, Lee J, Rowland K, Wen Y, Hua H, Carlson N, Lavania S, Parrish JZ, Kim MD. Regulation of dendrite growth and maintenance by exocytosis. J Cell Sci 2015; 128:4279-92. [PMID: 26483382 DOI: 10.1242/jcs.174771] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/08/2015] [Indexed: 01/07/2023] Open
Abstract
Dendrites lengthen by several orders of magnitude during neuronal development, but how membrane is allocated in dendrites to facilitate this growth remains unclear. Here, we report that Ras opposite (Rop), the Drosophila ortholog of the key exocytosis regulator Munc18-1 (also known as STXBP1), is an essential factor mediating dendrite growth. Neurons with depleted Rop function exhibit reduced terminal dendrite outgrowth followed by primary dendrite degeneration, suggestive of differential requirements for exocytosis in the growth and maintenance of different dendritic compartments. Rop promotes dendrite growth together with the exocyst, an octameric protein complex involved in tethering vesicles to the plasma membrane, with Rop-exocyst complexes and exocytosis predominating in primary dendrites over terminal dendrites. By contrast, membrane-associated proteins readily diffuse from primary dendrites into terminals, but not in the reverse direction, suggesting that diffusion, rather than targeted exocytosis, supplies membranous material for terminal dendritic growth, revealing key differences in the distribution of materials to these expanding dendritic compartments.
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Affiliation(s)
- Yun Peng
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Jiae Lee
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Kimberly Rowland
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Yuhui Wen
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Hope Hua
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Nicole Carlson
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Shweta Lavania
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Michael D Kim
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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18
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Role of Retinoic Acid-Metabolizing Cytochrome P450s, CYP26, in Inflammation and Cancer. ADVANCES IN PHARMACOLOGY 2015; 74:373-412. [PMID: 26233912 DOI: 10.1016/bs.apha.2015.04.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Vitamin A (retinol) and its active metabolite, all-trans-retinoic acid (atRA), play critical roles in regulating the differentiation, growth, and migration of immune cells. Similarly, as critical signaling molecules in the regulation of the cell cycle, retinoids are important in cancers. Concentrations of atRA are tightly regulated in tissues, predominantly by the availability of retinol, synthesis of atRA by ALDH1A enzymes and metabolism and clearance of atRA by CYP26 enzymes. The ALDH1A and CYP26 enzymes are expressed in several cell types in the immune system and in cancer cells. In the immune system, the ALDH1A and CYP26 enzymes appear to modulate RA concentrations. Consequently, alterations in the activity of ALDH1A and CYP26 enzymes are expected to change disease outcomes in inflammation. There is increasing evidence from various disease models of intestinal and skin inflammation that treatment with atRA has a positive effect on disease markers. However, whether aberrant atRA concentrations or atRA synthesis and metabolism play a role in inflammatory disease development and progression is not well understood. In cancers, especially in acute promyelocytic leukemia and neuroblastoma, increasing intracellular concentrations of atRA appears to provide clinical benefit. Inhibition of the CYP26 enzymes to increase atRA concentrations and combat therapy resistance has been pursued as a drug target in these cancers. This chapter covers the current knowledge of how atRA and retinol regulate the immune system and inflammation, how retinol and atRA metabolism is altered in inflammation and cancer, and what roles atRA-metabolizing enzymes have in immune responses and cancers.
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Wen J, Hanna CW, Martell S, Leung PC, Lewis SM, Robinson WP, Stephenson MD, Rajcan-Separovic E. Functional consequences of copy number variants in miscarriage. Mol Cytogenet 2015; 8:6. [PMID: 25674159 PMCID: PMC4324423 DOI: 10.1186/s13039-015-0109-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/09/2015] [Indexed: 02/01/2023] Open
Abstract
Background The presence of unique copy number variations (CNVs) in miscarriages suggests that their integral genes have a role in maintaining early pregnancy. In our previous work, we identified 19 unique CNVs in ~40% of studied euploid miscarriages, which were predominantly familial in origin. In our current work, we assessed their relevance to miscarriage by expression analysis of 14 genes integral to CNVs in available miscarriage chorionic villi. As familial CNVs could cause miscarriage due to imprinting effect, we investigated the allelic expression of one of the genes (TIMP2) previously suggested to be maternally expressed in placenta and involved in placental remodelling and embryo development. Results Six out of fourteen genes had detectable expression in villi and for three genes the RNA and protein expression was altered due to maternal CNVs. These genes were integral to duplication on Xp22.2 (TRAPPC2 and OFD1) or disrupted by a duplication mapping to 17q25.3 (TIMP2). RNA and protein expression was increased for TRAPPC2 and OFD1 and reduced for TIMP2 in carrier miscarriages. The three genes have roles in processes important for pregnancy development such as extracellular matrix homeostasis (TIMP2 and TRAPPC2) and cilia function (OFD1). TIMP2 allelic expression was not affected by the CNV in miscarriages in comparison to control elective terminations. Conclusion We propose that functional studies of CNVs could help determine if and how the miscarriage CNVs affect the expression of integral genes. In case of parental CNVs, assessment of the function of their integral genes in parental reproductive tissues should be also considered in the future, especially if they affect processes relevant for pregnancy development and support. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0109-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiadi Wen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5 Canada.,Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
| | - Courtney W Hanna
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Sally Martell
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
| | - Peter Ck Leung
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, V6Z 2 K5 Canada
| | - Suzanne Me Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Wendy P Robinson
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Mary D Stephenson
- Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, 60612 USA
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5 Canada.,Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
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Benítez-Burraco A, Boeckx C. FOXP2, retinoic acid, and language: a promising direction. Front Cell Neurosci 2014; 8:387. [PMID: 25431551 PMCID: PMC4230053 DOI: 10.3389/fncel.2014.00387] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 10/30/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Cedric Boeckx
- Catalan Institute for Advanced Studies and Research (ICREA) Barcelona, Spain ; Department of Linguistics, Universitat de Barcelona Barcelona, Spain
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Boeckx C, Benítez-Burraco A. Globularity and language-readiness: generating new predictions by expanding the set of genes of interest. Front Psychol 2014; 5:1324. [PMID: 25505436 PMCID: PMC4243498 DOI: 10.3389/fpsyg.2014.01324] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022] Open
Abstract
This study builds on the hypothesis put forth in Boeckx and Benítez-Burraco (2014), according to which the developmental changes expressed at the levels of brain morphology and neural connectivity that resulted in a more globular braincase in our species were crucial to understand the origins of our language-ready brain. Specifically, this paper explores the links between two well-known 'language-related' genes like FOXP2 and ROBO1 implicated in vocal learning and the initial set of genes of interest put forth in Boeckx and Benítez-Burraco (2014), with RUNX2 as focal point. Relying on the existing literature, we uncover potential molecular links that could be of interest to future experimental inquiries into the biological foundations of language and the testing of our initial hypothesis. Our discussion could also be relevant for clinical linguistics and for the interpretation of results from paleogenomics.
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Affiliation(s)
- Cedric Boeckx
- Catalan Institute for Advanced Studies and Research (ICREA)Barcelona, Spain
- Department of Linguistics, Universitat de BarcelonaBarcelona, Spain
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Evers C, Maas B, Koch KA, Jauch A, Janssen JWG, Sutter C, Parker MJ, Hinderhofer K, Moog U. Mosaic deletion of EXOC6B: further evidence for an important role of the exocyst complex in the pathogenesis of intellectual disability. Am J Med Genet A 2014; 164A:3088-94. [PMID: 25256811 DOI: 10.1002/ajmg.a.36770] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 08/07/2014] [Indexed: 12/21/2022]
Abstract
We describe a boy with developmental delay, speech delay, and minor dysmorphic features with a heterozygous de novo ∼460 kb deletion at 2p13.2 involving only parts of EXOC6B present in about 50% of lymphocytes. This widely expressed gene encodes the exocyst component 6B, which is part of a multiprotein complex required for targeted exocytosis. Little is known about the effect of EXOC6B haploinsufficiency. In 2008, a patient with a complex syndromic phenotype, including left renal agenesis, neutropenia, recurrent pulmonary infections, long bone diaphysis broadening, growth retardation, and developmental delay (DD) was found to carry a de novo translocation t(2;7) involving TSN3 and EXOC6B. Further characterization of the translocation indicated that disruption of TSN3 may be responsible for the skeletal phenotype. Recently, a heterozygous deletion of EXOC6B along with a deletion of the CYP26B1 gene has been reported in a boy with intellectual disability, speech delay, hyperactivity, facial asymmetry, a dysplastic ear, brachycephaly, and mild joint contractures. Additionally, disruption of EXOC6B by a de novo balanced translocation t(2;8) has been described in a patient with developmental delay, epilepsy, autistic and aggressive behavior. This is the first report of a de novo deletion affecting only EXOC6B in an individual with developmental delay. In conclusion, based on our findings and recent data from the literature, there is evidence that EXOC6B and the exocyst complex might play an important role in the molecular pathogenesis of intellectual disability.
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Affiliation(s)
- Christina Evers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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