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Kossack ME, Manz KE, Martin NR, Pennell KD, Plavicki J. Environmentally relevant uptake, elimination, and metabolic changes following early embryonic exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin in zebrafish. CHEMOSPHERE 2023; 310:136723. [PMID: 36241106 PMCID: PMC9835613 DOI: 10.1016/j.chemosphere.2022.136723] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 06/03/2023]
Abstract
Dioxin and dioxin-like compounds are ubiquitous environmental contaminants that induce toxicity by binding to the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor. The zebrafish model has been used to define the developmental toxicity observed following exposure to exogenous AHR ligands such as the potent agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin, TCDD). While the model has successfully identified cellular targets of TCDD and molecular mechanisms mediating TCDD-induced phenotypes, fundamental information such as the body burden produced by standard exposure models is still unknown. We performed targeted gas chromatography (GC) high-resolution mass spectrometry (HRMS) in tandem with non-targeted liquid chromatography (LC) HRMS to quantify TCDD uptake, model the elimination dynamics of TCDD, and determine how TCDD exposure affects the zebrafish metabolome. We found that 50 ppt, 10 ppb, and 1 ppb waterborne exposures to TCDD during early embryogenesis produced environmentally relevant body burdens: 38 ± 4.34, 26.6 ± 1.2, and 8.53 ± 0.341 pg/embryo, respectively, at 24 hours post fertilization. TCDD exposure was associated with the dysregulation of metabolic pathways that are associated with the AHR signaling pathway as well as pathways shown to be affected in mammals following TCDD exposure. In addition, we discovered that TCDD exposure affected several metabolic pathways that are critical for brain development and function including glutamate metabolism, chondroitin sulfate biosynthesis, and tyrosine metabolism. Together, these data demonstrate that existing exposure methods produce environmentally relevant body burdens of TCDD in zebrafish and provide insight into the biochemical pathways impacted by toxicant-induced AHR activation.
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Affiliation(s)
- Michelle E Kossack
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Katherine E Manz
- School of Engineering, Brown University, 184 Hope St, Box D, Providence, RI, 02903, USA
| | - Nathan R Martin
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Kurt D Pennell
- School of Engineering, Brown University, 184 Hope St, Box D, Providence, RI, 02903, USA
| | - Jessica Plavicki
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA.
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A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome. Hum Genet 2021; 141:217-227. [PMID: 34821995 DOI: 10.1007/s00439-021-02403-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Cooks syndrome (CS) is an ultrarare limb malformation due to in tandem microduplications involving KCNJ2 and extending to the 5' regulatory element of SOX9. To date, six CS families were resolved at the molecular level. Subsequent studies explored the evolutionary and pathological complexities of the SOX9-KCNJ2/Sox9-Kcnj2 locus, and suggested a key role for the formation of novel topologically associating domain (TAD) by inter-TAD duplications in causing CS. Here, we report a unique case of CS associated with a de novo 1;17 translocation affecting the KCNJ2 locus. On chromosome 17, the breakpoint mapped between KCNJ16 and KCNJ2, and combined with a ~ 5 kb deletion in the 5' of KCNJ2. Based on available capture Hi-C data, the breakpoint on chromosome 17 separated KCNJ2 from a putative enhancer. Gene expression analysis demonstrated downregulation of KCNJ2 in both patient's blood cells and cultured skin fibroblasts. Our findings suggest that a complex rearrangement falling in the 5' of KCNJ2 may mimic the developmental consequences of in tandem duplications affecting the SOX9-KCNJ2/Sox9-Kcnj2 locus. This finding adds weight to the notion of an intricate role of gene regulatory regions and, presumably, the related three-dimensional chromatin structure in normal and abnormal human morphology.
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Varadarajan S, Balaji TM, Raj AT, Gupta AA, Patil S, Alhazmi TH, Alaqi HAA, Al Omar NEM, Almutaher SABA, Jafer AA, Hedad IA. Genetic Mutations Associated with Pierre Robin Syndrome/Sequence: A Systematic Review. Mol Syndromol 2021; 12:69-86. [PMID: 34012376 DOI: 10.1159/000513217] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/20/2020] [Indexed: 01/16/2023] Open
Abstract
Pierre Robin syndrome/sequence (PRS) is associated with a triad of symptoms that includes micrognathia, cleft palate, and glossoptosis that may lead to respiratory obstruction. The syndrome occurs in 2 forms: nonsyndromic PRS (nsPRS), and PRS associated with other syndromes (sPRS). Studies have shown varying genetic mutations associated with both nsPRS and sPRS. The present systematic review aims to provide a comprehensive collection of published literature reporting genetic mutations in PRS. Web of Science, PubMed, and Scopus were searched using the keywords: "Pierre Robin syndrome/sequence AND gene mutation." The search resulted in 208 articles, of which 93 were excluded as they were duplicates/irrelevant. The full-text assessment led to the further exclusion of 76 articles. From the remaining 39 articles included in the review, details of 324 cases were extracted. 56% of the cases were sPRS, and 22% of the cases were associated with other malformations and the remaining were nsPRS. Genetic mutations were noted in 30.9% of the 300 cases. Based on the review, SOX9 was found to be the most common gene associated with both nsPRS and sPRS. The gene mutation in sPRS was specific to the associated syndrome. Due to the lack of original studies, a quantitative analysis was not possible. Thus, future studies must focus on conducting large-scale cohort studies. Along with generating data on genetic mutation, future studies must also conduct pedigree analysis to assess potential familial inheritance, which in turn could provide valuable insights into the etiopathogenesis of PRS.
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Affiliation(s)
- Saranya Varadarajan
- Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai, India
| | | | - A Thirumal Raj
- Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai, India
| | - Archana A Gupta
- Department of Oral Pathology and Microbiology, Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pune, India
| | - Shankargouda Patil
- Division of Oral Pathology, Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Tariq Hassan Alhazmi
- Community Dental Unit, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | - Neda Essa M Al Omar
- Community Dental Unit, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | | | - Ismaeel Abker Hedad
- Community Dental Unit, College of Dentistry, Jazan University, Jazan, Saudi Arabia
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Logjes RJH, Breugem CC, Van Haaften G, Paes EC, Sperber GH, van den Boogaard MJH, Farlie PG. The ontogeny of Robin sequence. Am J Med Genet A 2018; 176:1349-1368. [PMID: 29696787 DOI: 10.1002/ajmg.a.38718] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 12/17/2017] [Accepted: 03/23/2018] [Indexed: 02/06/2023]
Abstract
The triad of micrognathia, glossoptosis, and concomitant airway obstruction defined as "Robin sequence" (RS) is caused by oropharyngeal developmental events constrained by a reduced stomadeal space. This sequence of abnormal embryonic development also results in an anatomical configuration that might predispose the fetus to a cleft palate. RS is heterogeneous and many different etiologies have been described including syndromic, RS-plus, and isolated forms. For an optimal diagnosis, subsequent treatment and prognosis, a thorough understanding of the embryology and pathogenesis is necessary. This manuscript provides an update about our current understanding of the development of the mandible, tongue, and palate and possible mechanisms involved in the development of RS. Additionally, we provide the reader with an up-to-date summary of the different etiologies of this phenotype and link this to the embryologic, developmental, and genetic mechanisms.
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Affiliation(s)
- Robrecht J H Logjes
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Corstiaan C Breugem
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Gijs Van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emma C Paes
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Geoffrey H Sperber
- Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | | | - Peter G Farlie
- Royal Children's Hospital, Murdoch Children's Research Institute, Parkville, Australia
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Di Pasquo E, Amiel J, Roth P, Malan V, Lind K, Chalouhi C, Soupre V, Gordon CT, Lyonnet S, Salomon LJ, Abadie V. Efficiency of prenatal diagnosis in Pierre Robin sequence. Prenat Diagn 2017; 37:1169-1175. [DOI: 10.1002/pd.5162] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/13/2017] [Accepted: 09/19/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Elvira Di Pasquo
- Gynecology and Obstetrics Unit, Prenatal Diagnosis Centre; Necker Hospital; Paris France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité University; Paris France
| | - Philippe Roth
- Gynecology and Obstetrics Unit, Prenatal Diagnosis Centre; Necker Hospital; Paris France
| | - Valérie Malan
- Cytogenetics Laboratory; Necker Hospital; Paris France
| | - Katia Lind
- General Pediatrics Department and Rare Disease Reference Centre “Syndrome de Pierre Robin et Troubles de Succion Déglutition Congénitaux”; Necker Hospital; Paris France
| | - Christel Chalouhi
- General Pediatrics Department and Rare Disease Reference Centre “Syndrome de Pierre Robin et Troubles de Succion Déglutition Congénitaux”; Necker Hospital; Paris France
| | | | - Christopher T. Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité University; Paris France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité University; Paris France
| | - Laurent J. Salomon
- Gynecology and Obstetrics Unit, Prenatal Diagnosis Centre; Necker Hospital; Paris France
- Paris Descartes-Sorbonne Paris Cité University; Paris France
| | - Véronique Abadie
- Paris Descartes-Sorbonne Paris Cité University; Paris France
- General Pediatrics Department and Rare Disease Reference Centre “Syndrome de Pierre Robin et Troubles de Succion Déglutition Congénitaux”; Necker Hospital; Paris France
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Thieme F, Ludwig K. The Role of Noncoding Genetic Variation in Isolated Orofacial Clefts. J Dent Res 2017; 96:1238-1247. [DOI: 10.1177/0022034517720403] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past decade, medical genetic research has generated multiple discoveries, many of which were obtained via genome-wide association studies (GWASs). A major GWAS finding is that the majority of risk variants for complex traits map to noncoding regions. This has resulted in a paradigm shift in terms of the interpretation of human genomic sequence variation, with more attention now being paid to what was previously termed “junk DNA.” Translation of genetic findings into biologically meaningful results requires 1) large-scale and cell-specific efforts to annotate non-protein–coding regions and 2) the integration of comprehensive genomic data sets. However, this represents an enormous challenge, particularly in the case of human traits that arise during embryonic development, such as orofacial clefts (OFCs). OFC is a multifactorial trait and ranks among the most common of all human congenital malformations. These 2 attributes apply in particular to its isolated forms (nonsyndromic OFC [nsOFC]). Although genetic studies (including GWASs) have yielded novel insights into the genetic architecture of nsOFC, few data are available concerning causality and affected biological pathways. Reasons for this deficiency include the complex genetic architecture at risk loci and the limited availability of functional data sets from human tissues that represent relevant embryonic sites and time points. The present review summarizes current knowledge of the role of noncoding regions in nsOFC etiology. We describe the identification of genetic risk factors for nsOFC and several of the approaches used to identify causal variants at these loci. These strategies include the use of biological and genetic information from public databases, the assessment of the full spectrum of genetic variability within 1 locus, and comprehensive in vitro and in vivo experiments. This review also highlights the role of the emerging research field “functional genomics” and its increasing contribution to our biological understanding of nsOFC.
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Affiliation(s)
- F. Thieme
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - K.U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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Xu JX, Kilpatrick N, Baker NL, Penington A, Farlie PG, Tan TY. Clinical and Molecular Characterisation of Children with Pierre Robin Sequence and Additional Anomalies. Mol Syndromol 2016; 7:322-328. [PMID: 27920635 DOI: 10.1159/000449115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 12/21/2022] Open
Abstract
Pierre Robin Sequence (PRS) is usually classified into syndromic and nonsyndromic groups, with a further subclassification of the nonsyndromic group into isolated PRS and PRS with additional anomalies (PRS-Plus). The aim of this research is to provide an accurate phenotypic characterisation of nonsyndromic PRS, specifically the PRS-Plus subgroup. We sought to examine the frequency of sequence variants in previously defined conserved noncoding elements (CNEs) in the putative enhancer region upstream of SOX9, the regulation of which has been associated with PRS phenotypes. We identified 141 children with nonsyndromic PRS at the Royal Children's Hospital, Melbourne from 1985 to 2012 using 2 databases. Clinical and demographic data were extracted by file review and children categorized as 'isolated PRS' or 'PRS-Plus'. A subset of children with PRS-Plus was selected for detailed phenotyping and DNA sequencing of the upstream SOX9 CNEs. We found 83 children with isolated PRS and 58 with PRS-Plus. The most common PRS-Plus malformations involved the musculoskeletal and ocular systems. The most common coexisting craniofacial malformation was choanal stenosis/atresia. We identified 10 children with a family history of PRS or cleft palate. We found a single nucleotide substitution in a putative GATA1-binding site in one patient, but it was inherited from his phenotypically unaffected mother. PRS-Plus represents a broad phenotypic spectrum with uncertain pathogenesis. Dysmorphology assessment by a clinical geneticist is recommended. SOX9 CNE sequence variants are rare in our cohort and are unlikely to play a significant role in the pathogenesis of PRS-Plus.
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Affiliation(s)
- Jessie X Xu
- Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Vic., Australia; Department of Paediatrics, University of Melbourne, Melbourne, Vic., Australia
| | - Nicky Kilpatrick
- Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Vic., Australia; Department of Paediatrics, University of Melbourne, Melbourne, Vic., Australia; Royal Children's Hospital, Melbourne, Vic., Australia
| | - Naomi L Baker
- Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Vic., Australia
| | - Anthony Penington
- Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Vic., Australia; Department of Paediatrics, University of Melbourne, Melbourne, Vic., Australia; Royal Children's Hospital, Melbourne, Vic., Australia
| | - Peter G Farlie
- Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Vic., Australia; Department of Paediatrics, University of Melbourne, Melbourne, Vic., Australia
| | - Tiong Yang Tan
- Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Vic., Australia; Department of Paediatrics, University of Melbourne, Melbourne, Vic., Australia; Royal Children's Hospital, Melbourne, Vic., Australia; Victorian Clinical Genetics Services, Melbourne, Vic., Australia
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