1
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Song C, Li T, Zhang C, Li S, Lu S, Zou Y. RA-induced prominence-specific response resulted in distinctive regulation of Wnt and osteogenesis. Life Sci Alliance 2023; 6:e202302013. [PMID: 37541848 PMCID: PMC10403638 DOI: 10.26508/lsa.202302013] [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] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Proper retinoic acid (RA) signaling is essential for normal craniofacial development. Both excessive RA and RA deficiency in early embryonic stage may lead to a variety of craniofacial malformations, for example, cleft palate, which have been investigated extensively. Dysregulated Wnt and Shh signaling were shown to underlie the pathogenesis of RA-induced craniofacial defects. In our present study, we showed a spatiotemporal-specific effect of RA signaling in regulating early development of facial prominences. Although inhibited Wnt activities was observed in E12.5/E13.5 mouse palatal shelves, early exposure of excessive RA induced Wnt signaling and Wnt-related gene expression in E11.5/E12.5 mouse embryonic frontonasal/maxillary processes. A conserved regulatory network of miR-484-Fzd5 was identified to play critical roles in RA-regulated craniofacial development using RNA-seq. In addition, subsequent osteogenic/chondrogenic differentiation were differentially regulated in discrete mouse embryonic facial prominences in response to early RA induction, demonstrated using both in vitro and in vivo analyses.
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Affiliation(s)
- Chao Song
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Ting Li
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Chunlei Zhang
- First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Shufang Li
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Songhui Lu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yi Zou
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
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2
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Ozekin YH, O’Rourke R, Bates EA. Single cell sequencing of the mouse anterior palate reveals mesenchymal heterogeneity. Dev Dyn 2023; 252:713-727. [PMID: 36734036 PMCID: PMC10238667 DOI: 10.1002/dvdy.573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Cleft palate is one of the most prevalent birth defects. Mice are useful for studying palate development because of their morphological and genetic similarities to humans. In mice, palate development occurs between embryonic days (E)11.5 to 15.5. Single cell transcriptional profiles of palate cell populations have been a valuable resource for the craniofacial research community, but we lack a single cell transcriptional profile for anterior palate at E13.5, at the transition from proliferation to shelf elevation. RESULTS A detailed single cell RNA sequencing analysis reveals heterogeneity in expression profiles of the cell populations of the E13.5 anterior palate. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA FISH) reveals epithelial populations segregate into layers. Mesenchymal populations spatially segregate into four domains. One of these mesenchymal populations expresses ligands and receptors distinct from the rest of the mesenchyme, suggesting that these cells have a unique function. RNA velocity analysis shows two terminal cell states that contribute to either the proximal or distal palatal regions emerge from a single progenitor pool. CONCLUSION This single cell resolution expression data and detailed analysis from E13.5 anterior palate provides a powerful resource for mechanistic insight into secondary palate morphogenesis for the craniofacial research community.
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Affiliation(s)
- Yunus H. Ozekin
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rebecca O’Rourke
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emily Anne Bates
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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3
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Dąbrowska J, Biedziak B, Bogdanowicz A, Mostowska A. Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing. J Clin Med 2023; 12:2051. [PMID: 36902838 PMCID: PMC10004578 DOI: 10.3390/jcm12052051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Non-syndromic cleft palate (ns-CP) has a genetically heterogeneous aetiology. Numerous studies have suggested a crucial role of rare coding variants in characterizing the unrevealed component of genetic variation in ns-CP called the "missing heritability". Therefore, this study aimed to detect low-frequency variants that are implicated in ns-CP aetiology in the Polish population. For this purpose, coding regions of 423 genes associated with orofacial cleft anomalies and/or involved with facial development were screened in 38 ns-CP patients using the next-generation sequencing technology. After multistage selection and prioritisation, eight novel and four known rare variants that may influence an individual's risk of ns-CP were identified. Among detected alternations, seven were located in novel candidate genes for ns-CP, including COL17A1 (c.2435-1G>A), DLG1 (c.1586G>C, p.Glu562Asp), NHS (c.568G>C, p.Val190Leu-de novo variant), NOTCH2 (c.1997A>G, p.Tyr666Cys), TBX18 (c.647A>T, p.His225Leu), VAX1 (c.400G>A, p.Ala134Thr) and WNT5B (c.716G>T, p.Arg239Leu). The remaining risk variants were identified within genes previously linked to ns-CP, confirming their contribution to this anomaly. This list included ARHGAP29 (c.1706G>A, p.Arg569Gln), FLNB (c.3605A>G, Tyr1202Cys), IRF6 (224A>G, p.Asp75Gly-de novo variant), LRP6 (c.481C>A, p.Pro161Thr) and TP63 (c.353A>T, p.Asn118Ile). In summary, this study provides further insights into the genetic components contributing to ns-CP aetiology and identifies novel susceptibility genes for this craniofacial anomaly.
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Affiliation(s)
- Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781 Poznan, Poland
| | - Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Agnieszka Bogdanowicz
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781 Poznan, Poland
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4
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Warren EB, Briano JA, Ellegood J, DeYoung T, Lerch JP, Morrow EM. 17q12 deletion syndrome mouse model shows defects in craniofacial, brain and kidney development, and glucose homeostasis. Dis Model Mech 2022; 15:dmm049752. [PMID: 36373506 PMCID: PMC10655816 DOI: 10.1242/dmm.049752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
17q12 deletion (17q12Del) syndrome is a copy number variant (CNV) disorder associated with neurodevelopmental disorders and renal cysts and diabetes syndrome (RCAD). Using CRISPR/Cas9 genome editing, we generated a mouse model of 17q12Del syndrome on both inbred (C57BL/6N) and outbred (CD-1) genetic backgrounds. On C57BL/6N, the 17q12Del mice had severe head development defects, potentially mediated by haploinsufficiency of Lhx1, a gene within the interval that controls head development. Phenotypes included brain malformations, particularly disruption of the telencephalon and craniofacial defects. On the CD-1 background, the 17q12Del mice survived to adulthood and showed milder craniofacial and brain abnormalities. We report postnatal brain defects using automated magnetic resonance imaging-based morphometry. In addition, we demonstrate renal and blood glucose abnormalities relevant to RCAD. On both genetic backgrounds, we found sex-specific presentations, with male 17q12Del mice exhibiting higher penetrance and more severe phenotypes. Results from these experiments pinpoint specific developmental defects and pathways that guide clinical studies and a mechanistic understanding of the human 17q12Del syndrome. This mouse mutant represents the first and only experimental model to date for the 17q12 CNV disorder. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Emily B. Warren
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
| | - Juan A. Briano
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
| | - Jacob Ellegood
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
| | - Taylor DeYoung
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
| | - Jason P. Lerch
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford OX3 9DU, UK
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
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5
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Dąbrowska J, Biedziak B, Szponar-Żurowska A, Budner M, Jagodziński PP, Płoski R, Mostowska A. Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing. Mol Genet Genomics 2022; 297:1315-1327. [PMID: 35778651 DOI: 10.1007/s00438-022-01919-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/12/2022] [Indexed: 01/02/2023]
Abstract
For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.
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Affiliation(s)
- Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Szponar-Żurowska
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Margareta Budner
- Eastern Poland Burn Treatment and Reconstructive Center, Leczna, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland.
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6
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Hirschberger C, Sleight VA, Criswell KE, Clark SJ, Gillis JA. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Mol Biol Evol 2021; 38:4187-4204. [PMID: 33905525 PMCID: PMC8476176 DOI: 10.1093/molbev/msab123] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral (DV) patterning mechanisms within the developing mandibular, hyoid, and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralizing BMP and endothelin signaling pathways and their effectors, the joint markers nkx3.2 and gdf5 and prochondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, whereas differences in notch signaling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the DV axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
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Affiliation(s)
| | - Victoria A Sleight
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.,School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | | | | | - J Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.,Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
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7
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Fu C, Lou S, Zhu G, Fan L, Yu X, Zhu W, Ma L, Wang L, Pan Y. Identification of New miRNA-mRNA Networks in the Development of Non-syndromic Cleft Lip With or Without Cleft Palate. Front Cell Dev Biol 2021; 9:631057. [PMID: 33732700 PMCID: PMC7957012 DOI: 10.3389/fcell.2021.631057] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/18/2021] [Indexed: 12/18/2022] Open
Abstract
Objective: To identify new microRNA (miRNA)-mRNA networks in non-syndromic cleft lip with or without cleft palate (NSCL/P). Materials and Methods: Overlapping differentially expressed miRNAs (DEMs) were selected from cleft palate patients (GSE47939) and murine embryonic orofacial tissues (GSE20880). Next, the target genes of DEMs were predicted by Targetscan, miRDB, and FUNRICH, and further filtered through differentially expressed genes (DEGs) from NSCL/P patients and controls (GSE42589), MGI, MalaCards, and DECIPHER databases. The results were then confirmed by in vitro experiments. NSCL/P lip tissues were obtained to explore the expression of miRNAs and their target genes. Results: Let-7c-5p and miR-193a-3p were identified as DEMs, and their overexpression inhibited cell proliferation and promoted cell apoptosis. PIGA and TGFB2 were confirmed as targets of let-7c-5p and miR-193a-3p, respectively, and were involved in craniofacial development in mice. Negative correlation between miRNA and mRNA expression was detected in the NSCL/P lip tissues. They were also associated with the occurrence of NSCL/P based on the MGI, MalaCards, and DECIPHER databases. Conclusions: Let-7c-5p-PIGA and miR-193a-3p-TGFB2 networks may be involved in the development of NSCL/P.
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Affiliation(s)
- Chengyi Fu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Liwen Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Xin Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Weihao Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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8
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Roth DM, Bayona F, Baddam P, Graf D. Craniofacial Development: Neural Crest in Molecular Embryology. Head Neck Pathol 2021; 15:1-15. [PMID: 33723764 PMCID: PMC8010074 DOI: 10.1007/s12105-021-01301-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/02/2021] [Indexed: 12/22/2022]
Abstract
Craniofacial development, one of the most complex sequences of developmental events in embryology, features a uniquely transient, pluripotent stem cell-like population known as the neural crest (NC). Neural crest cells (NCCs) originate from the dorsal aspect of the neural tube and migrate along pre-determined routes into the developing branchial arches and frontonasal plate. The exceptional rates of proliferation and migration of NCCs enable their diverse contribution to a wide variety of craniofacial structures. Subsequent differentiation of these cells gives rise to cartilage, bones, and a number of mesenchymally-derived tissues. Deficiencies in any stage of differentiation can result in facial clefts and abnormalities associated with craniofacial syndromes. A small number of conserved signaling pathways are involved in controlling NC differentiation and craniofacial development. They are used in a reiterated fashion to help define precise temporospatial cell and tissue formation. Although many aspects of their cellular and molecular control have yet to be described, it is clear that together they form intricately integrated signaling networks required for spatial orientation and developmental stability and plasticity, which are hallmarks of craniofacial development. Mutations that affect the functions of these signaling pathways are often directly or indirectly identified in congenital syndromes. Clinical applications of NC-derived mesenchymal stem/progenitor cells, persistent into adulthood, hold great promise for tissue repair and regeneration. Realization of NCC potential for regenerative therapies motivates understanding of the intricacies of cell communication and differentiation that underlie the complexities of NC-derived tissues.
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Affiliation(s)
- Daniela Marta Roth
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, 7020N Katz Group Centre for Pharmacy & Health Research, 11361-87 Avenue, Edmonton, Alberta, AB T6G 2E1 Canada
| | - Francy Bayona
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, 7020N Katz Group Centre for Pharmacy & Health Research, 11361-87 Avenue, Edmonton, Alberta, AB T6G 2E1 Canada
| | - Pranidhi Baddam
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, 7020N Katz Group Centre for Pharmacy & Health Research, 11361-87 Avenue, Edmonton, Alberta, AB T6G 2E1 Canada
| | - Daniel Graf
- Alberta Dental Association & College Chair for Oral Health Research, School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, 7020N Katz Group Centre for Pharmacy & Health Research, 11361-87 Avenue, Edmonton, Alberta, AB T6G 2E1 Canada
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9
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Milmoe NJ, Tucker AS. Craniofacial transitions: the role of EMT and MET during head development. Development 2021; 148:148/4/dev196030. [DOI: 10.1242/dev.196030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
Within the developing head, tissues undergo cell-fate transitions to shape the forming structures. This starts with the neural crest, which undergoes epithelial-to-mesenchymal transition (EMT) to form, amongst other tissues, many of the skeletal tissues of the head. In the eye and ear, these neural crest cells then transform back into an epithelium, via mesenchymal-to-epithelial transition (MET), highlighting the flexibility of this population. Elsewhere in the head, the epithelium loses its integrity and transforms into mesenchyme. Here, we review these craniofacial transitions, looking at why they happen, the factors that trigger them, and the cell and molecular changes they involve. We also discuss the consequences of aberrant EMT and MET in the head.
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Affiliation(s)
- Natalie J. Milmoe
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Abigail S. Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
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10
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Ma L, Lou S, Miao Z, Yao S, Yu X, Kan S, Zhu G, Yang F, Zhang C, Zhang W, Wang M, Wang L, Pan Y. Identification of novel susceptibility loci for non-syndromic cleft lip with or without cleft palate. J Cell Mol Med 2020; 24:13669-13678. [PMID: 33108691 PMCID: PMC7754035 DOI: 10.1111/jcmm.15878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/29/2020] [Accepted: 08/17/2020] [Indexed: 12/25/2022] Open
Abstract
Although several genome‐wide association studies (GWAS) of non‐syndromic cleft lip with or without cleft palate (NSCL/P) have been reported, more novel association signals are remained to be exploited. Here, we performed an in‐depth analysis of our previously published Chinese GWAS cohort study with replication in an extra dbGaP case‐parent trios and another in‐house Nanjing cohort, and finally identified five novel significant association signals (rs11119445: 3’ of SERTAD4, P = 6.44 × 10−14; rs227227 and rs12561877: intron of SYT14, P = 5.02 × 10−13 and 2.80 × 10−11, respectively; rs643118: intron of TRAF3IP3, P = 4.45 × 10−6; rs2095293: intron of NR6A1, P = 2.98 × 10−5). The mean (standard deviation) of the weighted genetic risk score (wGRS) from these SNPs was 1.83 (0.65) for NSCL/P cases and 1.58 (0.68) for controls, respectively (P = 2.67 × 10−16). Rs643118 was identified as a shared susceptible factor of NSCL/P among Asians and Europeans, while rs227227 may contribute to the risk of NSCL/P as well as NSCPO. In addition, sertad4 knockdown zebrafish models resulted in down‐regulation of sox2 and caused oedema around the heart and mandibular deficiency, compared with control embryos. Taken together, this study has improved our understanding of the genetic susceptibility to NSCL/P and provided further clues to its aetiology in the Chinese population.
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Affiliation(s)
- Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ziyue Miao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Siyue Yao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Xin Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Shiyi Kan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Chi Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Weibing Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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11
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Barqué A, Jan K, De La Fuente E, Nicholas CL, Hynes RO, Naba A. Knockout of the gene encoding the extracellular matrix protein SNED1 results in early neonatal lethality and craniofacial malformations. Dev Dyn 2020; 250:274-294. [PMID: 33012048 DOI: 10.1002/dvdy.258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/10/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The extracellular matrix (ECM) is a fundamental component of multicellular organisms that orchestrates developmental processes and controls cell and tissue organization. We previously identified the novel ECM protein SNED1 as a promoter of breast cancer metastasis and showed that its level of expression negatively correlated with breast cancer patient survival. Here, we sought to identify the roles of SNED1 during murine development. RESULTS We generated two novel Sned1 knockout mouse strains and showed that Sned1 is essential since homozygous ablation of the gene led to early neonatal lethality. Phenotypic analysis of the surviving knockout mice revealed a role for SNED1 in the development of craniofacial and skeletal structures since Sned1 knockout resulted in growth defects, nasal cavity occlusion, and craniofacial malformations. Sned1 is widely expressed in embryos, notably by cell populations undergoing epithelial-to-mesenchymal transition, such as the neural crest cells. We further show that mice with a neural-crest-cell-specific deletion of Sned1 survive, but display facial anomalies partly phenocopying the global knockout mice. CONCLUSIONS Our results demonstrate requisite roles for SNED1 during development and neonatal survival. Importantly, the deletion of 2q37.3 in humans, a region that includes the SNED1 locus, has been associated with facial dysmorphism and short stature.
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Affiliation(s)
- Anna Barqué
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Kyleen Jan
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Emanuel De La Fuente
- Department of Orthodontics, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Christina L Nicholas
- Department of Orthodontics, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Anthropology, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Richard O Hynes
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
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12
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Samuels BD, Aho R, Brinkley JF, Bugacov A, Feingold E, Fisher S, Gonzalez-Reiche AS, Hacia JG, Hallgrimsson B, Hansen K, Harris MP, Ho TV, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Leslie EJ, Li H, Liao EC, Long H, Lu N, Maas RL, Marazita ML, Mohammed J, Prescott S, Schuler R, Selleri L, Spritz RA, Swigut T, van Bakel H, Visel A, Welsh I, Williams C, Williams TJ, Wysocka J, Yuan Y, Chai Y. FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research. Development 2020; 147:dev191213. [PMID: 32958507 PMCID: PMC7522026 DOI: 10.1242/dev.191213] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a 'big data' resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.
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Affiliation(s)
- Bridget D Samuels
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Robert Aho
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - James F Brinkley
- Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Alejandro Bugacov
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Shannon Fisher
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, and McCaig Bone and Joint Institute, University of Calgary, Alberta, Canada
| | - Karissa Hansen
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Harris
- Department of Orthopedic Research, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joan E Hooper
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Carl Kesselman
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Ophir D Klein
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Hong Li
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Eric C Liao
- Massachusetts General Hospital, Plastic and Reconstructive Surgery, Boston, MA 02114, USA
| | - Hannah Long
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Na Lu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard L Maas
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mary L Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Jaaved Mohammed
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sara Prescott
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert Schuler
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Tomek Swigut
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
| | - Ian Welsh
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cristina Williams
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Joanna Wysocka
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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13
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Hooper JE, Jones KL, Smith FJ, Williams T, Li H. An Alternative Splicing Program for Mouse Craniofacial Development. Front Physiol 2020; 11:1099. [PMID: 33013468 PMCID: PMC7498679 DOI: 10.3389/fphys.2020.01099] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing acts as a fundamental mechanism to increase the number of functional transcripts that can be derived from the genome - and its appropriate regulation is required to direct normal development, differentiation, and physiology, in many species. Recent studies have highlighted that mutation of splicing factors, resulting in the disruption of alternative splicing, can have profound consequences for mammalian craniofacial development. However, there has been no systematic analysis of the dynamics of differential splicing during the critical period of face formation with respect to age, tissue layer, or prominence. Here we used deep RNA sequencing to profile transcripts expressed in the developing mouse face for both ectodermal and mesenchymal tissues from the three facial prominences at critical ages for facial development, embryonic days 10.5, 11.5, and 12.5. We also derived separate expression data from the nasal pit relating to the differentiation of the olfactory epithelium for a total of 60 independent datasets. Analysis of these datasets reveals the differential expression of multiple genes, but we find a similar number of genes are regulated only via differential splicing, indicating that alternative splicing is a major source of transcript diversity during facial development. Notably, splicing changes between tissue layers and over time are more prevalent than between prominences, with exon skipping the most common event. We next examined how the variation in splicing correlated with the expression of RNA binding proteins across the various datasets. Further, we assessed how binding sites for splicing regulatory molecules mapped with respect to intron exon boundaries. Overall these studies help define an alternative splicing regulatory program that has important consequences for facial development.
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Affiliation(s)
- Joan E. Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kenneth L. Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado School of Medicine, Aurora, CO, United States
| | - Francis J. Smith
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
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14
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Li H, Jones KL, Hooper JE, Williams T. The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution. Development 2019; 146:dev.174888. [PMID: 31118233 DOI: 10.1242/dev.174888] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
The mammalian lip and primary palate form when coordinated growth and morphogenesis bring the nasal and maxillary processes into contact, and the epithelia co-mingle, remodel and clear from the fusion site to allow mesenchyme continuity. Although several genes required for fusion have been identified, an integrated molecular and cellular description of the overall process is lacking. Here, we employ single cell RNA sequencing of the developing mouse face to identify ectodermal, mesenchymal and endothelial populations associated with patterning and fusion of the facial prominences. This analysis indicates that key cell populations at the fusion site exist within the periderm, basal epithelial cells and adjacent mesenchyme. We describe the expression profiles that make each population unique, and the signals that potentially integrate their behaviour. Overall, these data provide a comprehensive high-resolution description of the various cell populations participating in fusion of the lip and primary palate, as well as formation of the nasolacrimal groove, and they furnish a powerful resource for those investigating the molecular genetics of facial development and facial clefting that can be mined for crucial mechanistic information concerning this prevalent human birth defect.
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Affiliation(s)
- Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Joan E Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
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15
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Li A, Qin G, Suzuki A, Gajera M, Iwata J, Jia P, Zhao Z. Network-based identification of critical regulators as putative drivers of human cleft lip. BMC Med Genomics 2019; 12:16. [PMID: 30704473 PMCID: PMC6357351 DOI: 10.1186/s12920-018-0458-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Cleft lip (CL) is one of the most common congenital birth defects with complex etiology. While genome-wide association studies (GWAS) have made significant advances in our understanding of mutations and their related genes with potential involvement in the etiology of CL, it remains unknown how these genes are functionally regulated and interact with each other in lip development. Currently, identifying the disease-causing genes in human CL is urgently needed. So far, the causative CL genes have been largely undiscovered, making it challenging to design experiments to validate the functional influence of the mutations identified from large genomic studies such as CL GWAS. RESULTS Transcription factors (TFs) and microRNAs (miRNAs) are two important regulators in cellular system. In this study, we aimed to investigate the genetic interactions among TFs, miRNAs and the CL genes curated from the previous studies. We constructed miRNA-TF co-regulatory networks, from which the critical regulators as putative drivers in CL were examined. Based on the constructed networks, we identified ten critical hub genes with prior evidence in CL. Furthermore, the analysis of partitioned regulatory modules highlighted a number of biological processes involved in the pathology of CL, including a novel pathway "Signaling pathway regulating pluripotency of stem cells". Our subnetwork analysis pinpointed two candidate miRNAs, hsa-mir-27b and hsa-mir-497, activating the Wnt pathway that was associated with CL. Our results were supported by an independent gene expression dataset in CL. CONCLUSIONS This study represents the first regulatory network analysis of CL genes. Our work presents a global view of the CL regulatory network and a novel approach on investigating critical miRNAs, TFs and genes via combinatory regulatory networks in craniofacial development. The top genes and miRNAs will be important candidates for future experimental validation of their functions in CL.
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Affiliation(s)
- Aimin Li
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA
| | - Guimin Qin
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.,School of Software, Xidian University, Xi'an, 710071, Shaanxi, China
| | - Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Mona Gajera
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA. .,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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16
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Sharma PP, MacLean AL, Meinecke L, Clouthier DE, Nie Q, Schilling TF. Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch. Genesis 2018; 57:e23275. [PMID: 30561090 DOI: 10.1002/dvg.23275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 11/06/2022]
Abstract
The mandibular or first pharyngeal arch forms the upper and lower jaws in all gnathostomes. A gene regulatory network that defines ventral, intermediate, and dorsal domains along the dorsal-ventral (D-V) axis of the arch has emerged from studies in zebrafish and mice, but the temporal dynamics of this process remain unclear. To define cell fate trajectories in the arches we have performed quantitative gene expression analyses of D-V patterning genes in pharyngeal arch primordia in zebrafish and mice. Using NanoString technology to measure transcript numbers per cell directly we show that, in many cases, genes expressed in similar D-V domains and induced by similar signals vary dramatically in their temporal profiles. This suggests that cellular responses to D-V patterning signals are likely shaped by the baseline kinetics of target gene expression. Furthermore, similarities in the temporal dynamics of genes that occupy distinct pathways suggest novel shared modes of regulation. Incorporating these gene expression kinetics into our computational models for the mandibular arch improves the accuracy of patterning, and facilitates temporal comparisons between species. These data suggest that the magnitude and timing of target gene expression help diversify responses to patterning signals during craniofacial development.
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Affiliation(s)
- Praveer P Sharma
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California
| | - Adam L MacLean
- Department of Mathematics, University of California, Irvine, Irvine, California
| | - Lina Meinecke
- Department of Mathematics, University of California, Irvine, Irvine, California
| | - David E Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California.,Department of Mathematics, University of California, Irvine, Irvine, California
| | - Thomas F Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California
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17
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Minoux M, Holwerda S, Vitobello A, Kitazawa T, Kohler H, Stadler MB, Rijli FM. Gene bivalency at Polycomb domains regulates cranial neural crest positional identity. Science 2017; 355:355/6332/eaal2913. [PMID: 28360266 DOI: 10.1126/science.aal2913] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/02/2017] [Indexed: 12/15/2022]
Abstract
The cranial neural crest cells are multipotent cells that provide head skeletogenic mesenchyme and are crucial for craniofacial patterning. We analyzed the chromatin landscapes of mouse cranial neural crest subpopulations in vivo. Early postmigratory subpopulations contributing to distinct mouse craniofacial structures displayed similar chromatin accessibility patterns yet differed transcriptionally. Accessible promoters and enhancers of differentially silenced genes carried H3K27me3/H3K4me2 bivalent chromatin marks embedded in large enhancer of zeste homolog 2-dependent Polycomb domains, indicating transcriptional poising. These postmigratory bivalent chromatin regions were already present in premigratory progenitors. At Polycomb domains, H3K27me3 antagonized H3K4me2 deposition, which was restricted to accessible sites. Thus, bivalent Polycomb domains provide a chromatin template for the regulation of cranial neural crest cell positional identity in vivo, contributing insights into the epigenetic regulation of face morphogenesis.
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Affiliation(s)
- Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4051 Basel, Switzerland.,INSERM UMR 1121, Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67 000 Strasbourg, France
| | - Sjoerd Holwerda
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4051 Basel, Switzerland
| | - Antonio Vitobello
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4051 Basel, Switzerland
| | - Taro Kitazawa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4051 Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4051 Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4051 Basel, Switzerland. .,Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4051 Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4051 Basel, Switzerland. .,University of Basel, 4003 Basel, Switzerland
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18
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Starbuck JM, Cole TM, Reeves RH, Richtsmeier JT. The Influence of trisomy 21 on facial form and variability. Am J Med Genet A 2017; 173:2861-2872. [PMID: 28941128 DOI: 10.1002/ajmg.a.38464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/16/2017] [Accepted: 08/14/2017] [Indexed: 01/25/2023]
Abstract
Triplication of chromosome 21 (trisomy 21) results in Down syndrome (DS), the most common live-born human aneuploidy. Individuals with DS have a unique facial appearance that can include form changes and altered variability. Using 3D photogrammatic images, 3D coordinate locations of 20 anatomical landmarks, and Euclidean Distance Matrix Analysis methods, we quantitatively test the hypothesis that children with DS (n = 55) exhibit facial form and variance differences relative to two different age-matched (4-12 years) control samples of euploid individuals: biological siblings of individuals with DS (n = 55) and euploid individuals without a sibling with DS (n = 55). Approximately 36% of measurements differ significantly between DS and DS-sibling samples, whereas 46% differ significantly between DS and unrelated control samples. Nearly 14% of measurements differ significantly in variance between DS and DS sibling samples, while 18% of measurements differ significantly in variance between DS and unrelated euploid control samples. Of those measures that showed a significant difference in variance, all were relatively increased in the sample of DS individuals. These results indicate that faces of children with DS are quantitatively more similar to their siblings than to unrelated euploid individuals and exhibit consistent, but slightly increased variation with most individuals falling within the range of normal variation established by euploid samples. These observations provide indirect evidence of the strength of the genetic underpinnings of the resemblance between relatives and the resistance of craniofacial development to genetic perturbations caused by trisomy 21, while underscoring the complexity of the genotype-phenotype map.
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Affiliation(s)
- John M Starbuck
- Department of Anthropology, University of Central Florida, Orlando, Florida
| | - Theodore M Cole
- Department of Biomedical Sciences, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Roger H Reeves
- Department of Physiology and Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joan T Richtsmeier
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania
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19
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Leach SM, Feng W, Williams T. Gene expression profile data for mouse facial development. Data Brief 2017; 13:242-247. [PMID: 28856179 PMCID: PMC5561971 DOI: 10.1016/j.dib.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/29/2017] [Accepted: 05/03/2017] [Indexed: 11/17/2022] Open
Abstract
This article contains data related to the research articles "Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences" (Feng et al., 2009) [1] and “Systems Biology of facial development: contributions of ectoderm and mesenchyme” (Hooper et al., 2017 In press) [2]. Embryonic mammalian craniofacial development is a complex process involving the growth, morphogenesis, and fusion of distinct facial prominences into a functional whole. Aberrant gene regulation during this process can lead to severe craniofacial birth defects, including orofacial clefting. As a means to understand the genes involved in facial development, we had previously dissected the embryonic mouse face into distinct prominences: the mandibular, maxillary or nasal between E10.5 and E12.5. The prominences were then processed intact, or separated into ectoderm and mesenchyme layers, prior analysis of RNA expression using microarrays (Feng et al., 2009, Hooper et al., 2017 in press) [1], [2]. Here, individual gene expression profiles have been built from these datasets that illustrate the timing of gene expression in whole prominences or in the separated tissue layers. The data profiles are presented as an indexed and clickable list of the genes each linked to a graphical image of that gene׳s expression profile in the ectoderm, mesenchyme, or intact prominence. These data files will enable investigators to obtain a rapid assessment of the relative expression level of any gene on the array with respect to time, tissue, prominence, and expression trajectory.
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Affiliation(s)
- Sonia M. Leach
- Department of Biomedical Research, Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA
| | - Weiguo Feng
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
- Corresponding author at: Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.Department of Craniofacial Biology, University of Colorado School of Dental Medicine12801 E 17th AvenueAuroraCO80045USA
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20
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Askary A, Xu P, Barske L, Bay M, Bump P, Balczerski B, Bonaguidi MA, Crump JG. Genome-wide analysis of facial skeletal regionalization in zebrafish. Development 2017; 144:2994-3005. [PMID: 28705894 DOI: 10.1242/dev.151712] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/10/2017] [Indexed: 12/16/2022]
Abstract
Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite the significance for craniofacial development, how genetic programs drive this regionalization remains incompletely understood. Here we use combinatorial labeling of zebrafish cranial neural crest-derived cells (CNCCs) to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region-specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin 1 (Edn1) signaling in the intermediate joint-forming region, yet a surprisingly minor role in ventralmost regions. Analysis of co-variance across multiple sequencing experiments further reveals clusters of co-regulated genes, with in situ hybridization confirming the domain-specific expression of novel genes. We then created loss-of-function alleles for 12 genes and uncovered antagonistic functions of two new Edn1 targets, follistatin a (fsta) and emx2, in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in zebrafish arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders.
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Affiliation(s)
- Amjad Askary
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Pengfei Xu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Lindsey Barske
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Maxwell Bay
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Paul Bump
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Bartosz Balczerski
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Michael A Bonaguidi
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - J Gage Crump
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
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21
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Gene and metabolite time-course response to cigarette smoking in mouse lung and plasma. PLoS One 2017; 12:e0178281. [PMID: 28575117 PMCID: PMC5456044 DOI: 10.1371/journal.pone.0178281] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 05/10/2017] [Indexed: 12/15/2022] Open
Abstract
Prolonged cigarette smoking (CS) causes chronic obstructive pulmonary disease (COPD), a prevalent serious condition that may persist or progress after smoking cessation. To provide insight into how CS triggers COPD, we investigated temporal patterns of lung transcriptome expression and systemic metabolome changes induced by chronic CS exposure and smoking cessation. Whole lung RNA-seq data was analyzed at transcript and exon levels from C57Bl/6 mice exposed to CS for 1- or 7 days, for 3-, 6-, or 9 months, or for 6 months followed by 3 months of cessation using age-matched littermate controls. We identified previously unreported dysregulation of pyrimidine metabolism and phosphatidylinositol signaling pathways and confirmed alterations in glutathione metabolism and circadian gene pathways. Almost all dysregulated pathways demonstrated reversibility upon smoking cessation, except the lysosome pathway. Chronic CS exposure was significantly linked with alterations in pathways encoding for energy, phagocytosis, and DNA repair and triggered differential expression of genes or exons previously unreported to associate with CS or COPD, including Lox, involved in matrix remodeling, Gp2, linked to goblet cells, and Slc22a12 and Agpat3, involved in purine and glycerolipid metabolism, respectively. CS-induced lung metabolic pathways changes were validated using metabolomic profiles of matched plasma samples, indicating that dynamic metabolic gene regulation caused by CS is reflected in the plasma metabolome. Using advanced technologies, our study uncovered novel pathways and genes altered by chronic CS exposure, including those involved in pyrimidine metabolism, phosphatidylinositol signaling and lysosome function, highlighting their potential importance in the pathogenesis or diagnosis of CS-associated conditions.
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22
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Hooper JE, Feng W, Li H, Leach SM, Phang T, Siska C, Jones KL, Spritz RA, Hunter LE, Williams T. Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev Biol 2017; 426:97-114. [PMID: 28363736 PMCID: PMC5530582 DOI: 10.1016/j.ydbio.2017.03.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 12/17/2022]
Abstract
The rapid increase in gene-centric biological knowledge coupled with analytic approaches for genomewide data integration provides an opportunity to develop systems-level understanding of facial development. Experimental analyses have demonstrated the importance of signaling between the surface ectoderm and the underlying mesenchyme are coordinating facial patterning. However, current transcriptome data from the developing vertebrate face is dominated by the mesenchymal component, and the contributions of the ectoderm are not easily identified. We have generated transcriptome datasets from critical periods of mouse face formation that enable gene expression to be analyzed with respect to time, prominence, and tissue layer. Notably, by separating the ectoderm and mesenchyme we considerably improved the sensitivity compared to data obtained from whole prominences, with more genes detected over a wider dynamic range. From these data we generated a detailed description of ectoderm-specific developmental programs, including pan-ectodermal programs, prominence- specific programs and their temporal dynamics. The genes and pathways represented in these programs provide mechanistic insights into several aspects of ectodermal development. We also used these data to identify co-expression modules specific to facial development. We then used 14 co-expression modules enriched for genes involved in orofacial clefts to make specific mechanistic predictions about genes involved in tongue specification, in nasal process patterning and in jaw development. Our multidimensional gene expression dataset is a unique resource for systems analysis of the developing face; our co-expression modules are a resource for predicting functions of poorly annotated genes, or for predicting roles for genes that have yet to be studied in the context of facial development; and our analytic approaches provide a paradigm for analysis of other complex developmental programs.
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Affiliation(s)
- Joan E Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Weiguo Feng
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA.
| | - Tzulip Phang
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Medicine, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Charlotte Siska
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, 12800 E 17th Avenue, Aurora, CO 80045, USA.
| | - Lawrence E Hunter
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
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23
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Marchant TW, Johnson EJ, McTeir L, Johnson CI, Gow A, Liuti T, Kuehn D, Svenson K, Bermingham ML, Drögemüller M, Nussbaumer M, Davey MG, Argyle DJ, Powell RM, Guilherme S, Lang J, Ter Haar G, Leeb T, Schwarz T, Mellanby RJ, Clements DN, Schoenebeck JJ. Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. Curr Biol 2017; 27:1573-1584.e6. [PMID: 28552356 PMCID: PMC5462623 DOI: 10.1016/j.cub.2017.04.057] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/14/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022]
Abstract
In morphological terms, “form” is used to describe an object’s shape and size. In dogs, facial form is stunningly diverse. Facial retrusion, the proximodistal shortening of the snout and widening of the hard palate is common to brachycephalic dogs and is a welfare concern, as the incidence of respiratory distress and ocular trauma observed in this class of dogs is highly correlated with their skull form. Progress to identify the molecular underpinnings of facial retrusion is limited to association of a missense mutation in BMP3 among small brachycephalic dogs. Here, we used morphometrics of skull isosurfaces derived from 374 pedigree and mixed-breed dogs to dissect the genetics of skull form. Through deconvolution of facial forms, we identified quantitative trait loci that are responsible for canine facial shapes and sizes. Our novel insights include recognition that the FGF4 retrogene insertion, previously associated with appendicular chondrodysplasia, also reduces neurocranium size. Focusing on facial shape, we resolved a quantitative trait locus on canine chromosome 1 to a 188-kb critical interval that encompasses SMOC2. An intronic, transposable element within SMOC2 promotes the utilization of cryptic splice sites, causing its incorporation into transcripts, and drastically reduces SMOC2 gene expression in brachycephalic dogs. SMOC2 disruption affects the facial skeleton in a dose-dependent manner. The size effects of the associated SMOC2 haplotype are profound, accounting for 36% of facial length variation in the dogs we tested. Our data bring new focus to SMOC2 by highlighting its clinical implications in both human and veterinary medicine. A population-based genetics study of dogs that required diagnostic imaging Resolution of a QTL associated with face length reduction (brachycephaly) Association of brachycephaly with a retrotransposon that disrupts SMOC2 splicing The SMOC2 locus explains up to 36% of face length variation in dogs
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Affiliation(s)
- Thomas W Marchant
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Edward J Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Lynn McTeir
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Craig I Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Adam Gow
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tiziana Liuti
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dana Kuehn
- Friendship Hospital for Animals, Washington, DC 20016, USA
| | | | - Mairead L Bermingham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Marc Nussbaumer
- Naturhistorisches Museum, Bernastrasse 15, 3005 Bern, Switzerland
| | - Megan G Davey
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - David J Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Roger M Powell
- Powell Torrance Diagnostic Services, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Sérgio Guilherme
- Davies Veterinary Specialists, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Johann Lang
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, University of Bern, 3001 Bern, Switzerland
| | - Gert Ter Haar
- Department of Clinical Sciences and Services, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Tobias Schwarz
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Richard J Mellanby
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Jeffrey J Schoenebeck
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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24
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Cole JB, Manyama M, Kimwaga E, Mathayo J, Larson JR, Liberton DK, Lukowiak K, Ferrara TM, Riccardi SL, Li M, Mio W, Prochazkova M, Williams T, Li H, Jones KL, Klein OD, Santorico SA, Hallgrimsson B, Spritz RA. Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape. PLoS Genet 2016; 12:e1006174. [PMID: 27560698 PMCID: PMC4999243 DOI: 10.1371/journal.pgen.1006174] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/15/2016] [Indexed: 12/16/2022] Open
Abstract
The human face is a complex assemblage of highly variable yet clearly heritable anatomic structures that together make each of us unique, distinguishable, and recognizable. Relatively little is known about the genetic underpinnings of normal human facial variation. To address this, we carried out a large genomewide association study and two independent replication studies of Bantu African children and adolescents from Mwanza, Tanzania, a region that is both genetically and environmentally relatively homogeneous. We tested for genetic association of facial shape and size phenotypes derived from 3D imaging and automated landmarking of standard facial morphometric points. SNPs within genes SCHIP1 and PDE8A were associated with measures of facial size in both the GWAS and replication cohorts and passed a stringent genomewide significance threshold adjusted for multiple testing of 34 correlated traits. For both SCHIP1 and PDE8A, we demonstrated clear expression in the developing mouse face by both whole-mount in situ hybridization and RNA-seq, supporting their involvement in facial morphogenesis. Ten additional loci demonstrated suggestive association with various measures of facial shape. Our findings, which differ from those in previous studies of European-derived whites, augment understanding of the genetic basis of normal facial development, and provide insights relevant to both human disease and forensics. The human face is made up of distinct yet related anatomic structures that together make both individuals and families recognizable. It is clear there is a strong genetic component to the human face, and though the genetics of the face have been studied for several years, there are relatively few genes known to impact normal human facial development and facial shape. We report here a large-scale human genetic study in which we successfully identify and replicate genetic markers associated with normal facial variation using advanced 3D facial imaging in African children. We identified two significant replicated genes associated with measures of human facial size, SCHIP1 and PDE8A, demonstrated their clear expression in the developing face in the mouse, and identified 10 additional candidate genetic loci for human facial shape. Gene discovery for human facial development is an important first step for both diagnosing and treating craniofacial syndromes and for developing forensic modeling of the human face.
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Affiliation(s)
- Joanne B. Cole
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Mange Manyama
- Department of Anatomy, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Emmanuel Kimwaga
- Department of Anatomy, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Joshua Mathayo
- Department of Anatomy, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Jacinda R. Larson
- Department of Anatomy and Cell Biology and McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Canada
| | - Denise K. Liberton
- Department of Anatomy and Cell Biology and McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Canada
| | - Ken Lukowiak
- Hotchkiss Brain Institute, Cummings School of Medicine, University of Calgary, Calgary, Canada
| | - Tracey M. Ferrara
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Sheri L. Riccardi
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Mao Li
- Department of Mathematics, Florida State University, Tallahassee, Florida, United States of America
| | - Washington Mio
- Department of Mathematics, Florida State University, Tallahassee, Florida, United States of America
| | - Michaela Prochazkova
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, Colorado, United States of America
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, Colorado, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Ophir D. Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America
| | - Stephanie A. Santorico
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Mathematical and Statistical Science, University of Colorado Denver, Denver, Colorado, United States of America
- Department of Biostatistics & Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Benedikt Hallgrimsson
- Department of Anatomy and Cell Biology and McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Canada
| | - Richard A. Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- * E-mail:
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25
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Brinkley JF, Fisher S, Harris MP, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Maas RL, Marazita ML, Selleri L, Spritz RA, van Bakel H, Visel A, Williams TJ, Wysocka J, Chai Y. The FaceBase Consortium: a comprehensive resource for craniofacial researchers. Development 2016; 143:2677-88. [PMID: 27287806 PMCID: PMC4958338 DOI: 10.1242/dev.135434] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/22/2016] [Indexed: 12/13/2022]
Abstract
The FaceBase Consortium, funded by the National Institute of Dental and Craniofacial Research, National Institutes of Health, is designed to accelerate understanding of craniofacial developmental biology by generating comprehensive data resources to empower the research community, exploring high-throughput technology, fostering new scientific collaborations among researchers and human/computer interactions, facilitating hypothesis-driven research and translating science into improved health care to benefit patients. The resources generated by the FaceBase projects include a number of dynamic imaging modalities, genome-wide association studies, software tools for analyzing human facial abnormalities, detailed phenotyping, anatomical and molecular atlases, global and specific gene expression patterns, and transcriptional profiling over the course of embryonic and postnatal development in animal models and humans. The integrated data visualization tools, faceted search infrastructure, and curation provided by the FaceBase Hub offer flexible and intuitive ways to interact with these multidisciplinary data. In parallel, the datasets also offer unique opportunities for new collaborations and training for researchers coming into the field of craniofacial studies. Here, we highlight the focus of each spoke project and the integration of datasets contributed by the spokes to facilitate craniofacial research.
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Affiliation(s)
- James F Brinkley
- Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Shannon Fisher
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Matthew P Harris
- Department of Orthopedic Research, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joan E Hooper
- Cell and Developmental Biology, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Carl Kesselman
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Ophir D Klein
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard L Maas
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology and of Developmental Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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26
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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27
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Percival CJ, Liberton DK, Pardo‐Manuel de Villena F, Spritz R, Marcucio R, Hallgrímsson B. Genetics of murine craniofacial morphology: diallel analysis of the eight founders of the Collaborative Cross. J Anat 2016; 228:96-112. [PMID: 26426826 PMCID: PMC4694168 DOI: 10.1111/joa.12382] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 11/28/2022] Open
Abstract
Using eight inbred founder strains of the mouse Collaborative Cross (CC) project and their reciprocal F1 hybrids, we quantified variation in craniofacial morphology across mouse strains, explored genetic contributions to craniofacial variation that distinguish the founder strains, and tested whether specific or summary measures of craniofacial shape display stronger additive genetic contributions. This study thus provides critical information about phenotypic diversity among CC founder strains and about the genetic contributions to this phenotypic diversity, which is relevant to understanding the basis of variation in standard laboratory strains and natural populations. Craniofacial shape was quantified as a series of size-adjusted linear dimensions (RDs) and by principal components (PC) analysis of morphological landmarks captured from computed tomography images from 62 of the 64 reciprocal crosses of the CC founder strains. We first identified aspects of skull morphology that vary between these phenotypically 'normal' founder strains and that are defining characteristics of these strains. We estimated the contributions of additive and various non-additive genetic factors to phenotypic variation using diallel analyses of a subset of these strongly differing RDs and the first eight PCs of skull shape variation. We find little difference in the genetic contributions to RD measures and PC scores, suggesting fundamental similarities in the magnitude of genetic contributions to both specific and summary measures of craniofacial phenotypes. Our results indicate that there are stronger additive genetic effects associated with defining phenotypic characteristics of specific founder strains, suggesting these distinguishing measures are good candidates for use in genotype-phenotype association studies of CC mice. Our results add significantly to understanding of genotype-phenotype associations in the skull, which serve as a foundation for modeling the origins of medically and evolutionarily relevant variation.
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Affiliation(s)
- Christopher J. Percival
- Alberta Children's Hospital Institute for Child and Maternal HealthUniversity of CalgaryCalgaryABCanada
- The McCaig Bone and Joint InstituteUniversity of CalgaryCalgaryABCanada
- Department of Cell Biology and AnatomyUniversity of CalgaryCalgaryABCanada
| | - Denise K. Liberton
- The McCaig Bone and Joint InstituteUniversity of CalgaryCalgaryABCanada
- Department of Cell Biology and AnatomyUniversity of CalgaryCalgaryABCanada
- Present address: National Institute of Dental and Craniofacial ResearchBethesdaMDUSA
| | | | - Richard Spritz
- Human Medical Genetics and Genomics ProgramUniversity of Colorado School of MedicineAuroraCOUSA
| | - Ralph Marcucio
- The Orthopaedic Trauma InstituteDepartment of Orthopaedic SurgeryUCSF School of MedicineSan FranciscoCAUSA
| | - Benedikt Hallgrímsson
- Alberta Children's Hospital Institute for Child and Maternal HealthUniversity of CalgaryCalgaryABCanada
- The McCaig Bone and Joint InstituteUniversity of CalgaryCalgaryABCanada
- Department of Cell Biology and AnatomyUniversity of CalgaryCalgaryABCanada
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28
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Ealba EL, Jheon AH, Hall J, Curantz C, Butcher KD, Schneider RA. Neural crest-mediated bone resorption is a determinant of species-specific jaw length. Dev Biol 2015; 408:151-63. [PMID: 26449912 PMCID: PMC4698309 DOI: 10.1016/j.ydbio.2015.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 11/28/2022]
Abstract
Precise control of jaw length during development is crucial for proper form and function. Previously we have shown that in birds, neural crest mesenchyme (NCM) confers species-specific size and shape to the beak by regulating molecular and histological programs for the induction and deposition of cartilage and bone. Here we reveal that a hitherto unrecognized but similarly essential mechanism for establishing jaw length is the ability of NCM to mediate bone resorption. Osteoclasts are considered the predominant cells that resorb bone, although osteocytes have also been shown to participate in this process. In adults, bone resorption is tightly coupled to bone deposition as a means to maintain skeletal homeostasis. Yet, the role and regulation of bone resorption during growth of the embryonic skeleton have remained relatively unexplored. We compare jaw development in short-beaked quail versus long-billed duck and find that quail have substantially higher levels of enzymes expressed by bone-resorbing cells including tartrate-resistant acid phosphatase (TRAP), Matrix metalloproteinase 13 (Mmp13), and Mmp9. Then, we transplant NCM destined to form the jaw skeleton from quail to duck and generate chimeras in which osteocytes arise from quail donor NCM and osteoclasts come exclusively from the duck host. Chimeras develop quail-like jaw skeletons coincident with dramatically elevated expression of TRAP, Mmp13, and Mmp9. To test for a link between bone resorption and jaw length, we block resorption using a bisphosphonate, osteoprotegerin protein, or an MMP13 inhibitor, and this significantly lengthens the jaw. Conversely, activating resorption with RANKL protein shortens the jaw. Finally, we find that higher resorption in quail presages their relatively lower adult jaw bone mineral density (BMD) and that BMD is also NCM-mediated. Thus, our experiments suggest that NCM not only controls bone resorption by its own derivatives but also modulates the activity of mesoderm-derived osteoclasts, and in so doing enlists bone resorption as a key patterning mechanism underlying the functional morphology and evolution of the jaw.
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Affiliation(s)
- Erin L Ealba
- Department of Orofacial Sciences, University of California, San Francisco, USA; Department of Orthopaedic Surgery, University of California, San Francisco, USA
| | - Andrew H Jheon
- Department of Orofacial Sciences, University of California, San Francisco, USA; Department of Orthopaedic Surgery, University of California, San Francisco, USA
| | - Jane Hall
- Department of Orthopaedic Surgery, University of California, San Francisco, USA
| | - Camille Curantz
- Department of Orthopaedic Surgery, University of California, San Francisco, USA
| | - Kristin D Butcher
- Department of Orthopaedic Surgery, University of California, San Francisco, USA
| | - Richard A Schneider
- Department of Orofacial Sciences, University of California, San Francisco, USA; Department of Orthopaedic Surgery, University of California, San Francisco, USA.
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Abstract
The NIH FACEBASE consortium was established in part to create a central resource for craniofacial researchers. One purpose is to provide a molecular anatomy of craniofacial development. To this end we have used a combination of laser capture microdissection and RNA-Seq to define the gene expression programs driving development of the murine palate. We focused on the E14.5 palate, soon after medial fusion of the two palatal shelves. The palate was divided into multiple compartments, including both medial and lateral, as well as oral and nasal, for both the anterior and posterior domains. A total of 25 RNA-Seq datasets were generated. The results provide a comprehensive view of the region specific expression of all transcription factors, growth factors and receptors. Paracrine interactions can be inferred from flanking compartment growth factor/receptor expression patterns. The results are validated primarily through very high concordance with extensive previously published gene expression data for the developing palate. In addition selected immunostain validations were carried out. In conclusion, this report provides an RNA-Seq based atlas of gene expression patterns driving palate development at microanatomic resolution. This FACEBASE resource is designed to promote discovery by the craniofacial research community.
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Maga AM, Navarro N, Cunningham ML, Cox TC. Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico. Front Physiol 2015; 6:92. [PMID: 25859222 PMCID: PMC4374467 DOI: 10.3389/fphys.2015.00092] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/05/2015] [Indexed: 11/17/2022] Open
Abstract
We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.
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Affiliation(s)
- A Murat Maga
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington Seattle, WA, USA ; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute Seattle, WA, USA
| | - Nicolas Navarro
- Laboratoire PALEVO, Ecole Pratique des Hautes Etudes Dijon, France ; UMR uB/CNRS 6282 - Biogéosciences, Université de Bourgogne Dijon, France
| | - Michael L Cunningham
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington Seattle, WA, USA ; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute Seattle, WA, USA
| | - Timothy C Cox
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington Seattle, WA, USA ; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute Seattle, WA, USA ; Department of Anatomy and Developmental Biology, Monash University Clayton, VIC, Australia
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31
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Bergeron KF, Cardinal T, Touré AM, Béland M, Raiwet DL, Silversides DW, Pilon N. Male-biased aganglionic megacolon in the TashT mouse line due to perturbation of silencer elements in a large gene desert of chromosome 10. PLoS Genet 2015; 11:e1005093. [PMID: 25786024 PMCID: PMC4364714 DOI: 10.1371/journal.pgen.1005093] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/23/2015] [Indexed: 01/13/2023] Open
Abstract
Neural crest cells (NCC) are a transient migratory cell population that generates diverse cell types such as neurons and glia of the enteric nervous system (ENS). Via an insertional mutation screen for loci affecting NCC development in mice, we identified one line—named TashT—that displays a partially penetrant aganglionic megacolon phenotype in a strong male-biased manner. Interestingly, this phenotype is highly reminiscent of human Hirschsprung’s disease, a neurocristopathy with a still unexplained male sex bias. In contrast to the megacolon phenotype, colonic aganglionosis is almost fully penetrant in homozygous TashT animals. The sex bias in megacolon expressivity can be explained by the fact that the male ENS ends, on average, around a “tipping point” of minimal colonic ganglionosis while the female ENS ends, on average, just beyond it. Detailed analysis of embryonic intestines revealed that aganglionosis in homozygous TashT animals is due to slower migration of enteric NCC. The TashT insertional mutation is localized in a gene desert containing multiple highly conserved elements that exhibit repressive activity in reporter assays. RNAseq analyses and 3C assays revealed that the TashT insertion results, at least in part, in NCC-specific relief of repression of the uncharacterized gene Fam162b; an outcome independently confirmed via transient transgenesis. The transcriptional signature of enteric NCC from homozygous TashT embryos is also characterized by the deregulation of genes encoding members of the most important signaling pathways for ENS formation—Gdnf/Ret and Edn3/Ednrb—and, intriguingly, the downregulation of specific subsets of X-linked genes. In conclusion, this study not only allowed the identification of Fam162b coding and regulatory sequences as novel candidate loci for Hirschsprung’s disease but also provides important new insights into its male sex bias. Hirschsprung’s disease (also known as aganglionic megacolon) is a severe congenital defect of the enteric nervous system (ENS) resulting in complete failure to pass stools. It is characterized by the absence of neural ganglia (aganglionosis) in the distal gut due to incomplete colonization of the embryonic intestines by neural crest cells (NCC), the ENS precursors. Hirschsprung’s disease has an incidence of 1 in 5000 newborns and a 4:1 male sex bias. Although many genes have been associated with this complex genetic disease, most of its heritability as well as its male sex bias remain unexplained. Here, we describe an insertional mutant mouse line (“TashT”) in which virtually all homozygotes display colonic aganglionosis due to defective migration of enteric NCC, but in which only a subset of homozygotes develops megacolon. Surprisingly, this group is almost exclusively male. The TashT ENS defect stems, at least in part, from the disruption of long-range interactions between evolutionarily conserved elements with silencer activity and Fam162b, resulting in NCC-specific upregulation of this uncharacterized protein coding gene. Global analysis of gene expression further revealed that several hundreds of genes are significantly deregulated in TashT enteric NCC. Interestingly, this dataset includes multiple X-linked candidate genes potentially underlying the male sex bias. Taken together, our data pave the way for a clearer understanding of the intriguing male sex bias of Hirschsprung’s disease.
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Affiliation(s)
- Karl-F. Bergeron
- Molecular Genetics of Development Laboratory, Department of Biological Sciences and BioMed Research Center, University of Quebec at Montreal (UQAM), Quebec, Canada
| | - Tatiana Cardinal
- Molecular Genetics of Development Laboratory, Department of Biological Sciences and BioMed Research Center, University of Quebec at Montreal (UQAM), Quebec, Canada
| | - Aboubacrine M. Touré
- Molecular Genetics of Development Laboratory, Department of Biological Sciences and BioMed Research Center, University of Quebec at Montreal (UQAM), Quebec, Canada
| | - Mélanie Béland
- Molecular Genetics of Development Laboratory, Department of Biological Sciences and BioMed Research Center, University of Quebec at Montreal (UQAM), Quebec, Canada
| | - Diana L. Raiwet
- Veterinary Genetics Laboratory, Faculty of Veterinary Medicine, University of Montreal, Quebec, Canada
| | - David W. Silversides
- Veterinary Genetics Laboratory, Faculty of Veterinary Medicine, University of Montreal, Quebec, Canada
| | - Nicolas Pilon
- Molecular Genetics of Development Laboratory, Department of Biological Sciences and BioMed Research Center, University of Quebec at Montreal (UQAM), Quebec, Canada
- * E-mail:
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Starbuck JM, Ghoneima A, Kula K. Bilateral cleft lip and palate: A morphometric analysis of facial skeletal form using cone beam computed tomography. Clin Anat 2015; 28:584-92. [DOI: 10.1002/ca.22530] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 12/20/2022]
Affiliation(s)
- John M. Starbuck
- Department of Orthodontics and Oral Facial Genetics, School of DentistryIndiana UniversityIndianapolis Indiana
- Department of Sociology and AnthropologyIndiana University NorthwestGary Indiana
- Department of AnthropologyUniversity of Central FloridaOrlando Florida
| | - Ahmed Ghoneima
- Department of Orthodontics and Oral Facial Genetics, School of DentistryIndiana UniversityIndianapolis Indiana
| | - Katherine Kula
- Department of Orthodontics and Oral Facial Genetics, School of DentistryIndiana UniversityIndianapolis Indiana
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Green RM, Feng W, Phang T, Fish JL, Li H, Spritz RA, Marcucio RS, Hooper J, Jamniczky H, Hallgrímsson B, Williams T. Tfap2a-dependent changes in mouse facial morphology result in clefting that can be ameliorated by a reduction in Fgf8 gene dosage. Dis Model Mech 2015; 8:31-43. [PMID: 25381013 PMCID: PMC4283648 DOI: 10.1242/dmm.017616] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/02/2014] [Indexed: 12/20/2022] Open
Abstract
Failure of facial prominence fusion causes cleft lip and palate (CL/P), a common human birth defect. Several potential mechanisms can be envisioned that would result in CL/P, including failure of prominence growth and/or alignment as well as a failure of fusion of the juxtaposed epithelial seams. Here, using geometric morphometrics, we analyzed facial outgrowth and shape change over time in a novel mouse model exhibiting fully penetrant bilateral CL/P. This robust model is based upon mutations in Tfap2a, the gene encoding transcription factor AP-2α, which has been implicated in both syndromic and non-syndromic human CL/P. Our findings indicate that aberrant morphology and subsequent misalignment of the facial prominences underlies the inability of the mutant prominences to fuse. Exencephaly also occured in some of the Tfap2a mutants and we observed additional morphometric differences that indicate an influence of neural tube closure defects on facial shape. Molecular analysis of the CL/P model indicates that Fgf signaling is misregulated in the face, and that reducing Fgf8 gene dosage can attenuate the clefting pathology by generating compensatory changes. Furthermore, mutations in either Tfap2a or Fgf8 increase variance in facial shape, but the combination of these mutations restores variance to normal levels. The alterations in variance provide a potential mechanistic link between clefting and the evolution and diversity of facial morphology. Overall, our findings suggest that CL/P can result from small gene-expression changes that alter the shape of the facial prominences and uncouple their coordinated morphogenesis, which is necessary for normal fusion.
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Affiliation(s)
- Rebecca M Green
- Department of Craniofacial Biology, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Weiguo Feng
- Department of Craniofacial Biology, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Tzulip Phang
- Department of Pharmacology, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Jennifer L Fish
- University of California San Francisco, Orthopaedic Trauma Institute, Department of Orthopaedic Surgery, San Francisco, CA 94110, USA
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, 12800 East 17th Avenue, Aurora, CO 80045, USA
| | - Ralph S Marcucio
- University of California San Francisco, Orthopaedic Trauma Institute, Department of Orthopaedic Surgery, San Francisco, CA 94110, USA
| | - Joan Hooper
- Department of Cell and Developmental Biology, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Heather Jamniczky
- McCaig Institute for Bone and Joint Health, Department of Cell Biology & Anatomy, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N3Z6, Canada
| | - Benedikt Hallgrímsson
- McCaig Institute for Bone and Joint Health, Department of Cell Biology & Anatomy, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N3Z6, Canada. Alberta Children's Hospital Research Institute, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N3Z6, Canada
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA. Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, 12800 East 17th Avenue, Aurora, CO 80045, USA. Department of Cell and Developmental Biology, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA.
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Mommaerts H, Esguerra CV, Hartmann U, Luyten FP, Tylzanowski P. Smoc2 modulates embryonic myelopoiesis during zebrafish development. Dev Dyn 2014; 243:1375-90. [PMID: 25044883 DOI: 10.1002/dvdy.24164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 06/14/2014] [Accepted: 07/02/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND SMOC2 is a member of the BM-40 (SPARC) family of matricellular proteins, reported to influence signaling in the extracellular compartment. In mice, Smoc2 is expressed in many different tissues and was shown to enhance the response to angiogenic growth factors, mediate cell adhesion, keratinocyte migration, and metastasis. Additionally, SMOC2 is associated with vitiligo and craniofacial and dental defects. The function of Smoc2 during early zebrafish development has not been determined to date. RESULTS In pregastrula zebrafish embryos, smoc2 is expressed ubiquitously. As development progresses, the expression pattern becomes more anteriorly restricted. At the onset of blood cell circulation, smoc2 morphants presented a mild ventralization of posterior structures. Molecular analysis of the smoc2 morphants indicated myelopoietic defects in the rostral blood islands during segmentation stages. Hemangioblast development and further specification of the myeloid progenitor cells were shown to be impaired. Additional experiments indicated that Bmp target genes were down-regulated in smoc2 morphants. CONCLUSIONS Our findings reveal that Smoc2 is an essential player in the development of myeloid cells of the anterior lateral plate mesoderm during embryonic zebrafish development. Furthermore, our data show that Smoc2 affects the transcription of Bmp target genes without affecting initial dorsoventral patterning or mesoderm development.
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Affiliation(s)
- Hendrik Mommaerts
- Laboratory for Developmental and Stem Cell Biology, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven - University of Leuven, Leuven, Belgium
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Starbuck JM, Friel MT, Ghoneima A, Flores RL, Tholpady S, Kula K. Nasal airway and septal variation in unilateral and bilateral cleft lip and palate. Clin Anat 2014; 27:999-1008. [PMID: 24976342 DOI: 10.1002/ca.22428] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 11/10/2022]
Abstract
Cleft lip and palate (CLP) affects the dentoalveolar and nasolabial facial regions. Internal and external nasal dysmorphology may persist in individuals born with CLP despite surgical interventions. 7-18 year old individuals born with unilateral and bilateral CLP (n = 50) were retrospectively assessed using cone beam computed tomography. Anterior, middle, and posterior nasal airway volumes were measured on each facial side. Septal deviation was measured at the anterior and posterior nasal spine, and the midpoint between these two locations. Data were evaluated using principal components analysis (PCA), multivariate analysis of variance (MANOVA), and post-hoc ANOVA tests. PCA results show partial separation in high dimensional space along PC1 (48.5% variance) based on age groups and partial separation along PC2 (29.8% variance) based on CLP type and septal deviation patterns. MANOVA results indicate that age (P = 0.007) and CLP type (P ≤ 0.001) significantly affect nasal airway volume and septal deviation. ANOVA results indicate that anterior nasal volume is significantly affected by age (P ≤ 0.001), whereas septal deviation patterns are significantly affected by CLP type (P ≤ 0.001). Age and CLP type affect nasal airway volume and septal deviation patterns. Nasal airway volumes tend to be reduced on the clefted sides of the face relative to non-clefted sides of the face. Nasal airway volumes tend to strongly increase with age, whereas septal deviation values tend to increase only slightly with age. These results suggest that functional nasal breathing may be impaired in individuals born with the unilateral and bilateral CLP deformity.
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Affiliation(s)
- John M Starbuck
- Department of Orthodontics and Oral Facial Genetics, School of Dentistry, Indiana University, Indianapolis, Indiana, 46202
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36
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Warner DR, Mukhopadhyay P, Brock G, Webb CL, Michele Pisano M, Greene RM. MicroRNA expression profiling of the developing murine upper lip. Dev Growth Differ 2014; 56:434-47. [PMID: 24849136 DOI: 10.1111/dgd.12140] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/28/2014] [Accepted: 04/01/2014] [Indexed: 12/21/2022]
Abstract
Clefts of the lip and palate are thought to be caused by genetic and environmental insults but the role of epigenetic mechanisms underlying this common birth defect are unknown. We analyzed the expression of over 600 microRNAs in the murine medial nasal and maxillary processes isolated on GD10.0-GD11.5 to identify those expressed during development of the upper lip and analyzed spatial expression of a subset. A total of 142 microRNAs were differentially expressed across gestation days 10.0-11.5 in the medial nasal processes, and 66 in the maxillary processes of the first branchial arch with 45 common to both. Of the microRNAs exhibiting the largest percent increase in both facial processes were five members of the Let-7 family. Among those with the greatest decrease in expression from GD10.0 to GD11.5 were members of the microRNA-302/367 family that have been implicated in cellular reprogramming. The distribution of expression of microRNA-199a-3p and Let-7i was determined by in situ hybridization and revealed widespread expression in both medial nasal and maxillary facial process, while that for microRNA-203 was much more limited. MicroRNAs are dynamically expressed in the tissues that form the upper lip and several were identified that target mRNAs known to be important for its development, including those that regulate the two main isoforms of p63 (microRNA-203 and microRNA-302/367 family). Integration of these data with corresponding proteomic datasets will lead to a greater appreciation of epigenetic regulation of lip development and provide a better understanding of potential causes of cleft lip.
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Affiliation(s)
- Dennis R Warner
- Department of Molecular, Cellular, and Craniofacial Biology, University of Louisville Birth Defects Center, Louisville, Kentucky, USA
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Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A. Fine tuning of craniofacial morphology by distant-acting enhancers. Science 2013; 342:1241006. [PMID: 24159046 PMCID: PMC3991470 DOI: 10.1126/science.1241006] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The shape of the human face and skull is largely genetically determined. However, the genomic basis of craniofacial morphology is incompletely understood and hypothesized to involve protein-coding genes, as well as gene regulatory sequences. We used a combination of epigenomic profiling, in vivo characterization of candidate enhancer sequences in transgenic mice, and targeted deletion experiments to examine the role of distant-acting enhancers in craniofacial development. We identified complex regulatory landscapes consisting of enhancers that drive spatially complex developmental expression patterns. Analysis of mouse lines in which individual craniofacial enhancers had been deleted revealed significant alterations of craniofacial shape, demonstrating the functional importance of enhancers in defining face and skull morphology. These results demonstrate that enhancers are involved in craniofacial development and suggest that enhancer sequence variation contributes to the diversity of human facial morphology.
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Affiliation(s)
- Catia Attanasio
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | - Alex S. Nord
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | - Yiwen Zhu
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | | | - Zirong Li
- Ludwig Institute for Cancer Research, and Department of
Cellular and Molecular Medicine, University of California, San Diego School of
Medicine, 9500 Gilman Drive, La Jolla, CA
| | - Denise K. Liberton
- Dept. of Cell Biology & Anatomy, McCaig Bone and
Joint Institute and the Alberta Children's Hospital Research Institute,
University of Calgary, Canada
| | - Harris Morrison
- MRC Human Genetics Unit, MRC Institute for Genetic and
Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Amy Holt
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | - Roya Hosseini
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | | | | | - Malak Shoukry
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | - Veena Afzal
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | - Edward M. Rubin
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
- DOE Joint Genome Institute, Walnut Creek, CA
| | - David R. FitzPatrick
- MRC Human Genetics Unit, MRC Institute for Genetic and
Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bing Ren
- Ludwig Institute for Cancer Research, and Department of
Cellular and Molecular Medicine, University of California, San Diego School of
Medicine, 9500 Gilman Drive, La Jolla, CA
| | - Benedikt Hallgrímsson
- Dept. of Cell Biology & Anatomy, McCaig Bone and
Joint Institute and the Alberta Children's Hospital Research Institute,
University of Calgary, Canada
| | - Len A. Pennacchio
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
- DOE Joint Genome Institute, Walnut Creek, CA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
- DOE Joint Genome Institute, Walnut Creek, CA
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Kobayashi GS, Alvizi L, Sunaga DY, Francis-West P, Kuta A, Almada BVP, Ferreira SG, de Andrade-Lima LC, Bueno DF, Raposo-Amaral CE, Menck CF, Passos-Bueno MR. Susceptibility to DNA damage as a molecular mechanism for non-syndromic cleft lip and palate. PLoS One 2013; 8:e65677. [PMID: 23776525 PMCID: PMC3680497 DOI: 10.1371/journal.pone.0065677] [Citation(s) in RCA: 29] [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: 12/20/2012] [Accepted: 04/26/2013] [Indexed: 01/03/2023] Open
Abstract
Non-syndromic cleft lip/palate (NSCL/P) is a complex, frequent congenital malformation, determined by the interplay between genetic and environmental factors during embryonic development. Previous findings have appointed an aetiological overlap between NSCL/P and cancer, and alterations in similar biological pathways may underpin both conditions. Here, using a combination of transcriptomic profiling and functional approaches, we report that NSCL/P dental pulp stem cells exhibit dysregulation of a co-expressed gene network mainly associated with DNA double-strand break repair and cell cycle control (p = 2.88×10(-2)-5.02×10(-9)). This network included important genes for these cellular processes, such as BRCA1, RAD51, and MSH2, which are predicted to be regulated by transcription factor E2F1. Functional assays support these findings, revealing that NSCL/P cells accumulate DNA double-strand breaks upon exposure to H2O2. Furthermore, we show that E2f1, Brca1 and Rad51 are co-expressed in the developing embryonic orofacial primordia, and may act as a molecular hub playing a role in lip and palate morphogenesis. In conclusion, we show for the first time that cellular defences against DNA damage may take part in determining the susceptibility to NSCL/P. These results are in accordance with the hypothesis of aetiological overlap between this malformation and cancer, and suggest a new pathogenic mechanism for the disease.
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Affiliation(s)
- Gerson Shigeru Kobayashi
- Human Genome Research Center, Institute for Biosciences, University of São Paulo, São Paulo, Brazil
| | - Lucas Alvizi
- Human Genome Research Center, Institute for Biosciences, University of São Paulo, São Paulo, Brazil
| | - Daniele Yumi Sunaga
- Human Genome Research Center, Institute for Biosciences, University of São Paulo, São Paulo, Brazil
| | - Philippa Francis-West
- Dental Institute, Department of Craniofacial Development and Stem Cell Biology, King’s College London, London, United Kingdom
| | - Anna Kuta
- Dental Institute, Department of Craniofacial Development and Stem Cell Biology, King’s College London, London, United Kingdom
| | | | - Simone Gomes Ferreira
- Human Genome Research Center, Institute for Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Daniela Franco Bueno
- Human Genome Research Center, Institute for Biosciences, University of São Paulo, São Paulo, Brazil
- SOBRAPAR Institute, Campinas, São Paulo, Brazil
| | | | | | - Maria Rita Passos-Bueno
- Human Genome Research Center, Institute for Biosciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
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Melvin VS, Feng W, Hernandez-Lagunas L, Artinger KB, Williams T. A morpholino-based screen to identify novel genes involved in craniofacial morphogenesis. Dev Dyn 2013; 242:817-31. [PMID: 23559552 DOI: 10.1002/dvdy.23969] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/11/2013] [Accepted: 03/24/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The regulatory mechanisms underpinning facial development are conserved between diverse species. Therefore, results from model systems provide insight into the genetic causes of human craniofacial defects. Previously, we generated a comprehensive dataset examining gene expression during development and fusion of the mouse facial prominences. Here, we used this resource to identify genes that have dynamic expression patterns in the facial prominences, but for which only limited information exists concerning developmental function. RESULTS This set of ∼80 genes was used for a high-throughput functional analysis in the zebrafish system using Morpholino gene knockdown technology. This screen revealed three classes of cranial cartilage phenotypes depending upon whether knockdown of the gene affected the neurocranium, viscerocranium, or both. The targeted genes that produced consistent phenotypes encoded proteins linked to transcription (meis1, meis2a, tshz2, vgll4l), signaling (pkdcc, vlk, macc1, wu:fb16h09), and extracellular matrix function (smoc2). The majority of these phenotypes were not altered by reduction of p53 levels, demonstrating that both p53-dependent and -independent mechanisms were involved in the craniofacial abnormalities. CONCLUSIONS This Morpholino-based screen highlights new genes involved in development of the zebrafish craniofacial skeleton with wider relevance to formation of the face in other species, particularly mouse and human.
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Affiliation(s)
- Vida Senkus Melvin
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Denver, Colorado, USA
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40
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Abstract
Orofacial clefts are the most frequent craniofacial defects, which affect 1.5 in 1,000 newborns worldwide. Orofacial clefting is caused by abnormal facial development. In human and mouse, initial growth and patterning of the face relies on several small buds of tissue, the facial prominences. The face is derived from six main prominences: paired frontal nasal processes (FNP), maxillary prominences (MxP) and mandibular prominences (MdP). These prominences consist of swellings of mesenchyme that are encased in an overlying epithelium. Studies in multiple species have shown that signaling crosstalk between facial ectoderm and mesenchyme is critical for shaping the face. Yet, mechanistic details concerning the genes involved in these signaling relays are lacking. One way to gain a comprehensive understanding of gene expression, transcription factor binding, and chromatin marks associated with the developing facial ectoderm and mesenchyme is to isolate and characterize the separated tissue compartments. Here we present a method for separating facial ectoderm and mesenchyme at embryonic day (E) 10.5, a critical developmental stage in mouse facial formation that precedes fusion of the prominences. Our method is adapted from the approach we have previously used for dissecting facial prominences. In this earlier study we had employed inbred C57BL/6 mice as this strain has become a standard for genetics, genomics and facial morphology. Here, though, due to the more limited quantities of tissue available, we have utilized the outbred CD-1 strain that is cheaper to purchase, more robust for husbandry, and tending to produce more embryos (12-18) per litter than any inbred mouse strain. Following embryo isolation, neutral protease Dispase II was used to treat the whole embryo. Then, the facial prominences were dissected out, and the facial ectoderm was separated from the mesenchyme. This method keeps both the facial ectoderm and mesenchyme intact. The samples obtained using this methodology can be used for techniques including protein detection, chromatin immunoprecipitation (ChIP) assay, microarray studies, and RNA-seq.
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Affiliation(s)
- Hong Li
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, USA
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Starbuck JM, Cole TM, Reeves RH, Richtsmeier JT. Trisomy 21 and facial developmental instability. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:49-57. [PMID: 23505010 DOI: 10.1002/ajpa.22255] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/06/2013] [Indexed: 01/03/2023]
Abstract
The most common live-born human aneuploidy is trisomy 21, which causes Down syndrome (DS). Dosage imbalance of genes on chromosome 21 (Hsa21) affects complex gene-regulatory interactions and alters development to produce a wide range of phenotypes, including characteristic facial dysmorphology. Little is known about how trisomy 21 alters craniofacial morphogenesis to create this characteristic appearance. Proponents of the "amplified developmental instability" hypothesis argue that trisomy 21 causes a generalized genetic imbalance that disrupts evolutionarily conserved developmental pathways by decreasing developmental homeostasis and precision throughout development. Based on this model, we test the hypothesis that DS faces exhibit increased developmental instability relative to euploid individuals. Developmental instability was assessed by a statistical analysis of fluctuating asymmetry. We compared the magnitude and patterns of fluctuating asymmetry among siblings using three-dimensional coordinate locations of 20 anatomic landmarks collected from facial surface reconstructions in four age-matched samples ranging from 4 to 12 years: (1) DS individuals (n = 55); (2) biological siblings of DS individuals (n = 55); 3) and 4) two samples of typically developing individuals (n = 55 for each sample), who are euploid siblings and age-matched to the DS individuals and their euploid siblings (samples 1 and 2). Identification in the DS sample of facial prominences exhibiting increased fluctuating asymmetry during facial morphogenesis provides evidence for increased developmental instability in DS faces. We found the highest developmental instability in facial structures derived from the mandibular prominence and lowest in facial regions derived from the frontal prominence.
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Affiliation(s)
- John M Starbuck
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
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Mutations in Hedgehog acyltransferase (Hhat) perturb Hedgehog signaling, resulting in severe acrania-holoprosencephaly-agnathia craniofacial defects. PLoS Genet 2012; 8:e1002927. [PMID: 23055936 PMCID: PMC3464201 DOI: 10.1371/journal.pgen.1002927] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 07/10/2012] [Indexed: 12/02/2022] Open
Abstract
Holoprosencephaly (HPE) is a failure of the forebrain to bifurcate and is the most common structural malformation of the embryonic brain. Mutations in SHH underlie most familial (17%) cases of HPE; and, consistent with this, Shh is expressed in midline embryonic cells and tissues and their derivatives that are affected in HPE. It has long been recognized that a graded series of facial anomalies occurs within the clinical spectrum of HPE, as HPE is often found in patients together with other malformations such as acrania, anencephaly, and agnathia. However, it is not known if these phenotypes arise through a common etiology and pathogenesis. Here we demonstrate for the first time using mouse models that Hedgehog acyltransferase (Hhat) loss-of-function leads to holoprosencephaly together with acrania and agnathia, which mimics the severe condition observed in humans. Hhat is required for post-translational palmitoylation of Hedgehog (Hh) proteins; and, in the absence of Hhat, Hh secretion from producing cells is diminished. We show through downregulation of the Hh receptor Ptch1 that loss of Hhat perturbs long-range Hh signaling, which in turn disrupts Fgf, Bmp and Erk signaling. Collectively, this leads to abnormal patterning and extensive apoptosis within the craniofacial primordial, together with defects in cartilage and bone differentiation. Therefore our work shows that Hhat loss-of-function underscrores HPE; but more importantly it provides a mechanism for the co-occurrence of acrania, holoprosencephaly, and agnathia. Future genetic studies should include HHAT as a potential candidate in the etiology and pathogenesis of HPE and its associated disorders. Craniofacial anomalies account for approximately one third of all birth defects, and holoprosencephaly (HPE) is the most common structural malformation of the embryonic brain. HPE is a failure of the forebrain to bifurcate and is a heterogeneous disorder that is often found in patients together with other craniofacial malformations. Currently, it is not known if these phenotypes arise through a common etiology and pathogenesis, as the genetic lesions responsible for HPE have only been identified in about 20% of affected individuals. Here we demonstrate for the first time that Hedgehog acyltransferase (Hhat) loss-of-function leads to holoprosencephaly together with acrania and agnathia, which highlights the importance of Hh signaling in complex craniofacial disorders.
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Starbuck J, Reeves RH, Richtsmeier J. Morphological integration of soft-tissue facial morphology in Down Syndrome and siblings. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:560-8. [PMID: 21996933 DOI: 10.1002/ajpa.21583] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/02/2011] [Indexed: 12/27/2022]
Abstract
Down syndrome (DS), resulting from trisomy of chromosome 21, is the most common live-born human aneuploidy. The phenotypic expression of trisomy 21 produces variable, though characteristic, facial morphology. Although certain facial features have been documented quantitatively and qualitatively as characteristic of DS (e.g., epicanthic folds, macroglossia, and hypertelorism), all of these traits occur in other craniofacial conditions with an underlying genetic cause. We hypothesize that the typical DS face is integrated differently than the face of non-DS siblings, and that the pattern of morphological integration unique to individuals with DS will yield information about underlying developmental associations between facial regions. We statistically compared morphological integration patterns of immature DS faces (N = 53) with those of non-DS siblings (N = 54), aged 6-12 years using 31 distances estimated from 3D coordinate data representing 17 anthropometric landmarks recorded on 3D digital photographic images. Facial features are affected differentially in DS, as evidenced by statistically significant differences in integration both within and between facial regions. Our results suggest a differential affect of trisomy on facial prominences during craniofacial development.
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Affiliation(s)
- John Starbuck
- The Pennsylvania State University-Anthropology, University Park, PA 16802, USA.
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Johnson CW, Hernandez-Lagunas L, Feng W, Melvin VS, Williams T, Artinger KB. Vgll2a is required for neural crest cell survival during zebrafish craniofacial development. Dev Biol 2011; 357:269-81. [PMID: 21741961 DOI: 10.1016/j.ydbio.2011.06.034] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 06/21/2011] [Accepted: 06/22/2011] [Indexed: 01/15/2023]
Abstract
Invertebrate and vertebrate vestigial (vg) and vestigial-like (VGLL) genes are involved in embryonic patterning and cell fate determination. These genes encode cofactors that interact with members of the Scalloped/TEAD family of transcription factors and modulate their activity. We have previously shown that, in mice, Vgll2 is differentially expressed in the developing facial prominences. In this study, we show that the zebrafish ortholog vgll2a is expressed in the pharyngeal endoderm and ectoderm surrounding the neural crest derived mesenchyme of the pharyngeal arches. Moreover, both the FGF and retinoic acid (RA) signaling pathways, which are critical components of the hierarchy controlling craniofacial patterning, regulate this domain of vgll2a expression. Consistent with these observations, vgll2a is required within the pharyngeal endoderm for NCC survival and pharyngeal cartilage development. Specifically, knockdown of Vgll2a in zebrafish embryos using Morpholino injection results in increased cell death within the pharyngeal arches, aberrant endodermal pouch morphogenesis, and hypoplastic cranial cartilages. Overall, our data reveal a novel non-cell autonomous role for Vgll2a in development of the NCC-derived vertebrate craniofacial skeleton.
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Affiliation(s)
- Christopher W Johnson
- Department of Craniofacial Biology, University of Colorado Denver, School of Dental Medicine, Aurora, 80045, USA
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45
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Billington CJ, Ng B, Forsman C, Schmidt B, Bagchi A, Symer DE, Schotta G, Gopalakrishnan R, Sarver AL, Petryk A. The molecular and cellular basis of variable craniofacial phenotypes and their genetic rescue in Twisted gastrulation mutant mice. Dev Biol 2011; 355:21-31. [PMID: 21549111 DOI: 10.1016/j.ydbio.2011.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/01/2011] [Accepted: 04/12/2011] [Indexed: 11/16/2022]
Abstract
The severity of numerous developmental abnormalities can vary widely despite shared genetic causes. Mice deficient in Twisted gastrulation (Twsg1(-/-)) display such phenotypic variation, developing a wide range of craniofacial malformations on an isogenic C57BL/6 strain background. To examine the molecular basis for this reduced penetrance and variable expressivity, we used exon microarrays to analyze gene expression in mandibular arches from several distinct, morphologically defined classes of Twsg1(-/-) and wild type (WT) embryos. Hierarchical clustering analysis of transcript levels identified numerous differentially expressed genes, clearly distinguishing severely affected and unaffected Twsg1(-/-) mutants from WT embryos. Several genes that play well-known roles in craniofacial development were upregulated in unaffected Twsg1(-/-) mutant embryos, suggesting that they may compensate for the loss of TWSG1. Imprinted genes were overrepresented among genes that were differentially expressed particularly between affected and unaffected mutants. The most severely affected embryos demonstrated increased p53 signaling and increased expression of its target, Trp53inp1. The frequency of craniofacial defects significantly decreased with a reduction of p53 gene dosage from 44% in Twsg1(-/-)p53(+/+) pups (N=675) to 30% in Twsg1(-/-)p53(+/-) (N=47, p=0.04) and 15% in Twsg1(-/-)p53(-/-) littermates (N=39, p=0.001). In summary, these results demonstrate that phenotypic variability in Twsg1(-/-) mice is associated with differential expression of certain developmentally regulated genes, and that craniofacial defects can be partially rescued by reduced p53 levels. We postulate that variable responses to stress may contribute to variable craniofacial phenotypes by triggering differential expression of genes and variable cellular apoptosis.
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Affiliation(s)
- Charles J Billington
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455-0356, USA
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46
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Meunier D, Patra K, Smits R, Hägebarth A, Lüttges A, Jaussi R, Wieduwilt MJ, Quintanilla-Fend L, Himmelbauer H, Fodde R, Fundele RH. Expression analysis of proline rich 15 (Prr15) in mouse and human gastrointestinal tumors. Mol Carcinog 2011; 50:8-15. [PMID: 21061267 DOI: 10.1002/mc.20692] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proline rich 15 (Prr15), which encodes a protein of unknown function, is expressed almost exclusively in postmitotic cells both during fetal development and in adult tissues, such as the intestinal epithelium and the testis. To determine if this specific expression is lost in intestinal neoplasias, we examined Prr15 expression by in situ hybridization (ISH) on mouse intestinal tumors caused by different gene mutations, and on human colorectal cancer (CRC) samples. Prr15/PRR15 expression was consistently observed in mouse gastrointestinal (GI) tumors caused by mutations in the Apc gene, as well as in several advanced stage human CRCs. In contrast, no Prr15 expression was detected in intestinal tumors derived from mice carrying mutations in the Smad3, Smad4, or Cdkn1b genes. These findings, combined with the fact that a majority of sporadic human CRCs carry APC mutations, strongly suggest that the expression of Prr15/PRR15 in mouse and human GI tumors is linked, directly or indirectly, to the absence of the APC protein or, more generally, to the disruption of the Wnt signaling pathway.
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Affiliation(s)
- Dominique Meunier
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
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47
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Ectodermal Wnt/β-catenin signaling shapes the mouse face. Dev Biol 2010; 349:261-9. [PMID: 21087601 DOI: 10.1016/j.ydbio.2010.11.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 10/14/2010] [Accepted: 11/05/2010] [Indexed: 01/11/2023]
Abstract
The canonical Wnt/β-catenin pathway is an essential component of multiple developmental processes. To investigate the role of this pathway in the ectoderm during facial morphogenesis, we generated conditional β-catenin mouse mutants using a novel ectoderm-specific Cre recombinase transgenic line. Our results demonstrate that ablating or stabilizing β-catenin in the embryonic ectoderm causes dramatic changes in facial morphology. There are accompanying alterations in the expression of Fgf8 and Shh, key molecules that establish a signaling center critical for facial patterning, the frontonasal ectodermal zone (FEZ). These data indicate that Wnt/β-catenin signaling within the ectoderm is critical for facial development and further suggest that this pathway is an important mechanism for generating the diverse facial shapes of vertebrates during evolution.
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48
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Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L. Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol 2009; 5:e1000215. [PMID: 19325874 PMCID: PMC2653649 DOI: 10.1371/journal.pcbi.1000215] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 02/12/2009] [Indexed: 01/17/2023] Open
Abstract
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work.
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Affiliation(s)
- Sonia M. Leach
- Center for Computational Pharmacology, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Hannah Tipney
- Center for Computational Pharmacology, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Weiguo Feng
- Department of Craniofacial Biology, University of Colorado at Denver, Denver, Colorado, United States of America
| | - William A. Baumgartner
- Center for Computational Pharmacology, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Priyanka Kasliwal
- Center for Computational Pharmacology, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Ronald P. Schuyler
- Center for Computational Pharmacology, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Richard A. Spritz
- Human Medical Genetics Program, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Lawrence Hunter
- Center for Computational Pharmacology, University of Colorado at Denver, Denver, Colorado, United States of America
- * E-mail:
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Tipney HJ, Leach SM, Feng W, Spritz R, Williams T, Hunter L. Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology. BMC Bioinformatics 2009; 10 Suppl 2:S12. [PMID: 19208187 PMCID: PMC2646237 DOI: 10.1186/1471-2105-10-s2-s12] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background In response to the frequently overwhelming output of high-throughput microarray experiments, we propose a methodology to facilitate interpretation of biological data in the context of existing knowledge. Through the probabilistic integration of explicit and implicit data sources a functional interaction network can be constructed. Each edge connecting two proteins is weighted by a confidence value capturing the strength and reliability of support for that interaction given the combined data sources. The resulting network is examined in conjunction with expression data to identify groups of genes with significant temporal or tissue specific patterns. In contrast to unstructured gene lists, these networks often represent coherent functional groupings. Results By linking from shared functional categorizations to primary biological resources we apply this method to craniofacial microarray data, generating biologically testable hypotheses and identifying candidate genes for craniofacial development. Conclusion The novel methodology presented here illustrates how the effective integration of pre-existing biological knowledge and high-throughput experimental data drives biological discovery and hypothesis generation.
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Affiliation(s)
- Hannah J Tipney
- Computational Pharmacology Department, University of Colorado at Denver and Health Sciences Center, Aurora, CO, USA.
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