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Flaherty SE, Bezy O, Paulhus BL, Song L, Piper M, Pang J, Park Y, Asano S, Lien YC, Griffin JD, Robertson A, Opsahl A, Shanthappa DH, Ahn Y, Pashos E, Simmons RA, Birnbaum MJ, Wu Z. SPAG7 deletion causes intrauterine growth restriction, resulting in adulthood obesity and metabolic dysfunction. eLife 2024; 12:RP91114. [PMID: 39056292 PMCID: PMC11281781 DOI: 10.7554/elife.91114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024] Open
Abstract
From a forward mutagenetic screen to discover mutations associated with obesity, we identified mutations in the Spag7 gene linked to metabolic dysfunction in mice. Here, we show that SPAG7 KO mice are born smaller and develop obesity and glucose intolerance in adulthood. This obesity does not stem from hyperphagia, but a decrease in energy expenditure. The KO animals also display reduced exercise tolerance and muscle function due to impaired mitochondrial function. Furthermore, SPAG7-deficiency in developing embryos leads to intrauterine growth restriction, brought on by placental insufficiency, likely due to abnormal development of the placental junctional zone. This insufficiency leads to loss of SPAG7-deficient fetuses in utero and reduced birth weights of those that survive. We hypothesize that a 'thrifty phenotype' is ingrained in SPAG7 KO animals during development that leads to adult obesity. Collectively, these results indicate that SPAG7 is essential for embryonic development and energy homeostasis later in life.
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Affiliation(s)
| | - Olivier Bezy
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | | | - LouJin Song
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | - Mary Piper
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | - Jincheng Pang
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | - Yoson Park
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | - Shoh Asano
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | - Yu-Chin Lien
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - John D Griffin
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | - Andrew Robertson
- Drug Safety Research and Development, Pfizer IncGrotonUnited States
| | - Alan Opsahl
- Drug Safety Research and Development, Pfizer IncGrotonUnited States
| | | | | | - Evanthia Pashos
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | | | - Zhidan Wu
- Internal Medicine Research Unit, Pfizer IncCambridgeUnited States
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2
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Andrade F, Howell L, Percival CJ, Richtsmeier JT, Marcucio RS, Hallgrímsson B, Cheverud JM. Genetic architecture of trait variance in craniofacial morphology. Genetics 2024; 226:iyae028. [PMID: 38386896 PMCID: PMC11090463 DOI: 10.1093/genetics/iyae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
The genetic architecture of trait variance has long been of interest in genetics and evolution. One of the earliest attempts to understand this architecture was presented in Lerner's Genetic Homeostasis (1954). Lerner proposed that heterozygotes should be better able to tolerate environmental perturbations because of functional differences between the alleles at a given locus, with each allele optimal for slightly different environments. This greater robustness to environmental variance, he argued, would result in smaller trait variance for heterozygotes. The evidence for Lerner's hypothesis has been inconclusive. To address this question using modern genomic methods, we mapped loci associated with differences in trait variance (vQTL) on 1,101 individuals from the F34 of an advanced intercross between LG/J and SM/J mice. We also mapped epistatic interactions for these vQTL in order to understand the influence of epistasis for the architecture of trait variance. We did not find evidence supporting Lerner's hypothesis, that heterozygotes tend to have smaller trait variances than homozygotes. We further show that the effects of most mapped loci on trait variance are produced by epistasis affecting trait means and that those epistatic effects account for about a half of the differences in genotypic-specific trait variances. Finally, we propose a model where the different interactions between the additive and dominance effects of the vQTL and their epistatic partners can explain Lerner's original observations but can also be extended to include other conditions where heterozygotes are not the least variable genotype.
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Affiliation(s)
- Fernando Andrade
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Lisa Howell
- Department of Anthropology, Penn State University, University Park, PA 16802, USA
| | | | - Joan T Richtsmeier
- Department of Anthropology, Penn State University, University Park, PA 16802, USA
| | - Ralph S Marcucio
- Department of Orthopedic Surgery, School of Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, Cumming School of Medicine, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - James M Cheverud
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
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3
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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4
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Zou J, Anai S, Ota S, Ishitani S, Oginuma M, Ishitani T. Determining zebrafish dorsal organizer size by a negative feedback loop between canonical/non-canonical Wnts and Tlr4/NFκB. Nat Commun 2023; 14:7194. [PMID: 37938219 PMCID: PMC10632484 DOI: 10.1038/s41467-023-42963-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
In vertebrate embryos, the canonical Wnt ligand primes the formation of dorsal organizers that govern dorsal-ventral patterns by secreting BMP antagonists. In contrast, in Drosophila embryos, Toll-like receptor (Tlr)-mediated NFκB activation initiates dorsal-ventral patterning, wherein Wnt-mediated negative feedback regulation of Tlr/NFκB generates a BMP antagonist-secreting signalling centre to control the dorsal-ventral pattern. Although both Wnt and BMP antagonist are conserved among species, the involvement of Tlr/NFκB and feedback regulation in vertebrate organizer formation remains unclear. By imaging and genetic modification, we reveal that a negative feedback loop between canonical and non-canonical Wnts and Tlr4/NFκB determines the size of zebrafish organizer, and that Tlr/NFκB and Wnts switch initial cue and feedback mediator roles between Drosophila and zebrafish. Here, we show that canonical Wnt signalling stimulates the expression of the non-canonical Wnt5b ligand, activating the Tlr4 receptor to stimulate NFκB-mediated transcription of the Wnt antagonist frzb, restricting Wnt-dependent dorsal organizer formation.
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Affiliation(s)
- Juqi Zou
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Satoshi Anai
- Yuuai Medical Center, Tomigusuku, Okinawa, 901-0224, Japan
| | - Satoshi Ota
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo, 153-8904, Japan
| | - Shizuka Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masayuki Oginuma
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
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5
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Li Y, Xiong Z, Zhang M, Hysi PG, Qian Y, Adhikari K, Weng J, Wu S, Du S, Gonzalez-Jose R, Schuler-Faccini L, Bortolini MC, Acuna-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Wang J, Tan J, Yuan Z, Jin L, Uitterlinden AG, Ghanbari M, Ikram MA, Nijsten T, Zhu X, Lei Z, Jia P, Ruiz-Linares A, Spector TD, Wang S, Kayser M, Liu F. Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci. PLoS Genet 2023; 19:e1010786. [PMID: 37459304 PMCID: PMC10351707 DOI: 10.1371/journal.pgen.1010786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/16/2023] [Indexed: 07/20/2023] Open
Abstract
Human ear morphology, a complex anatomical structure represented by a multidimensional set of correlated and heritable phenotypes, has a poorly understood genetic architecture. In this study, we quantitatively assessed 136 ear morphology traits using deep learning analysis of digital face images in 14,921 individuals from five different cohorts in Europe, Asia, and Latin America. Through GWAS meta-analysis and C-GWASs, a recently introduced method to effectively combine GWASs of many traits, we identified 16 genetic loci involved in various ear phenotypes, eight of which have not been previously associated with human ear features. Our findings suggest that ear morphology shares genetic determinants with other surface ectoderm-derived traits such as facial variation, mono eyebrow, and male pattern baldness. Our results enhance the genetic understanding of human ear morphology and shed light on the shared genetic contributors of different surface ectoderm-derived phenotypes. Additionally, gene editing experiments in mice have demonstrated that knocking out the newly ear-associated gene (Intu) and a previously ear-associated gene (Tbx15) causes deviating mouse ear morphology.
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Affiliation(s)
- Yi Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Manfei Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Yu Qian
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Beijing No.8 High School, Beijing, China
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, United Kingdom
| | - Jun Weng
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
| | - Sijie Wu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- University of Chinese Academy of Sciences, China
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Argentina
| | | | | | - Victor Acuna-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM-Instituto Nacional de Medicina Genomica, Mexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular), Universidad de Antioquia, Medellin, Colombia
| | | | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, China
| | - Li Jin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Fudan-Taizhou Institute of Health Sciences, China
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC, University Medical Center, the Netherlands
| | - Xiangyu Zhu
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Zhen Lei
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Aix-Marseille Universite, CNRS, EFS, ADES, France
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
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6
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Kidwai FK, Canalis E, Robey PG. Induced pluripotent stem cell technology in bone biology. Bone 2023; 172:116760. [PMID: 37028583 PMCID: PMC10228209 DOI: 10.1016/j.bone.2023.116760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Technologies on the development and differentiation of human induced pluripotent stem cells (hiPSCs) are rapidly improving, and have been applied to create cell types relevant to the bone field. Differentiation protocols to form bona fide bone-forming cells from iPSCs are available, and can be used to probe details of differentiation and function in depth. When applied to iPSCs bearing disease-causing mutations, the pathogenetic mechanisms of diseases of the skeleton can be elucidated, along with the development of novel therapeutics. These cells can also be used for development of cell therapies for cell and tissue replacement.
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Affiliation(s)
- Fahad K Kidwai
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, United States of America
| | - Ernesto Canalis
- Center for Skeletal Research, Orthopedic Surgery and Medicine, UConn Musculoskeletal Institute, UConn Health, Farmington, CT 06030-4037, United States of America
| | - Pamela G Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, United States of America.
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7
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Schrauwen I, Ghaffar A, Bharadwaj T, Shah K, Rehman S, Acharya A, Liaqat K, Lin NS, Everard JL, Khan A, Ahmed ZM, Ahmad W, Riazuddin S, Leal SM. Syntaxin 4 is essential for hearing in human and zebrafish. Hum Mol Genet 2023; 32:1184-1192. [PMID: 36355422 PMCID: PMC10026253 DOI: 10.1093/hmg/ddac257] [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: 04/19/2022] [Revised: 08/22/2022] [Accepted: 11/11/2022] [Indexed: 11/12/2022] Open
Abstract
Congenital hearing impairment (HI) is a genetically highly heterogeneous disorder in which prompt recognition and intervention are crucial to optimize outcomes. In this study, we used exome sequencing to investigate a large consanguineous Pakistani family with eight affected individuals showing bilateral severe-to-profound HI. This identified a homozygous splice region variant in STX4 (c.232 + 6T>C), which causes exon skipping and a frameshift, that segregated with HI (two-point logarithm of odds (LOD) score = 5.9). STX4, a member of the syntaxin family, is a component of the SNARE machinery involved in several vesicle transport and recycling pathways. In silico analysis showed that murine orthologue Stx4a is highly and widespread expressed in the developing and adult inner ear. Immunofluorescent imaging revealed localization of STX4A in the cell body, cell membrane and stereocilia of inner and outer hair cells. Furthermore, a morpholino-based knockdown of stx4 in zebrafish showed an abnormal startle response, morphological and developmental defects, and a disrupted mechanotransduction function in neuromast hair cells measured via FM1-43 uptake. Our findings indicate that STX4 dysfunction leads to HI in humans and zebrafish and supports the evolutionary conserved role of STX4 in inner ear development and hair cell functioning.
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Affiliation(s)
- Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Amama Ghaffar
- Department of Otorhinolaryngology - Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Khadim Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Khyber Pakhtunkhwa, Pakistan
| | - Sakina Rehman
- Department of Otorhinolaryngology - Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Khurram Liaqat
- Center for Statistical Genetics, Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Nicole S Lin
- Center for Statistical Genetics, Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Jenna L Everard
- Center for Statistical Genetics, Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Anwar Khan
- Department of Biochemistry, Hazara University Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Zubair M Ahmed
- Department of Otorhinolaryngology - Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology - Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
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8
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Paronett EM, Bryan CA, Maynard TM, LaMantia AS. Identity, lineage and fates of a temporally distinct progenitor population in the embryonic olfactory epithelium. Dev Biol 2023; 495:76-91. [PMID: 36627077 PMCID: PMC9926479 DOI: 10.1016/j.ydbio.2023.01.001] [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: 08/16/2021] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/09/2023]
Abstract
We defined a temporally and transcriptionally divergent precursor cohort in the medial olfactory epithelium (OE) shortly after it differentiates as a distinct tissue at mid-gestation in the mouse. This temporally distinct population of Ascl1+ cells in the dorsomedial OE is segregated from Meis1+/Pax7+ progenitors in the lateral OE, and does not appear to be generated by Pax7+ lateral OE precursors. The medial Ascl1+ precursors do not yield a substantial number of early-generated ORNs. Instead, they first generate additional proliferative precursors as well as a distinct population of frontonasal mesenchymal cells associated with the migratory mass that surrounds the nascent olfactory nerve. Parallel to these in vivo distinctions, isolated medial versus lateral OE precursors in vitro retain distinct proliferative capacities and modes of division that reflect their in vivo identities. At later fetal stages, these early dorsomedial Ascl1+ precursors cells generate spatially restricted subsets of ORNs as well as other non-neuronal cell classes. Accordingly, the initial compliment of ORNs and other OE cell types is derived from at least two distinct early precursor populations: lateral Meis1/Pax7+ precursors that generate primarily early ORNs, and a temporally, spatially, and transcriptionally distinct subset of medial Ascl1+ precursors that initially generate additional OE progenitors and apparent migratory mass cells before yielding a subset of ORNs and likely supporting cell classes.
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Affiliation(s)
- Elizabeth M Paronett
- Department of Pharmacology and Physiology, George Washington University School of Medicine, Washington, DC, 20037, USA
| | - Corey A Bryan
- Laboratory of Developmental Disorders and Genetics, The Fralin Biomedical Research Institute, Virginia Tech-Carilion School of Medicine, Roanoke, VA, USA
| | - Thomas M Maynard
- Center for Neurobiology Research, The Fralin Biomedical Research Institute, Virginia Tech-Carilion School of Medicine, Roanoke, VA, USA
| | - Anthony-S LaMantia
- Center for Neurobiology Research, The Fralin Biomedical Research Institute, Virginia Tech-Carilion School of Medicine, Roanoke, VA, USA; Department of Biological Sciences Virginia Tech, Blacksburg, VA, USA.
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9
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Adadey SM, Aboagye ET, Esoh K, Acharya A, Bharadwaj T, Lin NS, Amenga-Etego L, Awandare GA, Schrauwen I, Leal SM, Wonkam A. A novel autosomal dominant GREB1L variant associated with non-syndromic hearing impairment in Ghana. BMC Med Genomics 2022; 15:237. [PMID: 36357908 PMCID: PMC9648021 DOI: 10.1186/s12920-022-01391-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/08/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Childhood hearing impairment (HI) is genetically heterogeneous with many implicated genes, however, only a few of these genes are reported in African populations. METHODS This study used exome and Sanger sequencing to resolve the possible genetic cause of non-syndromic HI in a Ghanaian family. RESULTS We identified a novel variant c.3041G > A: p.(Gly1014Glu) in GREB1L (DFNA80) in the index case. The GREB1L: p.(Gly1014Glu) variant had a CADD score of 26.5 and was absent from human genomic databases such as TopMed and gnomAD. In silico homology protein modeling approaches displayed major structural differences between the wildtype and mutant proteins. Additionally, the variant was predicted to probably affect the secondary protein structure that may impact its function. Publicly available expression data shows a higher expression of Greb1L in the inner ear of mice during development and a reduced expression in adulthood, underscoring its importance in the development of the inner ear structures. CONCLUSION This report on an African individual supports the association of GREB1L variant with non-syndromic HI and extended the evidence of the implication of GREB1L variants in HI in diverse populations.
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Affiliation(s)
- Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Thashi Bharadwaj
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Nicole S Lin
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
| | - Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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10
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Hemkemeyer SA, Liu Z, Vollmer V, Xu Y, Lohmann B, Bähler M. The RhoGAP-myosin Myo9b regulates ocular lens pit morphogenesis. Dev Dyn 2022; 251:1897-1907. [PMID: 36008362 DOI: 10.1002/dvdy.522] [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: 01/19/2022] [Revised: 07/15/2022] [Accepted: 08/02/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND During eye development the lens placode invaginates to form the lens pit. Further bending of lens epithelium and separation from ectoderm leads eventually to a spherical lens vesicle with enclosed extracellular fluid. Changes in epithelial morphology involve the actin cytoskeleton and its regulators. The myosin Myo9b is simultaneously an actin-based motor and Rho GTPase-activating protein that regulates actin cytoskeleton organization. Myo9b-deficient adult mice and embryos were analyzed for eye malformations and alterations in lens development. RESULTS Myo9b-deficient mice showed a high incidence of microphthalmia and cataracts with occasional blepharitis. Formation of the lens vesicle during embryonic lens development was disordered in virtually all embryos. Lens placode invagination was less deep and gave rise to a conical structure instead of a spherical pit. At later stages either no lens vesicle was formed or a significantly smaller one that was not enclosed by the optic cup. Expression of the cell fate marker Pax6 was not altered. Staining of adherens junctions and F-actin was most intense at the tip of conical invaginations, suggesting that mechanical forces are not properly coordinated between epithelial cells that form the pit. CONCLUSIONS Myo9b is a critical regulator of ocular lens vesicle morphogenesis during eye development.
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Affiliation(s)
- Sandra A Hemkemeyer
- Institute of Integrative Cell Biology and Physiology, University of Muenster, Muenster, Germany
| | - Zhijun Liu
- Institute of Integrative Cell Biology and Physiology, University of Muenster, Muenster, Germany
| | - Veith Vollmer
- Institute of Integrative Cell Biology and Physiology, University of Muenster, Muenster, Germany
| | - Yan Xu
- Institute of Integrative Cell Biology and Physiology, University of Muenster, Muenster, Germany
| | - Birgit Lohmann
- Institute of Integrative Cell Biology and Physiology, University of Muenster, Muenster, Germany
| | - Martin Bähler
- Institute of Integrative Cell Biology and Physiology, University of Muenster, Muenster, Germany
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11
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Wonkam A, Adadey SM, Schrauwen I, Aboagye ET, Wonkam-Tingang E, Esoh K, Popel K, Manyisa N, Jonas M, deKock C, Nembaware V, Cornejo Sanchez DM, Bharadwaj T, Nasir A, Everard JL, Kadlubowska MK, Nouel-Saied LM, Acharya A, Quaye O, Amedofu GK, Awandare GA, Leal SM. Exome sequencing of families from Ghana reveals known and candidate hearing impairment genes. Commun Biol 2022; 5:369. [PMID: 35440622 PMCID: PMC9019055 DOI: 10.1038/s42003-022-03326-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/25/2022] [Indexed: 12/15/2022] Open
Abstract
We investigated hearing impairment (HI) in 51 families from Ghana with at least two affected members that were negative for GJB2 pathogenic variants. DNA samples from 184 family members underwent whole-exome sequencing (WES). Variants were found in 14 known non-syndromic HI (NSHI) genes [26/51 (51.0%) families], five genes that can underlie either syndromic HI or NSHI [13/51 (25.5%)], and one syndromic HI gene [1/51 (2.0%)]. Variants in CDH23 and MYO15A contributed the most to HI [31.4% (16/51 families)]. For DSPP, an autosomal recessive mode of inheritance was detected. Post-lingual expression was observed for a family segregating a MARVELD2 variant. To our knowledge, seven novel candidate HI genes were identified (13.7%), with six associated with NSHI (INPP4B, CCDC141, MYO19, DNAH11, POTEI, and SOX9); and one (PAX8) with Waardenburg syndrome. MYO19 and DNAH11 were replicated in unrelated Ghanaian probands. Six of the novel genes were expressed in mouse inner ear. It is known that Pax8-/- mice do not respond to sound, and depletion of Sox9 resulted in defective vestibular structures and abnormal utricle development. Most variants (48/60; 80.0%) have not previously been associated with HI. Identifying seven candidate genes in this study emphasizes the potential of novel HI genes discovery in Africa.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kalinka Popel
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Noluthando Manyisa
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Mario Jonas
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Carmen deKock
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Victoria Nembaware
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Diana M Cornejo Sanchez
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon-si, Republic of Korea
| | - Jenna L Everard
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Magda K Kadlubowska
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Geoffrey K Amedofu
- Department of Eye, Ear, Nose, and Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Centre, New York, NY, 10032, USA.
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12
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Munabi NCO, Mikhail S, Toubat O, Webb M, Auslander A, Sanchez-Lara PA, Manojlovic Z, Schmidt RJ, Craig D, Magee WP, Kumar SR. High prevalence of deleterious mutations in concomitant nonsyndromic cleft and outflow tract heart defects. Am J Med Genet A 2022; 188:2082-2095. [PMID: 35385219 PMCID: PMC9197864 DOI: 10.1002/ajmg.a.62748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/26/2022] [Accepted: 03/18/2022] [Indexed: 11/18/2022]
Abstract
Our previous work demonstrating enrichment of outflow tract (OFT) congenital heart disease (CHD) in children with cleft lip and/or palate (CL/P) suggests derangements in common underlying developmental pathways. The current pilot study examines the underlying genetics of concomitant nonsyndromic CL/P and OFT CHD phenotype. Of 575 patients who underwent CL/P surgery at Children's Hospital Los Angeles, seven with OFT CHD, negative chromosomal microarray analysis, and no recognizable syndromic association were recruited with their parents (as available). Whole genome sequencing of blood samples paired with whole‐blood‐based RNA sequencing for probands was performed. A pathogenic or potentially pathogenic variant was identified in 6/7 (85.7%) probands. A total of seven candidate genes were mutated (CHD7, SMARCA4, MED12, APOB, RNF213, SETX, and JAG1). Gene ontology analysis of variants predicted involvement in binding (100%), regulation of transcription (42.9%), and helicase activity (42.9%). Four patients (57.1%) expressed gene variants (CHD7, SMARCA4, MED12, and RNF213) previously involved in the Wnt signaling pathway. Our pilot analysis of a small cohort of patients with combined CL/P and OFT CHD phenotype suggests a potentially significant prevalence of deleterious mutations. In our cohort, an overrepresentation of mutations in molecules associated with Wnt‐signaling was found. These variants may represent an expanded phenotypic heterogeneity within known monogenic disease genes or provide novel evidence of shared developmental pathways. The mechanistic implications of these mutations and subsequent developmental derangements resulting in the CL/P and OFT CHD phenotype require further analysis in a larger cohort of patients.
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Affiliation(s)
- Naikhoba C O Munabi
- Division of Plastic and Reconstructive Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
| | | | - Omar Toubat
- Division of Cardiac Surgery, Department of Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Michelle Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | | | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Pathology, Keck School of Medicine of USC, Los Angeles, California, USA
| | - David Craig
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | - William P Magee
- Division of Plastic and Reconstructive Surgery, Keck School of Medicine of USC, Los Angeles, California, USA.,Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Plastic Surgery, Shriners Hospital for Children, Los Angeles, California, USA
| | - Subramanyan Ram Kumar
- Division of Cardiac Surgery, Department of Surgery, Keck School of Medicine of USC, Los Angeles, California, USA.,Heart Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
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13
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Li MJ, Shi JY, Zhu QS, Shi B, Jia ZL. Targeted Re-Sequencing of the 2p21 Locus Identifies Non-Syndromic Cleft Lip Only Novel Susceptibility Gene ZFP36L2. Front Genet 2022; 13:802229. [PMID: 35242166 PMCID: PMC8886408 DOI: 10.3389/fgene.2022.802229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
rs7590268 present on the 2p21 locus was identified to be associated with non-syndromic cleft lip with or without cleft palate (NSCL/P) in several populations, including the Chinese Han population, indicating that 2p21 was a susceptibility locus for NSCL/P. However, previous studies have only identified common single-nucleotide polymorphism (SNP) within the THADA gene, neglecting the rare variants and other genes in 2p21; thus, this study was designed to investigate additional variants and novel susceptibility genes in 2p21. A total of 159 NSCL/P patients and 542 controls were recruited in the discovery phase, whereas 1830 NSCL/P patients and 2,436 controls were recruited in the replication phase. After targeted region sequencing, we performed association and burden analyses for the common and rare variants, respectively. Furthermore, RNA-seq, proliferation assay and cell cycle analysis were performed to clarify the possible function of the candidate gene ZFP36L2. Association analysis showed that four SNPs were specifically associated with non-syndromic cleft lip only (NSCLO) and two SNPs were associated with both NSCLO and NSCL/P. Burden analysis indicated that ZFP36L2 was associated with NSCLO (p = .0489, OR = 2.41, 95% CI: 0.98–5.90). Moreover, SNPs in the ZFP36L2 targeted gene JUP were also associated with NSCLO. ZFP36L2 also inhibited cell proliferation and induced G2 phase arrest in the GMSM-K cell line. Therefore, we proposed that ZFP36L2 is a novel susceptibility gene of NSCLO in the 2p21 locus, which could lead to NSCLO by modulating cell proliferation and cycle.
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Affiliation(s)
- Mu-Jia Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Qiu-Shuang Zhu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China School of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Bing Shi, ; Zhong-Lin Jia,
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China School of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Bing Shi, ; Zhong-Lin Jia,
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14
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Boer EF, Maclary ET, Shapiro MD. Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons. Evol Dev 2021; 23:477-495. [PMID: 34914861 PMCID: PMC9119316 DOI: 10.1111/ede.12395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 10/28/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Abstract
Deciphering the genetic basis of vertebrate craniofacial variation is a longstanding biological problem with broad implications in evolution, development, and human pathology. One of the most stunning examples of craniofacial diversification is the adaptive radiation of birds, in which the beak serves essential roles in virtually every aspect of their life histories. The domestic pigeon (Columba livia) provides an exceptional opportunity to study the genetic underpinnings of craniofacial variation because of its unique balance of experimental accessibility and extraordinary phenotypic diversity within a single species. We used traditional and geometric morphometrics to quantify craniofacial variation in an F2 laboratory cross derived from the straight-beaked Pomeranian Pouter and curved-beak Scandaroon pigeon breeds. Using a combination of genome-wide quantitative trait locus scans and multi-locus modeling, we identified a set of genetic loci associated with complex shape variation in the craniofacial skeleton, including beak shape, braincase shape, and mandible shape. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. We find that in domestic pigeons, a complex blend of both independent and coupled genetic effects underlie three-dimensional craniofacial morphology.
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Affiliation(s)
- Elena F. Boer
- School of Biological SciencesUniversity of UtahSalt Lake CityUtahUSA
| | - Emily T. Maclary
- School of Biological SciencesUniversity of UtahSalt Lake CityUtahUSA
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15
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Cunningham AM, Walker DM, Ramakrishnan A, Doyle MA, Bagot RC, Cates HM, Peña CJ, Issler O, Lardner CK, Browne C, Russo SJ, Shen L, Nestler EJ. Sperm Transcriptional State Associated with Paternal Transmission of Stress Phenotypes. J Neurosci 2021; 41:6202-6216. [PMID: 34099514 PMCID: PMC8287983 DOI: 10.1523/jneurosci.3192-20.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/25/2021] [Accepted: 04/20/2021] [Indexed: 01/03/2023] Open
Abstract
Paternal stress can induce long-lasting changes in germ cells potentially propagating heritable changes across generations. To date, no studies have investigated differences in transmission patterns between stress-resilient and stress-susceptible mice. We tested the hypothesis that transcriptional alterations in sperm during chronic social defeat stress (CSDS) transmit increased susceptibility to stress phenotypes to the next generation. We demonstrate differences in offspring from stressed fathers that depend on paternal category (resilient vs susceptible) and offspring sex. Importantly, artificial insemination (AI) reveals that sperm mediates some of the behavioral phenotypes seen in offspring. Using RNA-sequencing (RNA-seq), we report substantial and distinct changes in the transcriptomic profiles of sperm following CSDS in susceptible versus resilient fathers, with alterations in long noncoding RNAs (lncRNAs) predominating especially in susceptibility. Correlation analysis revealed that these alterations were accompanied by a loss of regulation of protein-coding genes by lncRNAs in sperm of susceptible males. We also identify several co-expression gene modules that are enriched in differentially expressed genes (DEGs) in sperm from either resilient or susceptible fathers. Taken together, these studies advance our understanding of intergenerational epigenetic transmission of behavioral experience.SIGNIFICANCE STATEMENT This manuscript contributes to the complex factors that influence the paternal transmission of stress phenotypes. By leveraging the segregation of males exposed to chronic social defeat stress (CSDS) into either resilient or susceptible categories we were able to identify the phenotypic differences in the paternal transmission of stress phenotypes across generations between the two lineages. Importantly, this work also alludes to the significance of both long noncoding RNAs (lncRNAs) and protein coding genes (PCGs) mediating the paternal transmission of stress. The knowledge gained from these data are of particular interest in understanding the risk for the development of psychiatric disorders such as anxiety and depression.
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Affiliation(s)
- Ashley M Cunningham
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Deena M Walker
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Aarthi Ramakrishnan
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Marie A Doyle
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Rosemary C Bagot
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Hannah M Cates
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Catherine J Peña
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Orna Issler
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Casey K Lardner
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Caleb Browne
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Scott J Russo
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Li Shen
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Eric J Nestler
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
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16
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Punovuori K, Malaguti M, Lowell S. Cadherins in early neural development. Cell Mol Life Sci 2021; 78:4435-4450. [PMID: 33796894 PMCID: PMC8164589 DOI: 10.1007/s00018-021-03815-9] [Citation(s) in RCA: 12] [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: 10/22/2020] [Revised: 03/04/2021] [Accepted: 03/18/2021] [Indexed: 11/12/2022]
Abstract
During early neural development, changes in signalling inform the expression of transcription factors that in turn instruct changes in cell identity. At the same time, switches in adhesion molecule expression result in cellular rearrangements that define the morphology of the emerging neural tube. It is becoming increasingly clear that these two processes influence each other; adhesion molecules do not simply operate downstream of or in parallel with changes in cell identity but rather actively feed into cell fate decisions. Why are differentiation and adhesion so tightly linked? It is now over 60 years since Conrad Waddington noted the remarkable "Constancy of the Wild Type" (Waddington in Nature 183: 1654-1655, 1959) yet we still do not fully understand the mechanisms that make development so reproducible. Conversely, we do not understand why directed differentiation of cells in a dish is sometimes unpredictable and difficult to control. It has long been suggested that cells make decisions as 'local cooperatives' rather than as individuals (Gurdon in Nature 336: 772-774, 1988; Lander in Cell 144: 955-969, 2011). Given that the cadherin family of adhesion molecules can simultaneously influence morphogenesis and signalling, it is tempting to speculate that they may help coordinate cell fate decisions between neighbouring cells in the embryo to ensure fidelity of patterning, and that the uncoupling of these processes in a culture dish might underlie some of the problems with controlling cell fate decisions ex-vivo. Here we review the expression and function of cadherins during early neural development and discuss how and why they might modulate signalling and differentiation as neural tissues are formed.
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Affiliation(s)
- Karolina Punovuori
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Little France Drive, Edinburgh, EH16 4UU, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Little France Drive, Edinburgh, EH16 4UU, UK.
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17
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Crosstalk among Calcium ATPases: PMCA, SERCA and SPCA in Mental Diseases. Int J Mol Sci 2021; 22:ijms22062785. [PMID: 33801794 PMCID: PMC8000800 DOI: 10.3390/ijms22062785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Calcium in mammalian neurons is essential for developmental processes, neurotransmitter release, apoptosis, and signal transduction. Incorrectly processed Ca2+ signal is well-known to trigger a cascade of events leading to altered response to variety of stimuli and persistent accumulation of pathological changes at the molecular level. To counterbalance potentially detrimental consequences of Ca2+, neurons are equipped with sophisticated mechanisms that function to keep its concentration in a tightly regulated range. Calcium pumps belonging to the P-type family of ATPases: plasma membrane Ca2+-ATPase (PMCA), sarco/endoplasmic Ca2+-ATPase (SERCA) and secretory pathway Ca2+-ATPase (SPCA) are considered efficient line of defense against abnormal Ca2+ rises. However, their role is not limited only to Ca2+ transport, as they present tissue-specific functionality and unique sensitive to the regulation by the main calcium signal decoding protein—calmodulin (CaM). Based on the available literature, in this review we analyze the contribution of these three types of Ca2+-ATPases to neuropathology, with a special emphasis on mental diseases.
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18
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Lasić V, Kosović I, Jurić M, Racetin A, Čurčić J, Šolić I, Lozić M, Filipović N, Šoljić V, Martinović V, Saraga-Babić M, Vukojević K. GREB1L, CRELD2 and ITGA10 expression in the human developmental and postnatal kidneys: an immunohistochemical study. Acta Histochem 2021; 123:151679. [PMID: 33460985 DOI: 10.1016/j.acthis.2021.151679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/19/2020] [Accepted: 01/01/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Aim of our study is to provide an insight into the genetic expression landscape of GREB1L, ITGA10 and CRELD2 which are important in human genitourinary tract development which might help elucidate the critical stages for the onset of kidney anomalies. METHODS Morphological parameters were analyzed using immunohistochemistry on human foetal (13-38 w) and postnatal (1.5 and 7.5y) human kidney samples. RESULTS GREB1L marker had a strong intensity and the highest rate in proximal tubules (PTC) of 1.5 years' kidney (90.25%). In the distal tubules (DCT) there were statistically significant differences in 13 w, 15 w, 16 w, 21 w, 38 w and 7.5y regarding 1.5y (Kruskal-Wallis test, p < 0.001). There was significantly more GREB1L in the glomeruli at 21 w and 38 w in regard to all other stages (Kruskal-Wallis test, p < 0.01). ITGA10 staining intensity was strongest in PCT with the highest rate in 13 w (92.75%), while the lowest rate was found in glomeruli and DCT (Kruskal-Wallis test, p < 0.001). CRELD2 had the strongest staining intensity in PCT with the highest rate in 13 w and 1.5y (92.25%) and lowest in the glomeruli of 7.5 years (24.3 %). In DCT there were statistically significant differences in CRELD2 positive cells in 13 w, 15 w, 16 w, 21 w, 38 w and 7.5y regarding 1.5y (Kruskal-Wallis test, p < 0.01). ITGA10 and CRELD2 co-localised in the postnatal period in DCT. CONCLUSION High kidney expressions of GREB1L, ITGA10 and CRELD2 even in the postnatal period implicate their importance not only for the onset of CAKUT in the case of their mutation but also for maintenance of kidney homeostasis.
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19
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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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20
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Kidwai F, Mui BWH, Arora D, Iqbal K, Hockaday M, de Castro Diaz LF, Cherman N, Martin D, Myneni VD, Ahmad M, Futrega K, Ali S, Merling RK, Kaufman DS, Lee J, Robey PG. Lineage-specific differentiation of osteogenic progenitors from pluripotent stem cells reveals the FGF1-RUNX2 association in neural crest-derived osteoprogenitors. Stem Cells 2020; 38:1107-1123. [PMID: 32442326 PMCID: PMC7484058 DOI: 10.1002/stem.3206] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/01/2020] [Indexed: 12/16/2022]
Abstract
Human pluripotent stem cells (hPSCs) can provide a platform to model bone organogenesis and disease. To reflect the developmental process of the human skeleton, hPSC differentiation methods should include osteogenic progenitors (OPs) arising from three distinct embryonic lineages: the paraxial mesoderm, lateral plate mesoderm, and neural crest. Although OP differentiation protocols have been developed, the lineage from which they are derived, as well as characterization of their genetic and molecular differences, has not been well reported. Therefore, to generate lineage-specific OPs from human embryonic stem cells and human induced pluripotent stem cells, we employed stepwise differentiation of paraxial mesoderm-like cells, lateral plate mesoderm-like cells, and neural crest-like cells toward their respective OP subpopulation. Successful differentiation, confirmed through gene expression and in vivo assays, permitted the identification of transcriptomic signatures of all three cell populations. We also report, for the first time, high FGF1 levels in neural crest-derived OPs-a notable finding given the critical role of fibroblast growth factors (FGFs) in osteogenesis and mineral homeostasis. Our results indicate that FGF1 influences RUNX2 levels, with concomitant changes in ERK1/2 signaling. Overall, our study further validates hPSCs' power to model bone development and disease and reveals new, potentially important pathways influencing these processes.
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Affiliation(s)
- Fahad Kidwai
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Byron W. H. Mui
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Deepika Arora
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
- Biosystems and Biomaterials DivisionNational Institute of Standards and TechnologyGaithersburgMarylandUSA
| | - Kulsum Iqbal
- Department of Health and Human ServicesDental Consult Services, National Institute of Health Dental ClinicBethesdaMarylandUSA
| | - Madison Hockaday
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Luis Fernandez de Castro Diaz
- Department of Health and Human ServicesSkeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Natasha Cherman
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Daniel Martin
- Department of Health and Human ServicesGenomics and Computational Biology Core, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Vamsee D. Myneni
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch/Adult Stem Cell Section, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Moaz Ahmad
- Department of Health and Human ServicesMolecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Katarzyna Futrega
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Sania Ali
- Biology of Global Health, Department of BiologyGeorgetown UniversityWashingtonDistrict of ColumbiaUSA
| | - Randall K. Merling
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Dan S. Kaufman
- Department of MedicineUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Janice Lee
- Department of Health and Human ServicesCraniofacial Anomalies and Regeneration Section, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Pamela G. Robey
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
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21
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Autosomal Dominantly Inherited GREB1L Variants in Individuals with Profound Sensorineural Hearing Impairment. Genes (Basel) 2020; 11:genes11060687. [PMID: 32585897 PMCID: PMC7349314 DOI: 10.3390/genes11060687] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/16/2020] [Accepted: 06/20/2020] [Indexed: 01/15/2023] Open
Abstract
Congenital hearing impairment is a sensory disorder that is genetically highly heterogeneous. By performing exome sequencing in two families with congenital nonsyndromic profound sensorineural hearing loss (SNHL), we identified autosomal dominantly inherited missense variants [p.(Asn283Ser); p.(Thr116Ile)] in GREB1L, a neural crest regulatory molecule. The p.(Thr116Ile) variant was also associated with bilateral cochlear aplasia and cochlear nerve aplasia upon temporal bone imaging, an ultra-rare phenotype previously seen in patients with de novo GREB1L variants. An important role of GREB1L in normal ear development has also been demonstrated by greb1l-/- zebrafish, which show an abnormal sensory epithelia innervation. Last, we performed a review of all disease-associated variation described in GREB1L, as it has also been implicated in renal, bladder and genital malformations. We show that the spectrum of features associated with GREB1L is broad, variable and with a high level of reduced penetrance, which is typically characteristic of neurocristopathies. So far, seven GREB1L variants (14%) have been associated with ear-related abnormalities. In conclusion, these results show that autosomal dominantly inherited variants in GREB1L cause profound SNHL. Furthermore, we provide an overview of the phenotypic spectrum associated with GREB1L variants and strengthen the evidence of the involvement of GREB1L in human hearing.
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22
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Fan Z, Chen R, Chen X. SpatialDB: a database for spatially resolved transcriptomes. Nucleic Acids Res 2020; 48:D233-D237. [PMID: 31713629 PMCID: PMC7145543 DOI: 10.1093/nar/gkz934] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
Spatially resolved transcriptomic techniques allow the characterization of spatial organization of cells in tissues, which revolutionize the studies of tissue function and disease pathology. New strategies for detecting spatial gene expression patterns are emerging, and spatially resolved transcriptomic data are accumulating rapidly. However, it is not convenient for biologists to exploit these data due to the diversity of strategies and complexity in data analysis. Here, we present SpatialDB, the first manually curated database for spatially resolved transcriptomic techniques and datasets. The current version of SpatialDB contains 24 datasets (305 sub-datasets) from 5 species generated by 8 spatially resolved transcriptomic techniques. SpatialDB provides a user-friendly web interface for visualization and comparison of spatially resolved transcriptomic data. To further explore these data, SpatialDB also provides spatially variable genes and their functional enrichment annotation. SpatialDB offers a repository for research community to investigate the spatial cellular structure of tissues, and may bring new insights into understanding the cellular microenvironment in disease. SpatialDB is freely available at https://www.spatialomics.org/SpatialDB.
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Affiliation(s)
- Zhen Fan
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Runsheng Chen
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Chen
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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23
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Bajad P, Ebner F, Amman F, Szabó B, Kapoor U, Manjali G, Hildebrandt A, Janisiw MP, Jantsch MF. An internal deletion of ADAR rescued by MAVS deficiency leads to a minute phenotype. Nucleic Acids Res 2020; 48:3286-3303. [PMID: 31956894 PMCID: PMC7102943 DOI: 10.1093/nar/gkaa025] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022] Open
Abstract
The RNA-editing protein ADAR is essential for early development in the mouse. Genetic evidence suggests that A to I editing marks endogenous RNAs as ‘self’. Today, different Adar knockout alleles have been generated that show a common phenotype of apoptosis, liver disintegration, elevated immune response and lethality at E12.5. All the Adar knockout alleles can be rescued by a concomitant deletion of the innate immunity genes Mavs or Ifih1 (MDA5), albeit to different extents. This suggests multiple functions of ADAR. We analyze AdarΔ7-9 mice that show a unique growth defect phenotype when rescued by Mavs. We show that AdarΔ7-9 can form a truncated, unstable, editing deficient protein that is mislocalized. Histological and hematologic analysis of these mice indicate multiple tissue- and hematopoietic defects. Gene expression profiling shows dysregulation of Rps3a1 and Rps3a3 in rescued AdarΔ7-9. Consistently, a distortion in 40S and 60S ribosome ratios is observed in liver cells. This dysregulation is also seen in AdarΔ2-13; Mavs−/− but not in AdarE861A/E861A; Ifih1−/− mice, suggesting editing-independent functions of ADAR in regulating expression levels of Rps3a1 and Rps3a3. In conclusion, our study demonstrates the importance of ADAR in post-natal development which cannot be compensated by ADARB1.
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Affiliation(s)
- Prajakta Bajad
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Florian Ebner
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Fabian Amman
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.,Institute of Theoretical Biochemistry, University of Vienna, Währinger Strasse 17, A-1090 Vienna, Austria
| | - Brigitta Szabó
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Utkarsh Kapoor
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Greeshma Manjali
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Alwine Hildebrandt
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Michael P Janisiw
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
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24
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Yusuf L, Heatley MC, Palmer JPG, Barton HJ, Cooney CR, Gossmann TI. Noncoding regions underpin avian bill shape diversification at macroevolutionary scales. Genome Res 2020; 30:553-565. [PMID: 32269134 PMCID: PMC7197477 DOI: 10.1101/gr.255752.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022]
Abstract
Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence, and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein-coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1434 protein-coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein-coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cell pathways, including BMP and Wnt signaling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome-wide scale over macroevolutionary time is feasible. Although the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.
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Affiliation(s)
- Leeban Yusuf
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, KY16 9TF, United Kingdom
| | - Matthew C Heatley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Joseph P G Palmer
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, United Kingdom
| | - Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Organismal and Evolutionary Biology Research Programme, Viikinkaari 9 (PL 56), University of Helsinki, Helsinki, FI-00014, Finland
| | - Christopher R Cooney
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Department of Animal Behaviour, Bielefeld University, Bielefeld, DE-33501, Germany
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25
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Hussain S, Umm-E-Kalsoom, Ullah I, Liaqat K, Nawaz S, Ahmad W. A Novel Missense Variant in the ALX4 Gene Underlies Mild to Severe Frontonasal Dysplasia in a Consanguineous Family. Genet Test Mol Biomarkers 2020; 24:217-223. [PMID: 32216639 DOI: 10.1089/gtmb.2019.0203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Frontonasal dysplasia (FND) is a rare developmental disorder characterized by mild to severe changes in skull and brain structures. It is a phenotypically variable and heterogeneous disorder. This study was designed to provide a clinical and genetic analysis of FND in a consanguineous family of Pakistani origin. Methodology and Results: Affected individuals in the family showed characteristic features of frontonasal dysplasia type-2 (FND2), such as nasal bone hypoplasia, hypertelorism, and alopecia. Skull and brain imaging of affected members revealed ossification defects and various types of brain structural anomalies that created a split-brain. Sanger sequencing of the ALX4 gene revealed a homozygous missense variant [NM_021926.4: c.652C>T; p.(Arg218Trp)] in three affected members who demonstrated severe craniofacial anomalies. Heterozygous carriers in the family showed mild FND2 phenotypes. Conclusion: Clinical and genetic analysis of a family, exhibiting FND2 phenotypes, revealed several previously unreported clinical features and a novel missense variant in the ALX4 gene. These results will facilitate diagnosis and genetic counseling of the FND patients in the Pakistani population.
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Affiliation(s)
- Shabir Hussain
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Umm-E-Kalsoom
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Irfan Ullah
- Department of Biological Sciences, Shaheed Benazir Bhutto University, Upper Dir, Pakistan
| | - Khurram Liaqat
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shoaib Nawaz
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
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26
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Chen L, Pan X, Guo W, Gan Z, Zhang YH, Niu Z, Huang T, Cai YD. Investigating the gene expression profiles of cells in seven embryonic stages with machine learning algorithms. Genomics 2020; 112:2524-2534. [PMID: 32045671 DOI: 10.1016/j.ygeno.2020.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/26/2019] [Accepted: 02/07/2020] [Indexed: 12/15/2022]
Abstract
The development of embryonic cells involves several continuous stages, and some genes are related to embryogenesis. To date, few studies have systematically investigated changes in gene expression profiles during mammalian embryogenesis. In this study, a computational analysis using machine learning algorithms was performed on the gene expression profiles of mouse embryonic cells at seven stages. First, the profiles were analyzed through a powerful Monte Carlo feature selection method for the generation of a feature list. Second, increment feature selection was applied on the list by incorporating two classification algorithms: support vector machine (SVM) and repeated incremental pruning to produce error reduction (RIPPER). Through SVM, we extracted several latent gene biomarkers, indicating the stages of embryonic cells, and constructed an optimal SVM classifier that produced a nearly perfect classification of embryonic cells. Furthermore, some interesting rules were accessed by the RIPPER algorithm, suggesting different expression patterns for different stages.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, China; College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China; Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai 200241, China.
| | - XiaoYong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Key Laboratory of System Control and Information Processing, Ministry of Education of China, 200240 Shanghai, China.
| | - Wei Guo
- Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Zijun Gan
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Zhibin Niu
- College of Intelligence and Computing, Tianjin University, Tianjin 300072, China.
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
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27
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Belyaeva OV, Adams MK, Popov KM, Kedishvili NY. Generation of Retinaldehyde for Retinoic Acid Biosynthesis. Biomolecules 2019; 10:biom10010005. [PMID: 31861321 PMCID: PMC7022914 DOI: 10.3390/biom10010005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
The concentration of all-trans-retinoic acid, the bioactive derivative of vitamin A, is critically important for the optimal performance of numerous physiological processes. Either too little or too much of retinoic acid in developing or adult tissues is equally harmful. All-trans-retinoic acid is produced by the irreversible oxidation of all-trans-retinaldehyde. Thus, the concentration of retinaldehyde as the immediate precursor of retinoic acid has to be tightly controlled. However, the enzymes that produce all-trans-retinaldehyde for retinoic acid biosynthesis and the mechanisms responsible for the control of retinaldehyde levels have not yet been fully defined. The goal of this review is to summarize the current state of knowledge regarding the identities of physiologically relevant retinol dehydrogenases, their enzymatic properties, and tissue distribution, and to discuss potential mechanisms for the regulation of the flux from retinol to retinaldehyde.
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Affiliation(s)
- Olga V. Belyaeva
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
- Correspondence: ; Tel.: +1-205-996-4024
| | - Mark K. Adams
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA;
| | - Kirill M. Popov
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
| | - Natalia Y. Kedishvili
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
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28
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Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Rep 2019; 23:1581-1597. [PMID: 29719267 PMCID: PMC5965702 DOI: 10.1016/j.celrep.2018.03.129] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/29/2022] Open
Abstract
Defects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information located between genes and within intronic sequences. However, systematic identification of regulatory sequences important for forming the human face has not been performed. Here, we describe comprehensive epigenomic annotations from human embryonic craniofacial tissues and systematic comparisons with multiple tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences and likely causal regions for rare craniofacial abnormalities. We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.
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Affiliation(s)
- Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | | | - Jeffrey Kron
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - James P Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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29
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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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30
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Grimes T, Potter SS, Datta S. Integrating gene regulatory pathways into differential network analysis of gene expression data. Sci Rep 2019; 9:5479. [PMID: 30940863 PMCID: PMC6445151 DOI: 10.1038/s41598-019-41918-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/12/2019] [Indexed: 12/22/2022] Open
Abstract
The advent of next-generation sequencing has introduced new opportunities in analyzing gene expression data. Research in systems biology has taken advantage of these opportunities by gleaning insights into gene regulatory networks through the analysis of gene association networks. Contrasting networks from different populations can reveal the many different roles genes fill, which can lead to new discoveries in gene function. Pathologies can also arise from aberrations in these gene-gene interactions. Exposing these network irregularities provides a new avenue for understanding and treating diseases. A general framework for integrating known gene regulatory pathways into a differential network analysis between two populations is proposed. The framework importantly allows for any gene-gene association measure to be used, and inference is carried out through permutation testing. A simulation study investigates the performance in identifying differentially connected genes when incorporating known pathways, even if the pathway knowledge is partially inaccurate. Another simulation study compares the general framework with four state-of-the-art methods. Two RNA-seq datasets are analyzed to illustrate the use of this framework in practice. In both examples, the analysis reveals genes and pathways that are known to be biologically significant along with potentially novel findings that may be used to motivate future research.
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Affiliation(s)
- Tyler Grimes
- University of Florida, Department of Biostatistics, Gainesville, 32611, USA
| | - S Steven Potter
- University of Cincinnati, Department of Pediatrics, Cincinnati, 45229, USA
| | - Somnath Datta
- University of Florida, Department of Biostatistics, Gainesville, 32611, USA.
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31
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Abstract
The purpose of this chapter is to provide a step-by-step protocol to enable performance of laser capture microdissection (LCM) on tissue sections from mammalian embryos or postnatal organism stages in order to collect pure populations of neural crest cells from which sufficient amounts of nucleic acids and/or protein can be obtained for quantitative analysis. The methods (1) define a strategy to genetically and indelibly label mammalian neural crest-derived cells with a fluorescent marker, thus enabling their isolation throughout the pre- and postnatal life span of the organism, and (2) describe subsequent isolation by LCM of the labeled neural crest cells, or their derivatives, from embryonic/postnatal tissue cryosections. Details are provided for using the Arcturus PixCell®IIe Laser Capture Microdissection System (Arcturus) and CapSure LCM Caps (Thermo Fisher Scientific), to which the selected cells adhere upon laser-mediated capture. The protocol outlined herein can be applied in any situation wherein limited cellular samples are available for isolation by LCM. Nucleic acids or proteins can be extracted from LCM-isolated cells and processed for high-density gene expression profiling analyses (microarrays or RNA sequencing), Real-Time PCR (q-PCR) for specific candidate gene expression, investigation of DNA methylation, as well as for varied protein analyses.
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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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Brown JM, García-García MJ. Secretory pathway calcium ATPase 1 (SPCA1) controls mouse neural tube closure by regulating cytoskeletal dynamics. Development 2018; 145:dev.170019. [PMID: 30228103 DOI: 10.1242/dev.170019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/05/2018] [Indexed: 12/26/2022]
Abstract
Neural tube closure relies on the apical constriction of neuroepithelial cells. Research in frog and fly embryos has found links between the levels of intracellular calcium, actomyosin dynamics and apical constriction. However, genetic evidence for a role of calcium in apical constriction during mammalian neurulation is still lacking. Secretory pathway calcium ATPase (SPCA1) regulates calcium homeostasis by pumping cytosolic calcium into the Golgi apparatus. Loss of function in Spca1 causes cranial exencephaly and spinal cord defects in mice, phenotypes previously ascribed to apoptosis. However, our characterization of a novel allele of Spca1 revealed that neurulation defects in Spca1 mutants are not due to cell death, but rather to a failure of neuroepithelial cells to apically constrict. We show that SPCA1 influences cell contractility by regulating myosin II localization. Furthermore, we found that loss of Spca1 disrupts actin dynamics and the localization of the actin remodeling protein cofilin 1. Taken together, our results provide evidence that SPCA1 promotes neurulation by regulating the cytoskeletal dynamics that promote apical constriction and identify cofilin 1 as a downstream effector of SPCA1 function.
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Affiliation(s)
- Joel M Brown
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - María J García-García
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Schrauwen I, Kari E, Mattox J, Llaci L, Smeeton J, Naymik M, Raible DW, Knowles JA, Crump JG, Huentelman MJ, Friedman RA. De novo variants in GREB1L are associated with non-syndromic inner ear malformations and deafness. Hum Genet 2018; 137:459-470. [PMID: 29955957 PMCID: PMC6082420 DOI: 10.1007/s00439-018-1898-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/19/2018] [Indexed: 11/24/2022]
Abstract
Congenital inner ear malformations affecting both the osseous and membranous labyrinth can have a devastating impact on hearing and language development. With the exception of an enlarged vestibular aqueduct, non-syndromic inner ear malformations are rare, and their underlying molecular biology has thus far remained understudied. To identify molecular factors that might be important in the developing inner ear, we adopted a family-based trio exome sequencing approach in young unrelated subjects with severe inner ear malformations. We identified two previously unreported de novo loss-of-function variants in GREB1L [c.4368G>T;p.(Glu1410fs) and c.982C>T;p.(Arg328*)] in two affected subjects with absent cochleae and eighth cranial nerve malformations. The cochlear aplasia in these affected subjects suggests that a developmental arrest or problem at a very early stage of inner ear development exists, e.g., during the otic pit formation. Craniofacial Greb1l RNA expression peaks in mice during this time frame (E8.5). It also peaks in the developing inner ear during E13-E16, after which it decreases in adulthood. The crucial function of Greb1l in craniofacial development is also evidenced in knockout mice, which develop severe craniofacial abnormalities. In addition, we show that Greb1l-/- zebrafish exhibit a loss of abnormal sensory epithelia innervation. An important role for Greb1l in sensory epithelia innervation development is supported by the eighth cranial nerve deficiencies seen in both affected subjects. In conclusion, we demonstrate that GREB1L is a key player in early inner ear and eighth cranial nerve development. Abnormalities in cochleovestibular anatomy can provide challenges for cochlear implantation. Combining a molecular diagnosis with imaging techniques might aid the development of individually tailored therapeutic interventions in the future.
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Affiliation(s)
- Isabelle Schrauwen
- Molecular and Human Genetics Department, Center for Statistical Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA.
| | - Elina Kari
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
| | - Jacob Mattox
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, Keck University of Southern California School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Lorida Llaci
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Joanna Smeeton
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Marcus Naymik
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - James A Knowles
- Department of Cell Biology-MSC 5, SUNY Downstate Medical Center, 450 Clarkson Avenue, BSB 2-5, Brooklyn, NY, 11203, USA
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Matthew J Huentelman
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Rick A Friedman
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
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Schneider RA. Neural crest and the origin of species-specific pattern. Genesis 2018; 56:e23219. [PMID: 30134069 PMCID: PMC6108449 DOI: 10.1002/dvg.23219] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/20/2022]
Abstract
For well over half of the 150 years since the discovery of the neural crest, the special ability of these cells to function as a source of species-specific pattern has been clearly recognized. Initially, this observation arose in association with chimeric transplant experiments among differentially pigmented amphibians, where the neural crest origin for melanocytes had been duly noted. Shortly thereafter, the role of cranial neural crest cells in transmitting species-specific information on size and shape to the pharyngeal arch skeleton as well as in regulating the timing of its differentiation became readily apparent. Since then, what has emerged is a deeper understanding of how the neural crest accomplishes such a presumably difficult mission, and this includes a more complete picture of the molecular and cellular programs whereby neural crest shapes the face of each species. This review covers studies on a broad range of vertebrates and describes neural-crest-mediated mechanisms that endow the craniofacial complex with species-specific pattern. A major focus is on experiments in quail and duck embryos that reveal a hierarchy of cell-autonomous and non-autonomous signaling interactions through which neural crest generates species-specific pattern in the craniofacial integument, skeleton, and musculature. By controlling size and shape throughout the development of these systems, the neural crest underlies the structural and functional integration of the craniofacial complex during evolution.
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Affiliation(s)
- Richard A. Schneider
- Department of Orthopedic SurgeryUniversity of California at San Francisco, 513 Parnassus AvenueS‐1161San Francisco, California
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36
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Gu M, Zhang Y, Liu H, Liu J, Zhu D, Yang X. MSH homeobox 1 polymorphisms and the risk of non-syndromic orofacial clefts: a meta-analysis. Eur J Oral Sci 2018; 126:180-185. [PMID: 29664137 DOI: 10.1111/eos.12414] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Min Gu
- Department of Dentistry; The Third Affiliated Hospital of Soochow University; The First People's Hospital of Changzhou; Changzhou China
| | - Yan Zhang
- Department of Dentistry; The Third Affiliated Hospital of Soochow University; The First People's Hospital of Changzhou; Changzhou China
| | - Hualian Liu
- Department of Dentistry; The Third Affiliated Hospital of Soochow University; The First People's Hospital of Changzhou; Changzhou China
| | - Jue Liu
- Department of Dentistry; The Third Affiliated Hospital of Soochow University; The First People's Hospital of Changzhou; Changzhou China
| | - Danxia Zhu
- Department of Oncology; The Third Affiliated Hospital of Soochow University; The First People's Hospital of Changzhou; Changzhou China
| | - Xu Yang
- Department of Dentistry; The Third Affiliated Hospital of Soochow University; The First People's Hospital of Changzhou; Changzhou China
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37
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Pijuan-Sala B, Guibentif C, Göttgens B. Single-cell transcriptional profiling: a window into embryonic cell-type specification. Nat Rev Mol Cell Biol 2018; 19:399-412. [DOI: 10.1038/s41580-018-0002-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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38
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Percival CJ, Green R, Roseman CC, Gatti DM, Morgan JL, Murray SA, Donahue LR, Mayeux JM, Pollard KM, Hua K, Pomp D, Marcucio R, Hallgrímsson B. Developmental constraint through negative pleiotropy in the zygomatic arch. EvoDevo 2018; 9:3. [PMID: 29423138 PMCID: PMC5787316 DOI: 10.1186/s13227-018-0092-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/08/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Previous analysis suggested that the relative contribution of individual bones to regional skull lengths differ between inbred mouse strains. If the negative correlation of adjacent bone lengths is associated with genetic variation in a heterogeneous population, it would be an example of negative pleiotropy, which occurs when a genetic factor leads to opposite effects in two phenotypes. Confirming negative pleiotropy and determining its basis may reveal important information about the maintenance of overall skull integration and developmental constraint on skull morphology. RESULTS We identified negative correlations between the lengths of the frontal and parietal bones in the midline cranial vault as well as the zygomatic bone and zygomatic process of the maxilla, which contribute to the zygomatic arch. Through gene association mapping of a large heterogeneous population of Diversity Outbred (DO) mice, we identified a quantitative trait locus on chromosome 17 driving the antagonistic contribution of these two zygomatic arch bones to total zygomatic arch length. Candidate genes in this region were identified and real-time PCR of the maxillary processes of DO founder strain embryos indicated differences in the RNA expression levels for two of the candidate genes, Camkmt and Six2. CONCLUSIONS A genomic region underlying negative pleiotropy of two zygomatic arch bones was identified, which provides a mechanism for antagonism in component bone lengths while constraining overall zygomatic arch length. This type of mechanism may have led to variation in the contribution of individual bones to the zygomatic arch noted across mammals. Given that similar genetic and developmental mechanisms may underlie negative correlations in other parts of the skull, these results provide an important step toward understanding the developmental basis of evolutionary variation and constraint in skull morphology.
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Affiliation(s)
| | - Rebecca Green
- Alberta Children’s Hospital Institute for Child and Maternal Health, University of Calgary, Calgary, AB Canada
- The McCaig Bone and Joint Institute, University of Calgary, Calgary, AB Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB Canada
| | - Charles C. Roseman
- Program in Ecology Evolution and Conservation Biology, University of Illinois, Urbana, IL USA
| | | | | | | | | | - Jessica M. Mayeux
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - K. Michael Pollard
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Kunjie Hua
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC USA
| | - Daniel Pomp
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC USA
| | - Ralph Marcucio
- The Orthopaedic Trauma Institute, Department of Orthopaedic Surgery, UCSF School of Medicine, San Francisco, CA USA
| | - Benedikt Hallgrímsson
- Alberta Children’s Hospital Institute for Child and Maternal Health, University of Calgary, Calgary, AB Canada
- The McCaig Bone and Joint Institute, University of Calgary, Calgary, AB Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB Canada
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Munjal C, Jegga AG, Opoka AM, Stoilov I, Norris RA, Thomas CJ, Smith JM, Mecham RP, Bressan GM, Hinton RB. Inhibition of MAPK-Erk pathway in vivo attenuates aortic valve disease processes in Emilin1-deficient mouse model. Physiol Rep 2017; 5:5/5/e13152. [PMID: 28270590 PMCID: PMC5350168 DOI: 10.14814/phy2.13152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/08/2017] [Indexed: 12/20/2022] Open
Abstract
Aortic valve disease (AVD) is a common condition with a progressive natural history, and presently, there are no pharmacologic treatment strategies. Elastic fiber fragmentation (EFF) is a hallmark of AVD, and increasing evidence implicates developmental elastic fiber assembly defects. Emilin1 is a glycoprotein necessary for elastic fiber assembly that is present in both developing and mature human and mouse aortic valves. The Emilin1‐deficient mouse (Emilin1−/−) is a model of latent AVD, characterized by activated TGFβ/MEK/p‐Erk signaling and upregulated elastase activity. Emilin1−/− aortic valves demonstrate early EFF and aberrant angiogenesis followed by late neovascularization and fibrosis. The objective of this study was to test the effectiveness of three different targeted therapies. Aged (12–14 months) Emilin1−/− mice were treated with refametinib (RDEA‐119, MEK1/2 inhibitor), doxycycline (elastase inhibitor), or G6‐31 (anti‐VEGF‐A mouse antibody) for 4 weeks. Refametinib‐ and doxycycline‐treated Emilin1−/− mice markedly reduced MEK/p‐Erk activation in valve tissue. Furthermore, both refametinib and doxycycline attenuated elastolytic cathepsin K, L, MMP‐2, and MMP‐9 activation, and abrogated macrophage and neutrophil infiltration in Emilin1−/− aortic valves. RNAseq analysis was performed in aortic valve tissue from adult (4 months) and aged (14 months) Emilin1−/− and age‐matched wild‐type control mice, and demonstrated upregulation of genes associated with MAPK/MEK/p‐Erk signaling and elastases at the adult stage and inflammatory pathways at the aged stage controlling for age. These results suggest that Erk1/2 signaling is an important modulator of early elastase activation, and pharmacological inhibition using refametinib may be a promising treatment to halt AVD progression
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Affiliation(s)
- Charu Munjal
- Divisions of Cardiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Anil G Jegga
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Amy M Opoka
- Divisions of Cardiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ivan Stoilov
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Ohio
| | - Russell A Norris
- Department of Cell Biology, Medical University of South Carolina, Charleston, South Carolina
| | - Craig J Thomas
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences National Institutes of Health, Bethesda, Maryland
| | - J Michael Smith
- TriHealth Heart Institute, Cardio-Thoracic Surgery, Cincinnati, Ohio
| | - Robert P Mecham
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Ohio
| | - Giorgio M Bressan
- The Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Robert B Hinton
- Divisions of Cardiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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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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41
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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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42
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Dimitrova Y, Gruber AJ, Mittal N, Ghosh S, Dimitriades B, Mathow D, Grandy WA, Christofori G, Zavolan M. TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition. Biol Direct 2017; 12:8. [PMID: 28412966 PMCID: PMC5392957 DOI: 10.1186/s13062-017-0180-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/22/2017] [Indexed: 01/28/2023] Open
Abstract
Background The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master transcription factor (TF) regulators of this process are conserved between mouse and human. Methods From a computational analysis of a variety of high-throughput sequencing data sets we initially inferred that TFAP2A is connected to the core EMT network in both species. We then analysed publicly available human breast cancer data for TFAP2A expression and also studied the expression (by mRNA sequencing), activity (by monitoring the expression of its predicted targets), and binding (by electrophoretic mobility shift assay and chromatin immunoprecipitation) of this factor in a mouse mammary gland EMT model system (NMuMG) cell line. Results We found that upon induction of EMT, the activity of TFAP2A, reflected in the expression level of its predicted targets, is up-regulated in a variety of systems, both murine and human, while TFAP2A’s expression is increased in more “stem-like” cancers. We provide strong evidence for the direct interaction between the TFAP2A TF and the ZEB2 promoter and we demonstrate that this interaction affects ZEB2 expression. Overexpression of TFAP2A from an exogenous construct perturbs EMT, however, in a manner similar to the downregulation of endogenous TFAP2A that takes place during EMT. Conclusions Our study reveals that TFAP2A is a conserved component of the core network that regulates EMT, acting as a repressor of many genes, including ZEB2. Reviewers This article has been reviewed by Dr. Martijn Huynen and Dr. Nicola Aceto. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0180-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoana Dimitrova
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Andreas J Gruber
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Nitish Mittal
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Souvik Ghosh
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Beatrice Dimitriades
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Daniel Mathow
- Department of Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - William Aaron Grandy
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Gerhard Christofori
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland.
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Cheung LYM, Davis SW, Brinkmeier ML, Camper SA, Pérez-Millán MI. Regulation of pituitary stem cells by epithelial to mesenchymal transition events and signaling pathways. Mol Cell Endocrinol 2017; 445:14-26. [PMID: 27650955 PMCID: PMC5590650 DOI: 10.1016/j.mce.2016.09.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/11/2022]
Abstract
The anterior pituitary gland is comprised of specialized cell-types that produce and secrete polypeptide hormones in response to hypothalamic input and feedback from target organs. These specialized cells arise from stem cells that express SOX2 and the pituitary transcription factor PROP1, which is necessary to establish the stem cell pool and promote an epithelial to mesenchymal-like transition, releasing progenitors from the niche. The adult anterior pituitary responds to physiological challenge by mobilizing the SOX2-expressing progenitor pool and producing additional hormone-producing cells. Knowledge of the role of signaling pathways and extracellular matrix components in these processes may lead to improvements in the efficiency of differentiation of embryonic stem cells or induced pluripotent stem cells into hormone producing cells in vitro. Advances in our basic understanding of pituitary stem cell regulation and differentiation may lead to improved diagnosis and treatment for patients with hypopituitarism.
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Affiliation(s)
- Leonard Y M Cheung
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA.
| | - Shannon W Davis
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-0001, USA.
| | - Michelle L Brinkmeier
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA.
| | - Sally A Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA.
| | - María Inés Pérez-Millán
- Institute of Biomedical Investgations (UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina.
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Lumb R, Buckberry S, Secker G, Lawrence D, Schwarz Q. Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels. BMC DEVELOPMENTAL BIOLOGY 2017; 17:5. [PMID: 28407732 PMCID: PMC5390458 DOI: 10.1186/s12861-017-0147-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/03/2017] [Indexed: 01/13/2023]
Abstract
Background Cranial neural crest cells (NCCs) are a unique embryonic cell type which give rise to a diverse array of derivatives extending from neurons and glia through to bone and cartilage. Depending on their point of origin along the antero-posterior axis cranial NCCs are rapidly sorted into distinct migratory streams that give rise to axial specific structures. These migratory streams mirror the underlying segmentation of the brain with NCCs exiting the diencephalon and midbrain following distinct paths compared to those exiting the hindbrain rhombomeres (r). The genetic landscape of cranial NCCs arising at different axial levels remains unknown. Results Here we have used RNA sequencing to uncover the transcriptional profiles of mouse cranial NCCs arising at different axial levels. Whole transcriptome analysis identified over 120 transcripts differentially expressed between NCCs arising anterior to r3 (referred to as r1-r2 migratory stream for simplicity) and the r4 migratory stream. Eight of the genes differentially expressed between these populations were validated by RT-PCR with 2 being further validated by in situ hybridisation. We also explored the expression of the Neuropilins (Nrp1 and Nrp2) and their co-receptors and show that the A-type Plexins are differentially expressed in different cranial NCC streams. Conclusions Our analyses identify a large number of genes differentially regulated between cranial NCCs arising at different axial levels. This data provides a comprehensive description of the genetic landscape driving diversity of distinct cranial NCC streams and provides novel insight into the regulatory networks controlling the formation of specific skeletal elements and the mechanisms promoting migration along different paths. Electronic supplementary material The online version of this article (doi:10.1186/s12861-017-0147-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachael Lumb
- Centre for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5000, Australia.,University of Adelaide, Frome Road, Adelaide, SA, 5000, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, Perth, WA, 6008, Australia.,Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, 6009, WA, Australia
| | - Genevieve Secker
- Centre for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5000, Australia
| | - David Lawrence
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Quenten Schwarz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Frome Road, Adelaide, SA, 5000, Australia.
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Boughner JC. Implications of Vertebrate Craniodental Evo-Devo for Human Oral Health. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:321-333. [PMID: 28251806 DOI: 10.1002/jez.b.22734] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/21/2016] [Accepted: 01/30/2017] [Indexed: 12/12/2022]
Abstract
Highly processed diets eaten by postindustrial modern human populations coincide with higher frequencies of third molar impaction, malocclusion, and temporomandibular joint disorders that affect millions of people worldwide each year. Current treatments address symptoms, not causes, because the multifactorial etiologies of these three concerns mask which factors incline certain people to malocclusion, impaction, and/or joint issues. Deep scientific curiosity about the origins of jaws and dentitions continues to yield rich insights about the developmental genetic mechanisms that underpin healthy craniodental morphogenesis and integration. Mounting evidence from evolution and development (Evo-Devo) studies suggests that function is another mechanism important to healthy craniodental integration and fit. Starting as early as weaning, softer diets and thus lower bite forces appear to relax or disrupt integration of oral tissues, alter development and growth, and catalyze impaction, malocclusion, and jaw joint disorders. How developing oral tissues respond to bite forces remains poorly understood, but biomechanical feedback seems to alter balances of local bone resorption and deposition at the tooth-bone interface as well as affect tempos and amounts of facial outgrowth. Also, behavioral changes in jaw function and parafunction contribute to degeneration and pain in joint articular cartilages and masticatory muscles. The developmental genetic contribution to craniodental misfits and disorders is undeniable but still unclear; however, at present, human diet and jaw function remain important and much more actionable clinical targets. New Evo-Devo studies are needed to explain how function interfaces with craniodental phenotypic plasticity, variation, and evolvability to yield a spectrum of healthy and mismatched dentitions and jaws.
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Affiliation(s)
- Julia C Boughner
- Department of Anatomy and Cell Biology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Babbucci M, Ferraresso S, Pauletto M, Franch R, Papetti C, Patarnello T, Carnier P, Bargelloni L. An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax). Sci Rep 2016; 6:38673. [PMID: 27929136 PMCID: PMC5144136 DOI: 10.1038/srep38673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022] Open
Abstract
Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the “nervous system development” as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity.
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Affiliation(s)
- Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Chiara Papetti
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
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Fang Q, George AS, Brinkmeier ML, Mortensen AH, Gergics P, Cheung LYM, Daly AZ, Ajmal A, Pérez Millán MI, Ozel AB, Kitzman JO, Mills RE, Li JZ, Camper SA. Genetics of Combined Pituitary Hormone Deficiency: Roadmap into the Genome Era. Endocr Rev 2016; 37:636-675. [PMID: 27828722 PMCID: PMC5155665 DOI: 10.1210/er.2016-1101] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/31/2016] [Indexed: 02/08/2023]
Abstract
The genetic basis for combined pituitary hormone deficiency (CPHD) is complex, involving 30 genes in a variety of syndromic and nonsyndromic presentations. Molecular diagnosis of this disorder is valuable for predicting disease progression, avoiding unnecessary surgery, and family planning. We expect that the application of high throughput sequencing will uncover additional contributing genes and eventually become a valuable tool for molecular diagnosis. For example, in the last 3 years, six new genes have been implicated in CPHD using whole-exome sequencing. In this review, we present a historical perspective on gene discovery for CPHD and predict approaches that may facilitate future gene identification projects conducted by clinicians and basic scientists. Guidelines for systematic reporting of genetic variants and assigning causality are emerging. We apply these guidelines retrospectively to reports of the genetic basis of CPHD and summarize modes of inheritance and penetrance for each of the known genes. In recent years, there have been great improvements in databases of genetic information for diverse populations. Some issues remain that make molecular diagnosis challenging in some cases. These include the inherent genetic complexity of this disorder, technical challenges like uneven coverage, differing results from variant calling and interpretation pipelines, the number of tolerated genetic alterations, and imperfect methods for predicting pathogenicity. We discuss approaches for future research in the genetics of CPHD.
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Affiliation(s)
- Qing Fang
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Akima S George
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Michelle L Brinkmeier
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Amanda H Mortensen
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Peter Gergics
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Leonard Y M Cheung
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Alexandre Z Daly
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Adnan Ajmal
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - María Ines Pérez Millán
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - A Bilge Ozel
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Jacob O Kitzman
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Ryan E Mills
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Jun Z Li
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Sally A Camper
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
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Mammadova A, Zhou H, Carels CE, Von den Hoff JW. Retinoic acid signalling in the development of the epidermis, the limbs and the secondary palate. Differentiation 2016; 92:326-335. [DOI: 10.1016/j.diff.2016.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/20/2016] [Accepted: 05/02/2016] [Indexed: 01/06/2023]
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Cela P, Hampl M, Fu KK, Kunova Bosakova M, Krejci P, Richman JM, Buchtova M. MORN5 Expression during Craniofacial Development and Its Interaction with the BMP and TGFβ Pathways. Front Physiol 2016; 7:378. [PMID: 27630576 PMCID: PMC5005375 DOI: 10.3389/fphys.2016.00378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/17/2016] [Indexed: 12/23/2022] Open
Abstract
MORN5 (MORN repeat containing 5) is encoded by a locus positioned on chromosome 17 in the chicken genome. The MORN motif is found in multiple copies in several proteins including junctophilins or phosphatidylinositol phosphate kinase family and the MORN proteins themselves are found across the animal and plant kingdoms. MORN5 protein has a characteristic punctate pattern in the cytoplasm in immunofluorescence imaging. Previously, MORN5 was found among differentially expressed genes in a microarray profiling experiment of the chicken embryo head. Here, we provided in situ hybridization to analyse, in detail, the MORN5 expression in chick craniofacial structures. The expression of MORN5 was first observed at stage HH17-18 (E2.5). MORN5 expression gradually appeared on either side of the primitive oral cavity, within the maxillary region. At stage HH20 (E3), prominent expression was localized in the mandibular prominences lateral to the midline. From stage HH20 up to HH29 (E6), there was strong expression in restricted regions of the maxillary and mandibular prominences. The frontonasal mass (in the midline of the face) expressed MORN5, starting at HH27 (E5). The expression was concentrated in the corners or globular processes, which will ultimately fuse with the cranial edges of the maxillary prominences. MORN5 expression was maintained in the fusion zone up to stage HH29. In sections MORN5 expression was localized preferentially in the mesenchyme. Previously, we examined signals that regulate MORN5 expression in the face based on a previous microarray study. Here, we validated the array results with in situ hybridization and QPCR. MORN5 was downregulated 24 h after Noggin and/or RA treatment. We also determined that BMP pathway genes are downstream of MORN5 following siRNA knockdown. Based on these results, we conclude that MORN5 is both regulated by and required for BMP signaling. The restricted expression of MORN5 in the lip fusion zone shown here supports the human genetic data in which MORN5 variants were associated with increased risk of non-syndromic cleft lip with or without cleft palate.
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Affiliation(s)
- Petra Cela
- Institute of Animal Physiology and Genetics, v.v.i., Academy of Sciences of the Czech RepublicBrno, Czech Republic; Department of Animal Physiology and Immunology, Institute of Experimental Biology, Masaryk UniversityBrno, Czech Republic
| | - Marek Hampl
- Institute of Animal Physiology and Genetics, v.v.i., Academy of Sciences of the Czech RepublicBrno, Czech Republic; Department of Animal Physiology and Immunology, Institute of Experimental Biology, Masaryk UniversityBrno, Czech Republic
| | - Katherine K Fu
- Life Sciences Institute, University of British Columbia Vancouver, BC, Canada
| | | | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk UniversityBrno, Czech Republic; International Clinical Research Center, St. Anne's University HospitalBrno, Czech Republic
| | - Joy M Richman
- Life Sciences Institute, University of British Columbia Vancouver, BC, Canada
| | - Marcela Buchtova
- Institute of Animal Physiology and Genetics, v.v.i., Academy of Sciences of the Czech RepublicBrno, Czech Republic; Department of Animal Physiology and Immunology, Institute of Experimental Biology, Masaryk UniversityBrno, Czech Republic
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50
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Zheng Y, Cai J, Hutchins AP, Jia L, Liu P, Yang D, Chen S, Ge L, Pei D, Wei S. Remission for Loss of Odontogenic Potential in a New Micromilieu In Vitro. PLoS One 2016; 11:e0152893. [PMID: 27050091 PMCID: PMC4822848 DOI: 10.1371/journal.pone.0152893] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/21/2016] [Indexed: 12/29/2022] Open
Abstract
During embryonic organogenesis, the odontogenic potential resides in dental mesenchyme from the bud stage until birth. Mouse dental mesenchymal cells (mDMCs) isolated from the inductive dental mesenchyme of developing molars are frequently used in the context of tooth development and regeneration. We wondered if and how the odontogenic potential could be retained when mDMCs were cultured in vitro. In the present study, we undertook to test the odontogenic potential of cultured mDMCs and attempted to maintain the potential during culturing. We found that cultured mDMCs could retain the odontogenic potential for 24 h with a ratio of 60% for tooth formation, but mDMCs were incapable of supporting tooth formation after more than 24 h in culture. This loss of odontogenic potential was accompanied by widespread transcriptomic alteration and, specifically, the downregulation of some dental mesenchyme-specific genes, such as Pax9, Msx1, and Pdgfrα. To prolong the odontogenic potential of mDMCs in vitro, we then cultured mDMCs in a serum-free medium with Knockout Serum Replacement (KSR) and growth factors (fibroblastic growth factor 2 and epidermal growth factor). In this new micromilieu, mDMCs could maintain the odontogenic potential for 48 h with tooth formation ratio of 50%. Moreover, mDMCs cultured in KSR-supplemented medium gave rise to tooth-like structures when recombined with non-dental second-arch epithelium. Among the supplements, KSR is essential for the survival and adhesion of mDMCs, and both Egf and Fgf2 induced the expression of certain dental mesenchyme-related genes. Taken together, our results demonstrated that the transcriptomic changes responded to the alteration of odontogenic potential in cultured mDMCs and a new micromilieu partly retained this potential in vitro, providing insight into the long-term maintenance of odontogenic potential in mDMCs.
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Affiliation(s)
- Yunfei Zheng
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
- Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, P.R. China
| | - Jinglei Cai
- Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, P.R. China
| | - Andrew Paul Hutchins
- Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, P.R. China
| | - Lingfei Jia
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
| | - Pengfei Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, P.R. China
| | - Dandan Yang
- Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, P.R. China
| | - Shubin Chen
- Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, P.R. China
| | - Lihong Ge
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
| | - Duanqing Pei
- Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, P.R. China
- * E-mail: (DQP); (SCW)
| | - Shicheng Wei
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing 100081, P.R. China
- * E-mail: (DQP); (SCW)
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