1
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [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: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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2
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Moreno-Oñate M, Gallardo-Fuentes L, Martínez-García PM, Naranjo S, Jiménez-Gancedo S, Tena JJ, Santos-Pereira JM. Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development. Nucleic Acids Res 2024; 52:3682-3701. [PMID: 38321954 PMCID: PMC11040003 DOI: 10.1093/nar/gkae065] [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: 06/27/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Retinoic acid (RA) is the ligand of RA receptors (RARs), transcription factors that bind to RA response elements. RA signaling is required for multiple processes during embryonic development, including body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. Here, we stimulate the RA pathway by treating zebrafish embryos with all-trans-RA (atRA) and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which exogenously induced RA signaling controls gene expression. We find that RA signaling is involved in anterior/posterior patterning, central nervous system development, and the transition from pluripotency to differentiation. AtRA treatment also alters chromatin accessibility during early development and promotes chromatin binding of RARαa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that exogenous RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions involving target genes. Altogether, our findings identify genome-wide targets of RA signaling and provide a molecular mechanism by which developmental signaling pathways regulate target gene expression by altering chromatin topology.
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Affiliation(s)
- Marta Moreno-Oñate
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Pedro M Martínez-García
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Sandra Jiménez-Gancedo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - José M Santos-Pereira
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain
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3
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Wang C, Zhao Z, Zhao Y, Zhao J, Xia L, Xia Q. Macroscopic inhibition of DNA damage repair pathways by targeting AP-2α with LEI110 eradicates hepatocellular carcinoma. Commun Biol 2024; 7:342. [PMID: 38503825 PMCID: PMC10951303 DOI: 10.1038/s42003-024-05939-7] [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: 09/18/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
DNA damage repair (DDR) genes are known to be closely associated with the progression of Hepatocellular carcinoma (HCC). Here we report a unique cluster of "deletion-up" genes in HCC, which are accordantly overexpressed in HCC patients and predict the unfavorable prognosis. Binding motif analysis and further validation with ChIP-qPCR unveil that the AP-2α directly modulate the transcription of critical DNA repair genes including TOP2A, NUDT1, POLD1, and PARP1, which facilitates the sanitation of oxidized DNA lesions. Structural analysis and the following validation identify LEI110 as a potent AP-2α inhibitor. Together, we demonstrate that LEI110 stabilizes AP-2α and sensitizes HCC cells toward DNA-damaging reagents. Altogether, we identify AP-2α as a crucial transcription modulator in HCC and propose small-molecule inhibitors targeting AP-2α are a promising novel class of anticancer agents. Our study provides insights into the concept of macroscopic inhibition of DNA damage repair-related genes in cancer treatment.
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Affiliation(s)
- Chenchen Wang
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China.
- Shanghai Institute of Transplantation, Shanghai, China.
| | - Zhenjun Zhao
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
| | - Yudong Zhao
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
| | - Jie Zhao
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
| | - Lei Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
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4
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Uribe RA. Genetic regulation of enteric nervous system development in zebrafish. Biochem Soc Trans 2024; 52:177-190. [PMID: 38174765 PMCID: PMC10903509 DOI: 10.1042/bst20230343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
The enteric nervous system (ENS) is a complex series of interconnected neurons and glia that reside within and along the entire length of the gastrointestinal tract. ENS functions are vital to gut homeostasis and digestion, including local control of peristalsis, water balance, and intestinal cell barrier function. How the ENS develops during embryological development is a topic of great concern, as defects in ENS development can result in various diseases, the most common being Hirschsprung disease, in which variable regions of the infant gut lack ENS, with the distal colon most affected. Deciphering how the ENS forms from its progenitor cells, enteric neural crest cells, is an active area of research across various animal models. The vertebrate animal model, zebrafish, has been increasingly leveraged to understand early ENS formation, and over the past 20 years has contributed to our knowledge of the genetic regulation that underlies enteric development. In this review, I summarize our knowledge regarding the genetic regulation of zebrafish enteric neuronal development, and based on the most current literature, present a gene regulatory network inferred to underlie its construction. I also provide perspectives on areas for future zebrafish ENS research.
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Affiliation(s)
- Rosa A. Uribe
- Biosciences Department, Rice University, Houston, TX 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, TX 77005, U.S.A
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5
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Nguyen TT, Mitchell JM, Kiel MD, Kenny CP, Li H, Jones KL, Cornell RA, Williams TJ, Nichols JT, Van Otterloo E. TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. Development 2024; 151:dev202095. [PMID: 38063857 PMCID: PMC10820886 DOI: 10.1242/dev.202095] [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: 06/16/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underlies facial shape variation, yet how those networks in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both TFAP2 family members dysregulates numerous midface GRN components involved in midface morphogenesis, patterning and differentiation. Notably, Alx1, Alx3 and Alx4 (ALX) transcript levels are reduced, whereas ChIP-seq analyses suggest TFAP2 family members directly and positively regulate ALX gene expression. Tfap2a, Tfap2b and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish implies conservation of this regulatory axis across vertebrates. Consistent with this notion, tfap2a zebrafish mutants present with abnormal alx3 expression patterns, Tfap2a binds ALX loci and tfap2a-alx3 genetic interactions are observed. Together, these data demonstrate TFAP2 paralogs regulate vertebrate midfacial development in part by activating expression of ALX transcription factor genes.
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Affiliation(s)
- Timothy T. Nguyen
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Jennyfer M. Mitchell
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela D. Kiel
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Colin P. Kenny
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth L. Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Robert A. Cornell
- Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98195, USA
| | - Trevor J. Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James T. Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric Van Otterloo
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
- Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
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6
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Nguyen TT, Mitchell JM, Kiel MD, Jones KL, Williams TJ, Nichols JT, Van Otterloo E. TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545376. [PMID: 37398373 PMCID: PMC10312788 DOI: 10.1101/2023.06.16.545376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest even during the late migratory phase results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both Tfap2 members dysregulated numerous midface GRN components involved in midface fusion, patterning, and differentiation. Notably, Alx1/3/4 (Alx) transcript levels are reduced, while ChIP-seq analyses suggest TFAP2 directly and positively regulates Alx gene expression. TFAP2 and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish further implies conservation of this regulatory axis across vertebrates. Consistent with this notion, tfap2a mutant zebrafish present abnormal alx3 expression patterns, and the two genes display a genetic interaction in this species. Together, these data demonstrate a critical role for TFAP2 in regulating vertebrate midfacial development in part through ALX transcription factor gene expression.
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Affiliation(s)
- Timothy T Nguyen
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
| | - Jennyfer M Mitchell
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela D Kiel
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - James T Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric Van Otterloo
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
- Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA, 52242, USA
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7
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Collier AE, Piekos SN, Liu A, Pattison JM, Felix F, Bailetti AA, Sedov E, Gaddam S, Zhen H, Oro AE. GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development. iScience 2023; 26:106125. [PMID: 36843855 PMCID: PMC9950457 DOI: 10.1016/j.isci.2023.106125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Ectodermal dysplasias including skin abnormalities and cleft lip/palate result from improper surface ectoderm (SE) patterning. However, the connection between SE gene regulatory networks and disease remains poorly understood. Here, we dissect human SE differentiation with multiomics and establish GRHL2 as a key mediator of early SE commitment, which acts by skewing cell fate away from the neural lineage. GRHL2 and master SE regulator AP2a balance early cell fate output, with GRHL2 facilitating AP2a binding to SE loci. In turn, AP2a restricts GRHL2 DNA binding away from de novo chromatin contacts. Integration of these regulatory sites with ectodermal dysplasia-associated genomic variants annotated within the Biomedical Data Commons identifies 55 loci previously implicated in craniofacial disorders. These include ABCA4/ARHGAP29 and NOG regulatory regions where disease-linked variants directly affect GRHL2/AP2a binding and gene transcription. These studies elucidate the logic underlying SE commitment and deepen our understanding of human oligogenic disease pathogenesis.
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Affiliation(s)
- Ann E. Collier
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Samantha N. Piekos
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | - Angela Liu
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Franco Felix
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Egor Sedov
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Hanson Zhen
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Anthony E. Oro
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
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8
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Vöcking O, Van Der Meulen K, Patel MK, Famulski JK. Zebrafish anterior segment mesenchyme progenitors are defined by function of tfap2a but not sox10. Differentiation 2023; 130:32-42. [PMID: 36563566 PMCID: PMC10006344 DOI: 10.1016/j.diff.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
The anterior segment is a critical component of the visual system. Developing independent of the retina, the AS relies partially on cranial neural crest cells (cNCC) as its earliest progenitors. The cNCCs are thought to first adopt a periocular mesenchyme (POM) fate and subsequently target to the AS upon formation of the rudimentary retina. AS targeted POM is termed anterior segment mesenchyme (ASM). However, it remains unknown when and how the switch from cNCC to POM or POM to ASM takes place. As such, we sought to visualize the timing of these transitions and identify the regulators of this process using the zebrafish embryo model. Using two color fluorescence in situ hybridization, we tracked cNCC and ASM target gene expression from 12 to 24hpf. In doing so, we identified a tfap2a and foxC1a co-expression at 16hpf, identifying the earliest ASM to arrive at the AS. Interestingly, expression of two other key regulators of NCC, foxD3 and sox10 was not associated with early ASM. Functional analysis of tfap2a, foxD3 and sox10 revealed that tfap2a and foxD3 are both critical regulators of ASM specification and AS formation while sox10 was dispensable for either specification or development of the AS. Using genetic knockout lines, we show that in the absence of tfap2a or foxD3 function ASM cells are not specified, and subsequently the AS is malformed. Conversely, sox10 genetic mutants or CRISPR Cas9 injected embryos displayed no defects in ASM specification, migration or the AS. Lastly, using transcriptomic analysis, we show that GFP + cNCCs derived from Tg [foxD3:GFP] and Tg [foxC1b:GFP] share expression profiles consistent with ASM development whereas cNCCs isolated from Tg [sox10:GFP] exhibit expression profiles associated with vasculogenesis, muscle function and pigmentation. Taken together, we propose that the earliest stage of anterior segment mesenchyme (ASM) specification in zebrafish is approximately 16hpf and involves tfap2a/foxC1a positive cNCCs.
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Affiliation(s)
| | | | - M K Patel
- Department of Biology, University of Kentucky, USA
| | - J K Famulski
- Department of Biology, University of Kentucky, USA.
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9
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Yang K, Zhao J, Liu S, Man S. RELA promotes the progression of oral squamous cell carcinoma via TFAP2A-Wnt/β-catenin signaling. Mol Carcinog 2023; 62:641-651. [PMID: 36789977 DOI: 10.1002/mc.23512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/26/2023] [Indexed: 02/16/2023]
Abstract
Oral squamous cell carcinoma (OSCC) has emerged as the most prevailing oral malignancy worldwide, characterized by cervical solid lymph node metastasis and strong local invasiveness. Overexpression of Transcription Factor AP-2 alpha (TFAP2A) is observed in a significant proportion of OSCC cases. In this study, we aimed to elucidate the function of TFAP2A in the progression of OSCC and the related molecular signaling pathways. The role of RELA was predicted using bioinformatics analysis. The mRNA abundances of RELA, TFAP2A, and β-catenin were assessed by Western blot and quantitative real-timePCR. The relationship between RELA, TFAP2A, and β-catenin and their correlation with clinicopathological characteristics of OSCC was evaluated. The target of RELA and TFAP2A was identified by the chromatin immunoprecipitation as well as luciferase reporter assay. The colony formation assay and MTS assay were performed to determine the proliferative level of OSCC cells. OSCC cell motility was determined by Transwell assay and wound-healing assay. The protein expressions of epithelial-mesenchymal transition-associated factors were evaluated by Western blot. The expressions of RELA and TFAP2A were elevated in OSCC, and their expressions displayed a positive correlation. The expression levels of RELA and TFAP2A were found to be associated with TNM staging and lymphatic metastasis of OSCC patients. RELA upregulation promoted OSCC progression, as manifested by increased levels of proliferation, invasion, and migration of OSCC cells. We also demonstrated that RELA was directly bound to the promoter of TFAP2A transcription, which activated multiple malignant and metastatic phenotypes. Furthermore, TFAP2A activated the Wnt/β-catenin signaling by targeting the promoter regions of β-catenin. The study found that RELA is critical for promoting the progression of OSCC via the RELA-TFAP2A-Wnt/β-catenin signaling pathway. The RELA-TFAP2A-Wnt/β-catenin signaling pathway is a potential target for reducing the aggressiveness of OSCC.
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Affiliation(s)
- Kaicheng Yang
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Jianguang Zhao
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Shenghui Liu
- Department of Otolaryngology Head and Neck, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Shasha Man
- Department of Stomatology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
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10
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Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan A, Vadgama N, Balsubramani A, Wu JC, Engreitz JM, Farh K, Karakikes I, Wang KC, Quertermous T, Greenleaf WJ, Kundaje A. Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease. Cell 2022; 185:4937-4953.e23. [PMID: 36563664 PMCID: PMC10122433 DOI: 10.1016/j.cell.2022.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 09/13/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
To define the multi-cellular epigenomic and transcriptional landscape of cardiac cellular development, we generated single-cell chromatin accessibility maps of human fetal heart tissues. We identified eight major differentiation trajectories involving primary cardiac cell types, each associated with dynamic transcription factor (TF) activity signatures. We contrasted regulatory landscapes of iPSC-derived cardiac cell types and their in vivo counterparts, which enabled optimization of in vitro differentiation of epicardial cells. Further, we interpreted sequence based deep learning models of cell-type-resolved chromatin accessibility profiles to decipher underlying TF motif lexicons. De novo mutations predicted to affect chromatin accessibility in arterial endothelium were enriched in congenital heart disease (CHD) cases vs. controls. In vitro studies in iPSCs validated the functional impact of identified variation on the predicted developmental cell types. This work thus defines the cell-type-resolved cis-regulatory sequence determinants of heart development and identifies disruption of cell type-specific regulatory elements in CHD.
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Affiliation(s)
- Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Laksshman Sundaram
- Department of Computer Science, Stanford University, Stanford, CA, USA; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Mengcheng Shen
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Abhimanyu Banerjee
- Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA; Department of Physics, Stanford University, Stanford, CA, USA
| | - Soumya Kundu
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Mingxia Gu
- Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Avyay Varadarajan
- Department of Computer Science, California Institute of Technology, Pasadena, CA, USA
| | - Nirmal Vadgama
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | | | - Joseph C Wu
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA.
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA.
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA.
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11
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Norcross RG, Abdelmoti L, Rouchka EC, Andreeva K, Tussey O, Landestoy D, Galperin E. Shoc2 controls ERK1/2-driven neural crest development by balancing components of the extracellular matrix. Dev Biol 2022; 492:156-171. [PMID: 36265687 PMCID: PMC10019579 DOI: 10.1016/j.ydbio.2022.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 02/02/2023]
Abstract
The extracellular signal-regulated kinase (ERK1/2) pathway is essential in embryonic development. The scaffold protein Shoc2 is a critical modulator of ERK1/2 signals, and mutations in the shoc2 gene lead to the human developmental disease known as Noonan-like syndrome with loose anagen hair (NSLH). The loss of Shoc2 and the shoc2 NSLH-causing mutations affect the tissues of neural crest (NC) origin. In this study, we utilized the zebrafish model to dissect the role of Shoc2-ERK1/2 signals in the development of NC. These studies established that the loss of Shoc2 significantly altered the expression of transcription factors regulating the specification and differentiation of NC cells. Using comparative transcriptome analysis of NC-derived cells from shoc2 CRISPR/Cas9 mutant larvae, we found that Shoc2-mediated signals regulate gene programs at several levels, including expression of genes coding for the proteins of extracellular matrix (ECM) and ECM regulators. Together, our results demonstrate that Shoc2 is an essential regulator of NC development. This study also indicates that disbalance in the turnover of the ECM may lead to the abnormalities found in NSLH patients.
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Affiliation(s)
- Rebecca G Norcross
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Lina Abdelmoti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40292, USA
| | - Kalina Andreeva
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40292, USA; Department of Neuroscience Training, University of Louisville, Louisville, KY, 40292, USA; Department of Genetics, Stanford University, Palo Alto, CA, 94304, USA
| | - Olivia Tussey
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Daileen Landestoy
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
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12
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Martins TF, Braga Magalhães AF, Verardo LL, Santos GC, Silva Fernandes AA, Gomes Vieira JI, Irano N, dos Santos DB. Functional analysis of litter size and number of teats in pigs: From GWAS to post-GWAS. Theriogenology 2022; 193:157-166. [DOI: 10.1016/j.theriogenology.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 10/31/2022]
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13
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Candido-Ferreira IL, Lukoseviciute M, Sauka-Spengler T. Multi-layered transcriptional control of cranial neural crest development. Semin Cell Dev Biol 2022; 138:1-14. [PMID: 35941042 DOI: 10.1016/j.semcdb.2022.07.010] [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: 01/27/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
The neural crest (NC) is an emblematic population of embryonic stem-like cells with remarkable migratory ability. These distinctive attributes have inspired the curiosity of developmental biologists for over 150 years, however only recently the regulatory mechanisms controlling the complex features of the NC have started to become elucidated at genomic scales. Regulatory control of NC development is achieved through combinatorial transcription factor binding and recruitment of associated transcriptional complexes to distal cis-regulatory elements. Together, they regulate when, where and to what extent transcriptional programmes are actively deployed, ultimately shaping ontogenetic processes. Here, we discuss how transcriptional networks control NC ontogeny, with a special emphasis on the molecular mechanisms underlying specification of the cephalic NC. We also cover emerging properties of transcriptional regulation revealed in diverse developmental systems, such as the role of three-dimensional conformation of chromatin, and how they are involved in the regulation of NC ontogeny. Finally, we highlight how advances in deciphering the NC transcriptional network have afforded new insights into the molecular basis of human diseases.
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Affiliation(s)
- Ivan L Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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14
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Schock EN, York JR, LaBonne C. The developmental and evolutionary origins of cellular pluripotency in the vertebrate neural crest. Semin Cell Dev Biol 2022; 138:36-44. [PMID: 35534333 DOI: 10.1016/j.semcdb.2022.04.008] [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: 10/30/2021] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/30/2022]
Abstract
Neural crest cells are central to vertebrate development and evolution, endowing vertebrates with a "new head" that resulted in morphological, physiological, and behavioral features that allowed vertebrates to become active predators. One remarkable feature of neural crest cells is their multi-germ layer potential that allows for the formation of both ectodermal (pigmentation, peripheral glia, sensory neurons) and mesenchymal (connective tissue, cartilage/bone, dermis) cell types. Understanding the cellular and evolutionary origins of this broad cellular potential in the neural crest has been a long-standing focus for developmental biologists. Here, we review recent work that has demonstrated that neural crest cells share key features with pluripotent blastula stem cells, including expression of the Yamanaka stem cell factors (Oct3/4, Klf4, Sox2, c-Myc). These shared features suggest that pluripotency is either retained in the neural crest from blastula stages or subsequently reactivated as the neural crest forms. We highlight the cellular and molecular parallels between blastula stem cells and neural crest cells and discuss the work that has led to current models for the cellular origins of broad potential in the crest. Finally, we explore how these themes can provide new insights into how and when neural crest cells and pluripotency evolved in vertebrates and the evolutionary relationship between these populations.
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Affiliation(s)
| | | | - Carole LaBonne
- Dept. of Molecular Biosciences; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, United States.
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15
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McMahon R, Sibbritt T, Aryamanesh N, Masamsetti VP, Tam PPL. Loss of Foxd4 Impacts Neurulation and Cranial Neural Crest Specification During Early Head Development. Front Cell Dev Biol 2022; 9:777652. [PMID: 35178396 PMCID: PMC8843869 DOI: 10.3389/fcell.2021.777652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/30/2021] [Indexed: 11/19/2022] Open
Abstract
The specification of anterior head tissue in the late gastrulation mouse embryo relies on signaling cues from the visceral endoderm and anterior mesendoderm (AME). Genetic loss-of-function studies have pinpointed a critical requirement of LIM homeobox 1 (LHX1) transcription factor in these tissues for the formation of the embryonic head. Transcriptome analysis of embryos with gain-of-function LHX1 activity identified the forkhead box gene, Foxd4, as one downstream target of LHX1 in late-gastrulation E7.75 embryos. Our analysis of single-cell RNA-seq data show Foxd4 is co-expressed with Lhx1 and Foxa2 in the anterior midline tissue of E7.75 mouse embryos, and in the anterior neuroectoderm (ANE) at E8.25 alongside head organizer genes Otx2 and Hesx1. To study the role of Foxd4 during early development we used CRISPR-Cas9 gene editing in mouse embryonic stem cells (mESCs) to generate bi-allelic frameshift mutations in the coding sequence of Foxd4. In an in vitro model of the anterior neural tissues derived from Foxd4-loss of function (LOF) mESCs and extraembryonic endoderm cells, expression of head organizer genes as well as Zic1 and Zic2 was reduced, pointing to a need for FOXD4 in regulating early neuroectoderm development. Mid-gestation mouse chimeras harbouring Foxd4-LOF mESCs displayed craniofacial malformations and neural tube closure defects. Furthermore, our in vitro data showed a loss of FOXD4 impacts the expression of cranial neural crest markers Twist1 and Sox9. Our findings have demonstrated that FOXD4 is essential in the AME and later in the ANE for rostral neural tube closure and neural crest specification during head development.
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Affiliation(s)
- Riley McMahon
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, NSW, Australia
| | - Tennille Sibbritt
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia
| | - Nadar Aryamanesh
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia
| | - V Pragathi Masamsetti
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, NSW, Australia
| | - Patrick P L Tam
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, NSW, Australia
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16
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Mathiyalagan N, Dworkin S. Wholemount In-Situ Hybridization (WISH) in Zebrafish Embryos to Analyze Craniofacial Development. Methods Mol Biol 2022; 2403:19-32. [PMID: 34913113 DOI: 10.1007/978-1-0716-1847-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Wholemount in-situ hybridization in zebrafish is a powerful technique for visualizing spatiotemporal gene expression during development. Here we describe a technique to detect endogenous mRNA expression in zebrafish that can be adapted to use on embryos from the single-cell stage until 5 days postfertilization.
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Affiliation(s)
- Nishanthi Mathiyalagan
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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17
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Casey MA, Lusk S, Kwan KM. Build me up optic cup: Intrinsic and extrinsic mechanisms of vertebrate eye morphogenesis. Dev Biol 2021; 476:128-136. [PMID: 33811855 PMCID: PMC8848517 DOI: 10.1016/j.ydbio.2021.03.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/16/2022]
Abstract
The basic structure of the eye, which is crucial for visual function, is established during the embryonic process of optic cup morphogenesis. Molecular pathways of specification and patterning are integrated with spatially distinct cell and tissue shape changes to generate the eye, with discrete domains and structural features: retina and retinal pigment epithelium enwrap the lens, and the optic fissure occupies the ventral surface of the eye and optic stalk. Interest in the underlying cell biology of eye morphogenesis has led to a growing body of work, combining molecular genetics and imaging to quantify cellular processes such as adhesion and actomyosin activity. These studies reveal that intrinsic machinery and spatiotemporally specific extrinsic inputs collaborate to control dynamics of cell movements and morphologies. Here we consider recent advances in our understanding of eye morphogenesis, with a focus on the mechanics of eye formation throughout vertebrate systems, including insights and potential opportunities using organoids, which may provide a tractable system to test hypotheses from embryonic models.
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Affiliation(s)
- Macaulie A Casey
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Sarah Lusk
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Kristen M Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.
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18
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Howard AG, Baker PA, Ibarra-García-Padilla R, Moore JA, Rivas LJ, Tallman JJ, Singleton EW, Westheimer JL, Corteguera JA, Uribe RA. An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution. eLife 2021; 10:60005. [PMID: 33591267 PMCID: PMC7886338 DOI: 10.7554/elife.60005] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/31/2021] [Indexed: 02/06/2023] Open
Abstract
Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme cells, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.
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Affiliation(s)
- Aubrey Ga Howard
- Department of BioSciences, Rice University, Houston, United States
| | - Phillip A Baker
- Department of BioSciences, Rice University, Houston, United States
| | | | - Joshua A Moore
- Department of BioSciences, Rice University, Houston, United States
| | - Lucia J Rivas
- Department of BioSciences, Rice University, Houston, United States
| | - James J Tallman
- Department of BioSciences, Rice University, Houston, United States
| | | | | | | | - Rosa A Uribe
- Department of BioSciences, Rice University, Houston, United States
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19
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Fontenas L, Kucenas S. Spinal cord precursors utilize neural crest cell mechanisms to generate hybrid peripheral myelinating glia. eLife 2021; 10:64267. [PMID: 33554855 PMCID: PMC7886336 DOI: 10.7554/elife.64267] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/05/2021] [Indexed: 12/11/2022] Open
Abstract
During development, oligodendrocytes and Schwann cells myelinate central and peripheral nervous system axons, respectively, while motor exit point (MEP) glia are neural tube-derived, peripheral glia that myelinate axonal territory between these populations at MEP transition zones. From which specific neural tube precursors MEP glia are specified, and how they exit the neural tube to migrate onto peripheral motor axons, remain largely unknown. Here, using zebrafish, we found that MEP glia arise from lateral floor plate precursors and require foxd3 to delaminate and exit the spinal cord. Additionally, we show that similar to Schwann cells, MEP glial development depends on axonally derived neuregulin1. Finally, our data demonstrate that overexpressing axonal cues is sufficient to generate additional MEP glia in the spinal cord. Overall, these studies provide new insight into how a novel population of hybrid, peripheral myelinating glia are generated from neural tube precursors and migrate into the periphery.
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Affiliation(s)
- Laura Fontenas
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Sarah Kucenas
- Department of Biology, University of Virginia, Charlottesville, United States
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20
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Petratou K, Spencer SA, Kelsh RN, Lister JA. The MITF paralog tfec is required in neural crest development for fate specification of the iridophore lineage from a multipotent pigment cell progenitor. PLoS One 2021; 16:e0244794. [PMID: 33439865 PMCID: PMC7806166 DOI: 10.1371/journal.pone.0244794] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding how fate specification of distinct cell-types from multipotent progenitors occurs is a fundamental question in embryology. Neural crest stem cells (NCSCs) generate extraordinarily diverse derivatives, including multiple neural, skeletogenic and pigment cell fates. Key transcription factors and extracellular signals specifying NCSC lineages remain to be identified, and we have only a little idea of how and when they function together to control fate. Zebrafish have three neural crest-derived pigment cell types, black melanocytes, light-reflecting iridophores and yellow xanthophores, which offer a powerful model for studying the molecular and cellular mechanisms of fate segregation. Mitfa has been identified as the master regulator of melanocyte fate. Here, we show that an Mitf-related transcription factor, Tfec, functions as master regulator of the iridophore fate. Surprisingly, our phenotypic analysis of tfec mutants demonstrates that Tfec also functions in the initial specification of all three pigment cell-types, although the melanocyte and xanthophore lineages recover later. We show that Mitfa represses tfec expression, revealing a likely mechanism contributing to the decision between melanocyte and iridophore fate. Our data are consistent with the long-standing proposal of a tripotent progenitor restricted to pigment cell fates. Moreover, we investigate activation, maintenance and function of tfec in multipotent NCSCs, demonstrating for the first time its role in the gene regulatory network forming and maintaining early neural crest cells. In summary, we build on our previous work to characterise the gene regulatory network governing iridophore development, establishing Tfec as the master regulator driving iridophore specification from multipotent progenitors, while shedding light on possible cellular mechanisms of progressive fate restriction.
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Affiliation(s)
- Kleio Petratou
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Samantha A. Spencer
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
| | - Robert N. Kelsh
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - James A. Lister
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
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21
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Williams AL, Bohnsack BL. The Ocular Neural Crest: Specification, Migration, and Then What? Front Cell Dev Biol 2021; 8:595896. [PMID: 33425902 PMCID: PMC7785809 DOI: 10.3389/fcell.2020.595896] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022] Open
Abstract
During vertebrate embryonic development, a population of dorsal neural tube-derived stem cells, termed the neural crest (NC), undergo a series of morphogenetic changes and extensive migration to become a diverse array of cell types. Around the developing eye, this multipotent ocular NC cell population, called the periocular mesenchyme (POM), comprises migratory mesenchymal cells that eventually give rise to many of the elements in the anterior of the eye, such as the cornea, sclera, trabecular meshwork, and iris. Molecular cell biology and genetic analyses of congenital eye diseases have provided important information on the regulation of NC contributions to this area of the eye. Nevertheless, a complete understanding of the NC as a contributor to ocular development remains elusive. In addition, positional information during ocular NC migration and the molecular pathways that regulate end tissue differentiation have yet to be fully elucidated. Further, the clinical challenges of ocular diseases, such as Axenfeld-Rieger syndrome (ARS), Peters anomaly (PA) and primary congenital glaucoma (PCG), strongly suggest the need for better treatments. While several aspects of NC evolution have recently been reviewed, this discussion will consolidate the most recent current knowledge on the specification, migration, and contributions of the NC to ocular development, highlighting the anterior segment and the knowledge obtained from the clinical manifestations of its associated diseases. Ultimately, this knowledge can inform translational discoveries with potential for sorely needed regenerative therapies.
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Affiliation(s)
- Antionette L Williams
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Brenda L Bohnsack
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States.,Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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22
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Chong-Morrison V, Sauka-Spengler T. The Cranial Neural Crest in a Multiomics Era. Front Physiol 2021; 12:634440. [PMID: 33732166 PMCID: PMC7956944 DOI: 10.3389/fphys.2021.634440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Neural crest ontogeny plays a prominent role in craniofacial development. In this Perspective article, we discuss recent advances to the understanding of mechanisms underlying the cranial neural crest gene regulatory network (cNC-GRN) stemming from omics-based studies. We briefly summarize how parallel considerations of transcriptome, interactome, and epigenome data significantly elaborated the roles of key players derived from pre-omics era studies. Furthermore, the growing cohort of cNC multiomics data revealed contribution of the non-coding genomic landscape. As technological improvements are constantly being developed, we reflect on key questions we are poised to address by taking advantage of the unique perspective a multiomics approach has to offer.
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Weigele J, Bohnsack BL. Genetics Underlying the Interactions between Neural Crest Cells and Eye Development. J Dev Biol 2020; 8:jdb8040026. [PMID: 33182738 PMCID: PMC7712190 DOI: 10.3390/jdb8040026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/03/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
The neural crest is a unique, transient stem cell population that is critical for craniofacial and ocular development. Understanding the genetics underlying the steps of neural crest development is essential for gaining insight into the pathogenesis of congenital eye diseases. The neural crest cells play an under-appreciated key role in patterning the neural epithelial-derived optic cup. These interactions between neural crest cells within the periocular mesenchyme and the optic cup, while not well-studied, are critical for optic cup morphogenesis and ocular fissure closure. As a result, microphthalmia and coloboma are common phenotypes in human disease and animal models in which neural crest cell specification and early migration are disrupted. In addition, neural crest cells directly contribute to numerous ocular structures including the cornea, iris, sclera, ciliary body, trabecular meshwork, and aqueous outflow tracts. Defects in later neural crest cell migration and differentiation cause a constellation of well-recognized ocular anterior segment anomalies such as Axenfeld–Rieger Syndrome and Peters Anomaly. This review will focus on the genetics of the neural crest cells within the context of how these complex processes specifically affect overall ocular development and can lead to congenital eye diseases.
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Affiliation(s)
- Jochen Weigele
- Division of Ophthalmology, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 E. Chicago Ave, Chicago, IL 60611, USA;
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, 645 N. Michigan Ave, Chicago, IL 60611, USA
| | - Brenda L. Bohnsack
- Division of Ophthalmology, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 E. Chicago Ave, Chicago, IL 60611, USA;
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, 645 N. Michigan Ave, Chicago, IL 60611, USA
- Correspondence: ; Tel.: +1-312-227-6180; Fax: +1-312-227-9411
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McCallum S, Obata Y, Fourli E, Boeing S, Peddie CJ, Xu Q, Horswell S, Kelsh RN, Collinson L, Wilkinson D, Pin C, Pachnis V, Heanue TA. Enteric glia as a source of neural progenitors in adult zebrafish. eLife 2020; 9:56086. [PMID: 32851974 PMCID: PMC7521928 DOI: 10.7554/elife.56086] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/26/2020] [Indexed: 12/23/2022] Open
Abstract
The presence and identity of neural progenitors in the enteric nervous system (ENS) of vertebrates is a matter of intense debate. Here, we demonstrate that the non-neuronal ENS cell compartment of teleosts shares molecular and morphological characteristics with mammalian enteric glia but cannot be identified by the expression of canonical glial markers. However, unlike their mammalian counterparts, which are generally quiescent and do not undergo neuronal differentiation during homeostasis, we show that a relatively high proportion of zebrafish enteric glia proliferate under physiological conditions giving rise to progeny that differentiate into enteric neurons. We also provide evidence that, similar to brain neural stem cells, the activation and neuronal differentiation of enteric glia are regulated by Notch signalling. Our experiments reveal remarkable similarities between enteric glia and brain neural stem cells in teleosts and open new possibilities for use of mammalian enteric glia as a potential source of neurons to restore the activity of intestinal neural circuits compromised by injury or disease.
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Affiliation(s)
- Sarah McCallum
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Yuuki Obata
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Evangelia Fourli
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Stefan Boeing
- Bionformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Qiling Xu
- Neural Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Stuart Horswell
- Bionformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Robert N Kelsh
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - David Wilkinson
- Neural Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Carmen Pin
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Vassilis Pachnis
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tiffany A Heanue
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
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25
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Van Der Meulen KL, Vöcking O, Weaver ML, Meshram NN, Famulski JK. Spatiotemporal Characterization of Anterior Segment Mesenchyme Heterogeneity During Zebrafish Ocular Anterior Segment Development. Front Cell Dev Biol 2020; 8:379. [PMID: 32528955 PMCID: PMC7266958 DOI: 10.3389/fcell.2020.00379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Assembly of the ocular anterior segment (AS) is a critical event during development of the vertebrate visual system. Failure in this process leads to anterior segment dysgenesis (ASD), which is characterized by congenital blindness and predisposition to glaucoma. The anterior segment is largely formed via a neural crest-derived population, the Periocular Mesenchyme (POM). In this study, we aimed to characterize POM behaviors and transcriptional identities during early establishment of the zebrafish AS. Two-color fluorescent in situ hybridization suggested that early AS associated POM comprise of a heterogenous population. In vivo and time-course imaging analysis of POM distribution and migratory dynamics analyzed using transgenic zebrafish embryos (Tg[foxc1b:GFP], Tg[foxd3:GFP], Tg[pitx2:GFP], Tg[lmx1b.1:GFP], and Tg[sox10:GFP]) revealed unique AS distribution and migratory behavior among the reporter lines. Based on fixed timepoint and real-time analysis of POM cell behavior a comprehensive model for colonization of the zebrafish AS was assembled. Furthermore, we generated single cell transcriptomic profiles (scRNA) from our POM reporter lines and characterized unique subpopulation expression patterns. Based on scRNA clustering analysis we observed cluster overlap between neural crest associated (sox10/foxd3), POM (pitx2) and finally AS specified cells (lmx1b, and foxc1b). scRNA clustering also revealed several novel markers potentially associated with AS development and/or function including lum, fmoda, adcyap1b, tgfbi, and hmng2. Taken together, our data indicates that AS-associated POM, or Anterior Segment Mesenchyme (ASM), is not homogeneous but rather comprised of several subpopulations with differing colonization patterns, migration behavior, and transcriptomic profiles.
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Affiliation(s)
| | - Oliver Vöcking
- Department of Biology, University of Kentucky, Lexington, KY, United States
| | - Megan L Weaver
- Department of Biology, University of Kentucky, Lexington, KY, United States
| | - Nishita N Meshram
- Department of Biology, University of Kentucky, Lexington, KY, United States
| | - Jakub K Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
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26
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Bahrami N, Childs SJ. Development of vascular regulation in the zebrafish embryo. Development 2020; 147:147/10/dev183061. [PMID: 32423977 DOI: 10.1242/dev.183061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 04/07/2020] [Indexed: 01/03/2023]
Abstract
The thin endothelial wall of a newly formed vessel is under enormous stress at the onset of blood flow, rapidly acquiring support from mural cells (pericytes and vascular smooth muscle cells; vSMCs) during development. Mural cells then develop vasoactivity (contraction and relaxation) but we have little information as to when this first develops or the extent to which pericytes and vSMCs contribute. For the first time, we determine the dynamic developmental acquisition of vasoactivity in vivo in the cerebral vasculature of zebrafish. We show that pericyte-covered vessels constrict in response to α1-adrenergic receptor agonists and dilate in response to nitric oxide donors at 4 days postfertilization (dpf) but have heterogeneous responses later, at 6 dpf. In contrast, vSMC-covered vessels constrict at 6 dpf, and dilate at both stages. Using genetic ablation, we demonstrate that vascular constriction and dilation is an active response. Our data suggest that both pericyte- and vSMC-covered vessels regulate their diameter in early development, and that their relative contributions change over developmental time.
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Affiliation(s)
- Nabila Bahrami
- Alberta Children's Hospital Research Institute and Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Sarah J Childs
- Alberta Children's Hospital Research Institute and Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
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27
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Bryan CD, Casey MA, Pfeiffer RL, Jones BW, Kwan KM. Optic cup morphogenesis requires neural crest-mediated basement membrane assembly. Development 2020; 147:dev181420. [PMID: 31988185 PMCID: PMC7044464 DOI: 10.1242/dev.181420] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
Organogenesis requires precise interactions between a developing tissue and its environment. In vertebrates, the developing eye is surrounded by a complex extracellular matrix as well as multiple mesenchymal cell populations. Disruptions to either the matrix or periocular mesenchyme can cause defects in early eye development, yet in many cases the underlying mechanism is unknown. Here, using multidimensional imaging and computational analyses in zebrafish, we establish that cell movements in the developing optic cup require neural crest. Ultrastructural analysis reveals that basement membrane formation around the developing eye is also dependent on neural crest, but only specifically around the retinal pigment epithelium. Neural crest cells produce the extracellular matrix protein nidogen: impairing nidogen function disrupts eye development, and, strikingly, expression of nidogen in the absence of neural crest partially restores optic cup morphogenesis. These results demonstrate that eye formation is regulated in part by extrinsic control of extracellular matrix assembly.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Chase D Bryan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Macaulie A Casey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Rebecca L Pfeiffer
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Bryan W Jones
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Kristen M Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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28
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Lin S, Liu W, Chen CL, Sun D, Hu JX, Li L, Ye J, Mei L, Xiong WC. Neogenin-loss in neural crest cells results in persistent hyperplastic primary vitreous formation. J Mol Cell Biol 2020; 12:17-31. [PMID: 31336386 PMCID: PMC7053014 DOI: 10.1093/jmcb/mjz076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/07/2019] [Accepted: 06/12/2019] [Indexed: 01/25/2023] Open
Abstract
Neogenin is a transmembrane receptor critical for multiple cellular processes, including neurogenesis, astrogliogenesis, endochondral bone formation, and iron homeostasis. Here we present evidence that loss of neogenin contributes to pathogenesis of persistent hyperplastic primary vitreous (PHPV) formation, a genetic disorder accounting for ~ 5% of blindness in the USA. Selective loss of neogenin in neural crest cells (as observed in Wnt1-Cre; Neof/f mice), but not neural stem cells (as observed in GFAP-Cre and Nestin-Cre; Neof/f mice), resulted in a dysregulation of neural crest cell migration or delamination, exhibiting features of PHPV-like pathology (e.g. elevated retrolental mass), unclosed retinal fissure, and microphthalmia. These results demonstrate an unrecognized function of neogenin in preventing PHPV pathogenesis, implicating neogenin regulation of neural crest cell delamination/migration and retinal fissure formation as potential underlying mechanisms of PHPV.
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Affiliation(s)
- Sen Lin
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
- Department of Ophthalmology, Daping Hospital, Army Medical Center of PLA, Chongqing, China
| | - Wei Liu
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
- Department of Ophthalmology, Daping Hospital, Army Medical Center of PLA, Chongqing, China
| | - Chun-Lin Chen
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
- Department of Ophthalmology, Daping Hospital, Army Medical Center of PLA, Chongqing, China
| | - Dong Sun
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jin-Xia Hu
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
| | - Lei Li
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
| | - Jian Ye
- Department of Ophthalmology, Daping Hospital, Army Medical Center of PLA, Chongqing, China
| | - Lin Mei
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Wen-Cheng Xiong
- Department of Neuroscience & Regenerative Medicine and Department of Neurology, Augusta University, Augusta, GA 30912, USA
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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29
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Skuplik I, Cobb J. Animal Models for Understanding Human Skeletal Defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:157-188. [DOI: 10.1007/978-981-15-2389-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Jurynec MJ, Bai X, Bisgrove BW, Jackson H, Nechiporuk A, Palu RAS, Grunwald HA, Su YC, Hoshijima K, Yost HJ, Zon LI, Grunwald DJ. The Paf1 complex and P-TEFb have reciprocal and antagonist roles in maintaining multipotent neural crest progenitors. Development 2019; 146:dev.180133. [PMID: 31784460 DOI: 10.1242/dev.180133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/21/2019] [Indexed: 01/01/2023]
Abstract
Multipotent progenitor populations are necessary for generating diverse tissue types during embryogenesis. We show the RNA polymerase-associated factor 1 complex (Paf1C) is required to maintain multipotent progenitors of the neural crest (NC) lineage in zebrafish. Mutations affecting each Paf1C component result in near-identical NC phenotypes; alyron mutant embryos carrying a null mutation in paf1 were analyzed in detail. In the absence of zygotic paf1 function, definitive premigratory NC progenitors arise but fail to maintain expression of the sox10 specification gene. The mutant NC progenitors migrate aberrantly and fail to differentiate appropriately. Blood and germ cell progenitor development is affected similarly. Development of mutant NC could be rescued by additional loss of positive transcription elongation factor b (P-TEFb) activity, a key factor in promoting transcription elongation. Consistent with the interpretation that inhibiting/delaying expression of some genes is essential for maintaining progenitors, mutant embryos lacking the CDK9 kinase component of P-TEFb exhibit a surfeit of NC progenitors and their derivatives. We propose Paf1C and P-TEFb act antagonistically to regulate the timing of the expression of genes needed for NC development.
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Affiliation(s)
- Michael J Jurynec
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Xiaoying Bai
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brent W Bisgrove
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA
| | - Haley Jackson
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Alex Nechiporuk
- Department of Cell and Developmental Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rebecca A S Palu
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Hannah A Grunwald
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Yi-Chu Su
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA
| | - Kazuyuki Hoshijima
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - H Joseph Yost
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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31
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Is There a Noninvasive Source of MSCs Isolated with GMP Methods with Better Osteogenic Potential? Stem Cells Int 2019; 2019:7951696. [PMID: 31781247 PMCID: PMC6875366 DOI: 10.1155/2019/7951696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/11/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Background A new trend in the treatment for alveolar clefts in patients with cleft lip and palate involves the use of bone tissue engineering strategies to reduce or eliminate the morbidity associated with autologous bone grafting. The use of mesenchymal stem cells—autologous cells obtained from tissues such as bone marrow and fat—combined with various biomaterials has been proposed as a viable option for use in cleft patients. However, invasive procedures are necessary to obtain the mesenchymal stem cells from these two sources. To eliminate donor site morbidity, noninvasive stem cell sources such as the umbilical cord, orbicularis oris muscle, and deciduous dental pulp have been studied for use in alveolar cleft bone tissue engineering. In this study, we evaluate the osteogenic potential of these various stem cell types. Methods Ten cellular strains obtained from each different source (umbilical cord, orbicularis oris muscle, or deciduous dental pulp) were induced to osteogenic differentiation in vitro, and the bone matrix deposition of each primary culture was quantified. To evaluate whether greater osteogenic potential of the established mesenchymal stem cell strains was associated with an increase in the expression profile of neural crest genes, real-time qPCR was performed on the following genes: SRY-box 9, SRY-box 10, nerve growth factor receptor, transcription factor AP-2 alpha, and paired box 3. Results The mesenchymal stem cells obtained from deciduous dental pulp and orbicularis oris muscle demonstrated increased osteogenic potential with significantly more extracellular bone matrix deposition when compared to primary cultures obtained from the umbilical cord after twenty-one days in culture (p = 0.007 and p = 0.005, respectively). The paired box 3 gene was more highly expressed in the MSCs obtained from deciduous dental pulp and orbicularis oris muscle than in those obtained from the umbilical cord. Conclusion These results suggest that deciduous dental pulp and orbicularis oris muscle stem cells demonstrate superior osteogenic differentiation potential relative to umbilical cord-derived stem cells and that this increased potential is related to their neural crest origins. Based on these observations, and the distinct translational advantage of incorporating stem cells from noninvasive tissue sources into tissue engineering protocols, greater study of these specific cell lines in the setting of alveolar cleft repair is indicated.
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32
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Rocha M, Singh N, Ahsan K, Beiriger A, Prince VE. Neural crest development: insights from the zebrafish. Dev Dyn 2019; 249:88-111. [PMID: 31591788 DOI: 10.1002/dvdy.122] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/21/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022] Open
Abstract
Our understanding of the neural crest, a key vertebrate innovation, is built upon studies of multiple model organisms. Early research on neural crest cells (NCCs) was dominated by analyses of accessible amphibian and avian embryos, with mouse genetics providing complementary insights in more recent years. The zebrafish model is a relative newcomer to the field, yet it offers unparalleled advantages for the study of NCCs. Specifically, zebrafish provide powerful genetic and transgenic tools, coupled with rapidly developing transparent embryos that are ideal for high-resolution real-time imaging of the dynamic process of neural crest development. While the broad principles of neural crest development are largely conserved across vertebrate species, there are critical differences in anatomy, morphogenesis, and genetics that must be considered before information from one model is extrapolated to another. Here, our goal is to provide the reader with a helpful primer specific to neural crest development in the zebrafish model. We focus largely on the earliest events-specification, delamination, and migration-discussing what is known about zebrafish NCC development and how it differs from NCC development in non-teleost species, as well as highlighting current gaps in knowledge.
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Affiliation(s)
- Manuel Rocha
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, Illinois
| | - Noor Singh
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois
| | - Kamil Ahsan
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, Illinois
| | - Anastasia Beiriger
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, Illinois
| | - Victoria E Prince
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, Illinois.,Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois
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33
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Stage-dependent differential gene expression profiles of cranial neural crest-like cells derived from mouse-induced pluripotent stem cells. Med Mol Morphol 2019; 53:28-41. [PMID: 31297611 PMCID: PMC7033077 DOI: 10.1007/s00795-019-00229-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022]
Abstract
Cranial neural crest cells are multipotent cells that migrate into the pharyngeal arches of the vertebrate embryo and differentiate into various craniofacial organ derivatives. Therefore, migrating cranial neural crest cells are considered one of the most attractive candidate cell sources in regenerative medicine. We generated cranial neural crest like cell (cNCCs) using mouse-induced pluripotent stem cells cultured in neural crest-inducing medium for 14 days. Subsequently, we conducted RNA sequencing experiments to analyze gene expression profiles of cNCCs at different time points after induction. cNCCs expressed several neural crest specifier genes; however, some previously reported specifier genes such as paired box 3 and Forkhead box D3, which are essential for embryonic neural crest development, were not expressed. Moreover, ETS proto-oncogene 1, transcription factor and sex-determining region Y-box 10 were only expressed after 14 days of induction. Finally, cNCCs expressed multiple protocadherins and a disintegrin and metalloproteinase with thrombospondin motifs enzymes, which may be crucial for their migration.
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34
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Ahi EP, Richter F, Lecaudey LA, Sefc KM. Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species. Sci Rep 2019; 9:9052. [PMID: 31227799 PMCID: PMC6588699 DOI: 10.1038/s41598-019-45599-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/11/2019] [Indexed: 01/09/2023] Open
Abstract
Comparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. Here, we address a fin shape phenotype that evolved multiple times independently across teleost fish, including several species within the family Cichlidae. In a previous study, we proposed a gene regulatory network (GRN) involved in the formation and regeneration of conspicuous filamentous elongations adorning the unpaired fins of the Neolamprologus brichardi. Here, we tested the members of this network in the blockhead cichlid, Steatocranus casuarius, which displays conspicuously elongated dorsal and moderately elongated anal fins. Our study provided evidence for differences in the anatomy of fin elongation and suggested gene regulatory divergence between the two cichlid species. Only a subset of the 20 genes tested in S. casuarius showed the qPCR expression patterns predicted from the GRN identified in N. brichardi, and several of the gene-by-gene expression correlations differed between the two cichlid species. In comparison to N. brichardi, gene expression patterns in S. casuarius were in better (but not full) agreement with gene regulatory interactions inferred in zebrafish. Within S. casuarius, the dorsoventral asymmetry in ornament expression was accompanied by differences in gene expression patterns, including potential regulatory differentiation, between the anal and dorsal fin.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria. .,Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, SE-75 236, Uppsala, Sweden.
| | - Florian Richter
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | | | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
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35
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Dooley CM, Wali N, Sealy IM, White RJ, Stemple DL, Collins JE, Busch-Nentwich EM. The gene regulatory basis of genetic compensation during neural crest induction. PLoS Genet 2019; 15:e1008213. [PMID: 31199790 PMCID: PMC6594659 DOI: 10.1371/journal.pgen.1008213] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/26/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcription factors. NC induction robustness is ensured through the ability of some of these transcription factors to compensate loss of function of gene family members. However the gene regulatory events underlying compensation are poorly understood. We have used gene knockout and RNA sequencing strategies to dissect NC induction and compensation in zebrafish. We genetically ablate the NC using double mutants of tfap2a;tfap2c or remove specific subsets of the NC with sox10 and mitfa knockouts and characterise genome-wide gene expression levels across multiple time points. We find that compensation through a single wild-type allele of tfap2c is capable of maintaining early NC induction and differentiation in the absence of tfap2a function, but many target genes have abnormal expression levels and therefore show sensitivity to the reduced tfap2 dosage. This separation of morphological and molecular phenotypes identifies a core set of genes required for early NC development. We also identify the 15 somites stage as the peak of the molecular phenotype which strongly diminishes at 24 hpf even as the morphological phenotype becomes more apparent. Using gene knockouts, we associate previously uncharacterised genes with pigment cell development and establish a role for maternal Hippo signalling in melanocyte differentiation. This work extends and refines the NC GRN while also uncovering the transcriptional basis of genetic compensation via paralogues. Embryonic development is an intricate process that requires genes to be active at the right time and place. Organisms have evolved mechanisms that ensure faithful execution of developmental programmes even if genes fail to function. For example, in a process called genetic compensation, one or more genes become activated in response to loss of function of another. In this work we use the zebrafish model to investigate how two related genes, tfap2a and tfap2c, interact to ensure establishment of the neural crest, a vertebrate-specific cell type that contributes to many different tissues. Losing tfap2a activity causes mild morphological defects and losing tfap2c has no visible effect. Yet when both are inactive, embryos are severely abnormal due to lack of neural crest-derived tissues. Here we show that loss of tfap2a triggers upregulation of tfap2c which prevents the loss of neural crest tissue. However, the genes normally regulated by tfap2a respond differently to tfap2c allowing us to identify the first tier of the Ap2 network and new players in neural crest biology. Our work demonstrates that the expression signature of partial, but morphologically sufficient, genetic compensation provides an opportunity to dissect gene regulatory networks.
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Affiliation(s)
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ian M. Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Richard J. White
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - John E. Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elisabeth M. Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Lukoseviciute M, Gavriouchkina D, Williams RM, Hochgreb-Hagele T, Senanayake U, Chong-Morrison V, Thongjuea S, Repapi E, Mead A, Sauka-Spengler T. From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo. Dev Cell 2019; 47:608-628.e6. [PMID: 30513303 PMCID: PMC6286384 DOI: 10.1016/j.devcel.2018.11.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 08/15/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023]
Abstract
The neural crest (NC) is a transient embryonic stem cell-like population characterized by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that, during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes. Strikingly, foxd3 then gradually switches from an activator to its well-described role as a transcriptional repressor and potentially uses differential partners for each role. Taken together, these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from “permissive” to “repressive” nucleosome and chromatin organization to maintain multipotency and define cell fates. FoxD3 primes neural crest specification by modulating distal enhancers FoxD3 represses a number of neural crest migration and differentiation genes In neural crest, FoxD3 acts to switch chromatin from “permissive” to “repressive” Distinctive gene regulatory mechanisms underlie the bimodal action of FoxD3
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Affiliation(s)
- Martyna Lukoseviciute
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ruth M Williams
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatiana Hochgreb-Hagele
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Supat Thongjuea
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam Mead
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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Xu BN, Zhang L, Zhang DD, Song CY, Tian DL, Jiang WJ. Serum Fork-Head Box D3 (FOXD3) Expression Is Down-Regulated in and Associated with Diagnosis of Patients with Non-Small Cell Lung Cancer. Med Sci Monit 2018; 24:9504-9508. [PMID: 30596382 PMCID: PMC6324864 DOI: 10.12659/msm.896748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The aim of this study was to detect the expression of fork-head box D3 (FOXD3) and investigate its diagnostic value in patients with non-small cell lung cancer (NSCLC). Material/Methods The relative expression of FOXD3 at mRNA and protein levels was determined by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blotting analysis, respectively. Chi-square test was used to explore the relevance of FOXD3 expression with clinical features of NSCLC patients. A receiver operating characteristic (ROC) curve was built to estimate the diagnostic value of FOXD3 in distinguishing NSCLC patients from healthy controls. Results Serum FOXD3 expression was weakly expressed in NSCLC patients compared to the controls at mRNA and protein levels (P<0.001) and low FOXD3 expression was positively correlated with TNM stage, lymph node metastasis, and differentiation. The ROC curve indicated that FOXD3 acts as a diagnostic bio-marker for NSCLC patients, with an AUC of 0.826 corresponding to a sensitivity of 77.1% and a specificity of 74.6%, and an optimal cutoff point of 2.38. Conclusions Decreased expression of serum FOXD3 was observed in NSCLC patients, and it was found to be a potential molecular marker for the diagnosis of NSCLC.
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Affiliation(s)
- Bao-Ning Xu
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Lei Zhang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Dan-Dan Zhang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Cheng-Yang Song
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Da-Li Tian
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Wen-Jun Jiang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
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Jamal M, Lewandowski SL, Lawton ML, Huang GTJ, Ikonomou L. Derivation and characterization of putative craniofacial mesenchymal progenitor cells from human induced pluripotent stem cells. Stem Cell Res 2018; 33:100-109. [PMID: 30340089 PMCID: PMC6294687 DOI: 10.1016/j.scr.2018.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/28/2018] [Accepted: 10/08/2018] [Indexed: 12/23/2022] Open
Abstract
The introduction and widespread adoption of induced pluripotent stem cell (iPSC) technology has opened new avenues for craniofacial regenerative medicine. Neural crest cells (NCCs) are the precursor population to many craniofacial structures, including dental and periodontal structures, and iPSC-derived NCCs may, in the near future, offer an unlimited supply of patient-specific cells for craniofacial repair interventions. Here, we used an established protocol involving simultaneous Wnt signaling activation and TGF-β signaling inhibition to differentiate three human iPSC lines to cranial NCCs. We then derived a mesenchymal progenitor cell (NCC-MPCs) population with chondrogenic and osteogenic potential from cranial NCCs and investigated their similarity to widely studied human postnatal dental or periodontal stem/progenitor cells. NCC-MPCs were quite distinct from both their precursor cells (NCCs) and bone-marrow mesenchymal stromal cells, a stromal population of mesodermal origin. Despite their similarity with dental stem/progenitor cells, NCC-MPCs were clearly differentiated by a core set of 43 genes, including ACKR3 (CXCR7), whose expression (both at transcript and protein level) appear to be specific to NCC-MPCs. Altogether, our data demonstrate the feasibility of craniofacial mesenchymal progenitor derivation from human iPSCs through a neural crest-intermediate and set the foundation for future studies regarding their full differentiation repertoire and their in vivo existence.
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Affiliation(s)
- Mohamed Jamal
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - Sara L Lewandowski
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - Matthew L Lawton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
| | - George T-J Huang
- Department of Bioscience Research, College of Dentistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Laertis Ikonomou
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA; Pulmonary Center, Boston University School of Medicine, Boston, MA, USA.
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Ahi EP, Sefc KM. Towards a gene regulatory network shaping the fins of the Princess cichlid. Sci Rep 2018; 8:9602. [PMID: 29942008 PMCID: PMC6018552 DOI: 10.1038/s41598-018-27977-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/01/2018] [Indexed: 02/08/2023] Open
Abstract
Variation in fin shape and size contributes to the outstanding morphological diversity of teleost fishes, but the regulation of fin growth has not yet been studied extensively outside the zebrafish model. A previous gene expression study addressing the ornamental elongations of unpaired fins in the African cichlid fish Neolamprologus brichardi identified three genes (cx43, mmp9 and sema3d) with strong and consistent expression differences between short and elongated fin regions. Remarkably, the expression patterns of these genes were not consistent with inferences on their regulatory interactions in zebrafish. Here, we identify a gene expression network (GRN) comprising cx43, mmp9, and possibly also sema3d by a stepwise approach of identifying co-expression modules and predicting their upstream regulators. Among the transcription factors (TFs) predicted as potential upstream regulators of 11 co-expressed genes, six TFs (foxc1, foxp1, foxd3, myc, egr2, irf8) showed expression patterns consistent with their cooperative transcriptional regulation of the gene network. Some of these TFs have already been implicated in teleost fish fin regeneration and formation. We particularly discuss the potential function of foxd3 as driver of the network and its role in the unexpected gene expression correlations observed in N. brichardi.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria.
| | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
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40
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Abstract
TGF-β family ligands function in inducing and patterning many tissues of the early vertebrate embryonic body plan. Nodal signaling is essential for the specification of mesendodermal tissues and the concurrent cellular movements of gastrulation. Bone morphogenetic protein (BMP) signaling patterns tissues along the dorsal-ventral axis and simultaneously directs the cell movements of convergence and extension. After gastrulation, a second wave of Nodal signaling breaks the symmetry between the left and right sides of the embryo. During these processes, elaborate regulatory feedback between TGF-β ligands and their antagonists direct the proper specification and patterning of embryonic tissues. In this review, we summarize the current knowledge of the function and regulation of TGF-β family signaling in these processes. Although we cover principles that are involved in the development of all vertebrate embryos, we focus specifically on three popular model organisms: the mouse Mus musculus, the African clawed frog of the genus Xenopus, and the zebrafish Danio rerio, highlighting the similarities and differences between these species.
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Affiliation(s)
- Joseph Zinski
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Benjamin Tajer
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Mary C Mullins
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
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41
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Rogers CD, Nie S. Specifying neural crest cells: From chromatin to morphogens and factors in between. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e322. [PMID: 29722151 DOI: 10.1002/wdev.322] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 12/16/2022]
Abstract
Neural crest (NC) cells are a stem-like multipotent population of progenitor cells that are present in vertebrate embryos, traveling to various regions in the developing organism. Known as the "fourth germ layer," these cells originate in the ectoderm between the neural plate (NP), which will become the brain and spinal cord, and nonneural tissues that will become the skin and the sensory organs. NC cells can differentiate into more than 30 different derivatives in response to the appropriate signals including, but not limited to, craniofacial bone and cartilage, sensory nerves and ganglia, pigment cells, and connective tissue. The molecular and cellular mechanisms that control the induction and specification of NC cells include epigenetic control, multiple interactive and redundant transcriptional pathways, secreted signaling molecules, and adhesion molecules. NC cells are important not only because they transform into a wide variety of tissue types, but also because their ability to detach from their epithelial neighbors and migrate throughout developing embryos utilizes mechanisms similar to those used by metastatic cancer cells. In this review, we discuss the mechanisms required for the induction and specification of NC cells in various vertebrate species, focusing on the roles of early morphogenesis, cell adhesion, signaling from adjacent tissues, and the massive transcriptional network that controls the formation of these amazing cells. This article is categorized under: Nervous System Development > Vertebrates: General Principles Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Signaling Pathways > Cell Fate Signaling.
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Affiliation(s)
- Crystal D Rogers
- Department of Biology, College of Science and Mathematics, California State University Northridge, Northridge, California
| | - Shuyi Nie
- School of Biological Sciences and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
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Miranda P, Enkhmandakh B, Bayarsaihan D. TFII-I and AP2α Co-Occupy the Promoters of Key Regulatory Genes Associated with Craniofacial Development. Cleft Palate Craniofac J 2018; 55:865-870. [PMID: 28085512 DOI: 10.1597/15-214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES The aim of this study is to define the candidate target genes for TFII-I and AP2α regulation in neural crest progenitor cells. DESIGN The GTF2I and GTF2IRD1 genes encoding the TFII-I family of transcription factors are prime candidates for the Williams-Beuren syndrome, a complex multisystem disorder characterized by craniofacial, skeletal, and neurocognitive deficiencies. AP2α, a product of the TFAP2A gene, is a master regulator of neural crest cell lineage. Mutations in TFAP2A cause branchio-oculo-facial syndrome characterized by dysmorphic facial features and orofacial clefts. In this study, we examined the genome-wide promoter occupancy of TFII-I and AP2α in neural crest progenitor cells derived from in vitro-differentiated human embryonic stem cells. RESULTS Our study revealed that TFII-I and AP2α co-occupy a selective set of genes that control the specification of neural crest cells. CONCLUSIONS The data suggest that TFII-I and AP2α may coordinately control the expression of genes encoding chromatin-modifying proteins, epigenetic enzymes, transcription factors, and signaling proteins.
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Abstract
The zebrafish is an outstanding model for studying vascular biology in vivo. Pericytes and vascular smooth muscle cells can be imaged as they associate with vessels and provide stability and integrity to the vasculature. In zebrafish, pericytes associate with the cerebral and trunk vasculature on the second day of development, as assayed by pdgfrβ and notch3 markers. In the head, cerebral pericytes are neural crest derived, except for the pericytes of the hindbrain vasculature, which are mesoderm derived. Similar to the hindbrain, pericytes on the trunk vasculature are also mesoderm derived. Regardless of their location, pericyte development depends on a complex interaction between blood flow and signalling pathways, such as Notch, SONIC HEDGEHOG and BMP signalling, all of which positively regulate pericyte numbers.Pericyte numbers rapidly increase as development proceeds in order to stabilize both the blood-brain barrier and the vasculature and hence, prevent haemorrhage. Consequently, compromised pericyte development results in compromised vascular integrity, which then evolves into detrimental pathologies. Some of these pathologies have been modelled in zebrafish by inducing mutations in the notch3, foxc1 and foxf2 genes. These zebrafish models provide insights into the mechanisms of disease as associated with pericyte biology. Going forward, these models may be key contributors in elucidating the role of vascular mural cells in regulating vessel diameter and hence, blood flow.
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Affiliation(s)
- Nabila Bahrami
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Sarah J Childs
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
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Li C, Hu R, Hou N, Wang Y, Wang Z, Yang T, Gu Y, He M, Shi Y, Chen J, Song W, Li T. Alteration of the Retinoid Acid-CBP Signaling Pathway in Neural Crest Induction Contributes to Enteric Nervous System Disorder. Front Pediatr 2018; 6:382. [PMID: 30560112 PMCID: PMC6287626 DOI: 10.3389/fped.2018.00382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/16/2018] [Indexed: 12/21/2022] Open
Abstract
Hirschsprung Disease (HSCR) and/or hypoganglionosis are common pediatric disorders that arise from developmental deficiencies of enteric neural crest cells (ENCCs). Retinoid acid (RA) signaling has been shown to affect neural crest (NC) development. However, the mechanisms underlying RA deficiency-induced HSCR or hypoganglionosis are not well-defined. In this report, we found that in HSCR patient bowels, the RA nuclear receptor RARα and its interacting coregulator CREB-binding protein (CBP) were expressed in enteric neural plexuses in the normal ganglionic segment. However, the expression of these two genes was significantly inhibited in the pathological aganglionic segment. In a Xenopus laevis animal model, endogenous RARα interacted with CBP and was expressed in NC territory. Morpholino-mediated knockdown of RARα blocked expression of the NC marker genes Sox10 and FoxD3 and inhibited NC induction. The morphant embryos exhibited reduced nervous cells in the gastrointestinal anlage, a typical enteric nervous deficiency-associated phenotype. Injection of CBP mRNA rescued NC induction and reduced enteric nervous deficiency-associated phenotypes. Our work demonstrates that RARα regulates Sox10 expression via CBP during NC induction, and alteration of the RA-CBP signaling pathway may contribute to the development of enteric nervous system disorders.
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Affiliation(s)
- Cheng Li
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders and Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Rong Hu
- Ministry of Education Key Laboratory of Child Development and Disorders and Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Nali Hou
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yi Wang
- Department of Gastrointestinal Surgery and Neonatal Surgery, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhili Wang
- Department of Gastrointestinal Surgery and Neonatal Surgery, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ting Yang
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Gu
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Mulan He
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Shi
- Ministry of Education Key Laboratory of Child Development and Disorders and Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Chen
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Weihong Song
- Ministry of Education Key Laboratory of Child Development and Disorders and Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Tingyu Li
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders and Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
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45
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Perineurial Glial Plasticity and the Role of TGF-β in the Development of the Blood-Nerve Barrier. J Neurosci 2017; 37:4790-4807. [PMID: 28389474 DOI: 10.1523/jneurosci.2875-16.2017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 12/28/2022] Open
Abstract
Precisely orchestrated interactions between spinal motor axons and their ensheathing glia are vital for forming and maintaining functional spinal motor nerves. Following perturbations to peripheral myelinating glial cells, centrally derived oligodendrocyte progenitor cells (OPCs) ectopically exit the spinal cord and myelinate peripheral nerves in myelin with CNS characteristics. However, whether remaining peripheral ensheathing glia, such as perineurial glia, properly encase the motor nerve despite this change in glial cell and myelin composition, remains unknown. Using zebrafish mutants in which OPCs migrate out of the spinal cord and myelinate peripheral motor axons, we assayed perineurial glial development, maturation, and response to injury. Surprisingly, in the presence of OPCs, perineurial glia exited the CNS normally. However, aspects of their development, response to injury, and function were altered compared with wildtype larvae. In an effort to better understand the plasticity of perineurial glia in response to myelin perturbations, we identified transforming growth factor-β1 as a partial mediator of perineurial glial development. Together, these results demonstrate the incredible plasticity of perineurial glia in the presence of myelin perturbations.SIGNIFICANCE STATEMENT Peripheral neuropathies can result from damage or dysregulation of the insulating myelin sheath surrounding spinal motor axons, causing pain, inefficient nerve conduction, and the ectopic migration of oligodendrocyte progenitor cells (OPCs), the resident myelinating glial cell of the CNS, into the periphery. How perineurial glia, the ensheathing cells that form the protective blood-nerve barrier, are impacted by this myelin composition change is unknown. Here, we report that certain aspects of perineurial glial development and injury responses are mostly unaffected in the presence of ectopic OPCs. However, perineurial glial function is disrupted along nerves containing centrally derived myelin, demonstrating that, although perineurial glial cells display plasticity despite myelin perturbations, the blood-nerve barrier is compromised in the presence of ectopic OPCs.
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Hockman D, Burns AJ, Schlosser G, Gates KP, Jevans B, Mongera A, Fisher S, Unlu G, Knapik EW, Kaufman CK, Mosimann C, Zon LI, Lancman JJ, Dong PDS, Lickert H, Tucker AS, Baker CVH. Evolution of the hypoxia-sensitive cells involved in amniote respiratory reflexes. eLife 2017; 6:e21231. [PMID: 28387645 PMCID: PMC5438250 DOI: 10.7554/elife.21231] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/07/2017] [Indexed: 01/01/2023] Open
Abstract
The evolutionary origins of the hypoxia-sensitive cells that trigger amniote respiratory reflexes - carotid body glomus cells, and 'pulmonary neuroendocrine cells' (PNECs) - are obscure. Homology has been proposed between glomus cells, which are neural crest-derived, and the hypoxia-sensitive 'neuroepithelial cells' (NECs) of fish gills, whose embryonic origin is unknown. NECs have also been likened to PNECs, which differentiate in situ within lung airway epithelia. Using genetic lineage-tracing and neural crest-deficient mutants in zebrafish, and physical fate-mapping in frog and lamprey, we find that NECs are not neural crest-derived, but endoderm-derived, like PNECs, whose endodermal origin we confirm. We discover neural crest-derived catecholaminergic cells associated with zebrafish pharyngeal arch blood vessels, and propose a new model for amniote hypoxia-sensitive cell evolution: endoderm-derived NECs were retained as PNECs, while the carotid body evolved via the aggregation of neural crest-derived catecholaminergic (chromaffin) cells already associated with blood vessels in anamniote pharyngeal arches.
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Affiliation(s)
- Dorit Hockman
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Alan J Burns
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerhard Schlosser
- School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Keith P Gates
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Benjamin Jevans
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Alessandro Mongera
- Department of Genetics, Max-Planck Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Shannon Fisher
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, United States
| | - Gokhan Unlu
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, United States
| | - Ela W Knapik
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, United States
| | - Charles K Kaufman
- Children’s Hospital Boston, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Christian Mosimann
- Children’s Hospital Boston, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Leonard I Zon
- Children’s Hospital Boston, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Joseph J Lancman
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - P Duc S Dong
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Abigail S Tucker
- Department of Craniofacial Development and Stem Cell Biology, King’s College London, London, United Kingdom
| | - Clare V H Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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47
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Leslie EJ, Carlson JC, Shaffer JR, Butali A, Buxó CJ, Castilla EE, Christensen K, Deleyiannis FWB, Leigh Field L, Hecht JT, Moreno L, Orioli IM, Padilla C, Vieira AR, Wehby GL, Feingold E, Weinberg SM, Murray JC, Beaty TH, Marazita ML. Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with or without cleft palate. Hum Genet 2017; 136:275-286. [PMID: 28054174 PMCID: PMC5317097 DOI: 10.1007/s00439-016-1754-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/11/2016] [Indexed: 02/07/2023]
Abstract
Nonsyndromic orofacial clefts (OFCs) are a heterogeneous group of common craniofacial birth defects with complex etiologies that include genetic and environmental risk factors. OFCs are commonly categorized as cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which have historically been analyzed as distinct entities. Genes for both CL/P and CP have been identified via multiple genome-wide linkage and association studies (GWAS); however, altogether, known variants account for a minority of the estimated heritability in risk to these craniofacial birth defects. We performed genome-wide meta-analyses of CL/P, CP, and all OFCs across two large, multiethnic studies. We then performed population-specific meta-analyses in sub-samples of Asian and European ancestry. In addition to observing associations with known variants, we identified a novel genome-wide significant association between SNPs located in an intronic TP63 enhancer and CL/P (p = 1.16 × 10-8). Several novel loci with compelling candidate genes approached genome-wide significance on 4q21.1 (SHROOM3), 12q13.13 (KRT18), and 8p21 (NRG1). In the analysis of all OFCs combined, SNPs near FOXE1 reached genome-wide significance (p = 1.33 × 10-9). Our results support the highly heterogeneous nature of OFCs and illustrate the utility of meta-analysis for discovering new genetic risk factors.
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Affiliation(s)
- Elizabeth J Leslie
- Department of Oral Biology, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Jenna C Carlson
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - John R Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, Dows Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Carmen J Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, 00936, Puerto Rico
| | - Eduardo E Castilla
- CEMIC: Center for Medical Education and Clinical Research, Buenos Aires, 1431, Argentina
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, Brazil
- Laboratory of Congenital Malformation Epidemiology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, 21941-617, Brazil
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, 5230, Odense, Denmark
| | - Fred W B Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO, 80045, USA
| | - L Leigh Field
- Department of Medical Genetics, University of British Columbia, Vancouver, V6H 3N1, Canada
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry UT Health at Houston, Houston, TX, 77030, USA
| | - Lina Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Ieda M Orioli
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, Brazil
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine; and Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Manila, 1101, The Philippines
| | - Alexandre R Vieira
- Department of Oral Biology, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Eleanor Feingold
- Department of Oral Biology, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Seth M Weinberg
- Department of Oral Biology, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Mary L Marazita
- Department of Oral Biology, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA.
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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Chen CC, Hsia CW, Ho CW, Liang CM, Chen CM, Huang KL, Kang BH, Chen YH. Hypoxia and hyperoxia differentially control proliferation of rat neural crest stem cells via distinct regulatory pathways of the HIF1α-CXCR4 and TP53-TPM1 proteins. Dev Dyn 2017; 246:162-185. [PMID: 28002632 DOI: 10.1002/dvdy.24481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Neural crest stem cells (NCSCs) are a population of adult multipotent stem cells. We are interested in studying whether oxygen tensions affect the capability of NCSCs to self-renew and repair damaged tissues. NCSCs extracted from the hair follicle bulge region of the rat whisker pad were cultured in vitro under different oxygen tensions. RESULTS We found significantly increased and decreased rates of cell proliferation in rat NCSCs (rNCSCs) cultured, respectively, at 0.5% and 80% oxygen levels. At 0.5% oxygen, the expression of both hypoxia-inducible factor (HIF) 1α and CXCR4 was greatly enhanced in the rNCSC nuclei and was suppressed by incubation with the CXCR4-specific antagonist AMD3100. In addition, the rate of cell apoptosis in the rNCSCs cultured at 80% oxygen was dramatically increased, associated with increased nuclear expression of TP53, decreased cytoplasmic expression of TPM1 (tropomyosin-1), and increased nuclear-to-cytoplasmic translocation of S100A2. Incubation of rNCSCs with the antioxidant N-acetylcysteine (NAC) overcame the inhibitory effect of 80% oxygen on proliferation and survival of rNCSCs. CONCLUSIONS Our results show for the first time that extreme oxygen tensions directly control NCSC proliferation differentially via distinct regulatory pathways of proteins, with hypoxia via the HIF1α-CXCR4 pathway and hyperoxia via the TP53-TPM1 pathway. Developmental Dynamics 246:162-185, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Chien-Cheng Chen
- Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Neihu District, Taipei City, Taiwan
| | - Ching-Wu Hsia
- Department of Finance, School of Management, Shih Hsin University, Wenshan District, Taipei City, Taiwan
| | - Cheng-Wen Ho
- Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Neihu District, Taipei City, Taiwan
- Division of Rehabilitation Medicine, Taoyuan Armed Forces General Hospital, Longtan District, Taoyuan City, Taiwan
| | - Chang-Min Liang
- Department of Ophthalmology, Tri-Service General Hospital, Neihu District, Taipei City, Taiwan
| | - Chieh-Min Chen
- Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Neihu District, Taipei City, Taiwan
| | - Kun-Lun Huang
- Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Neihu District, Taipei City, Taiwan
- Department of Undersea and Hyperbaric Medicine, Tri-Service General Hospital, Neihu District, Taipei City, Taiwan
| | - Bor-Hwang Kang
- Division of Diving Medicine, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Zuoying District, Kaohsiung City, Taiwan
- Department of Otorhinolaryngology - Head and Neck Surgery, Tri-Service General Hospital, Taipei City, Taiwan
| | - Yi-Hui Chen
- Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Neihu District, Taipei City, Taiwan
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49
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Boer EF, Jette CA, Stewart RA. Neural Crest Migration and Survival Are Susceptible to Morpholino-Induced Artifacts. PLoS One 2016; 11:e0167278. [PMID: 28005909 PMCID: PMC5179070 DOI: 10.1371/journal.pone.0167278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023] Open
Abstract
The neural crest (NC) is a stem cell-like embryonic population that is essential for generating and patterning the vertebrate body, including the craniofacial skeleton and peripheral nervous system. Defects in NC development underlie many birth defects and contribute to formation of some of the most malignant cancers in humans, such as melanoma and neuroblastoma. For these reasons, significant research efforts have been expended to identify genes that control NC development, as it is expected to lead to a deeper understanding of the genetic mechanisms controlling vertebrate development and identify new treatments for NC-derived diseases and cancers. However, a number of inconsistencies regarding gene function during NC development have emerged from comparative analyses of gene function between mammalian and non-mammalian systems (chick, frog, zebrafish). This poses a significant barrier to identification of single genes and/or redundant pathways to target in NC diseases. Here, we determine whether technical differences, namely morpholino-based approaches used in non-mammalian systems, could contribute to these discrepancies, by examining the extent to which NC phenotypes in fascin1a (fscn1a) morphant embryos are similar to or different from fscn1a null mutants in zebrafish. Analysis of fscn1a morphants showed that they mimicked early NC phenotypes observed in fscn1a null mutants; however, these embryos also displayed NC migration and derivative phenotypes not observed in null mutants, including accumulation of p53-independent cell death. These data demonstrate that morpholinos can cause seemingly specific NC migration and derivative phenotypes, and thus have likely contributed to the inconsistencies surrounding NC gene function between species. We suggest that comparison of genetic mutants between different species is the most rigorous method for identifying conserved genetic mechanisms controlling NC development and is critical to identify new treatments for NC diseases.
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Affiliation(s)
- Elena F. Boer
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Cicely A. Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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50
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Krishnakumar R, Chen AF, Pantovich MG, Danial M, Parchem RJ, Labosky PA, Blelloch R. FOXD3 Regulates Pluripotent Stem Cell Potential by Simultaneously Initiating and Repressing Enhancer Activity. Cell Stem Cell 2016; 18:104-17. [PMID: 26748757 DOI: 10.1016/j.stem.2015.10.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/22/2015] [Accepted: 10/10/2015] [Indexed: 12/18/2022]
Abstract
Early development is governed by the ability of pluripotent cells to retain the full range of developmental potential and respond accurately to developmental cues. This property is achieved in large part by the temporal and contextual regulation of gene expression by enhancers. Here, we evaluated regulation of enhancer activity during differentiation of embryonic stem to epiblast cells and uncovered the forkhead transcription factor FOXD3 as a major regulator of the developmental potential of both pluripotent states. FOXD3 bound to distinct sites in the two cell types priming enhancers through a dual-functional mechanism. It recruited the SWI/SNF chromatin remodeling complex ATPase BRG1 to promote nucleosome removal while concurrently inhibiting maximal activation of the same enhancers by recruiting histone deacetylases1/2. Thus, FOXD3 prepares cognate genes for future maximal expression by establishing and simultaneously repressing enhancer activity. Through switching of target sites, FOXD3 modulates the developmental potential of pluripotent cells as they differentiate.
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Affiliation(s)
- Raga Krishnakumar
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amy F Chen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marisol G Pantovich
- Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Muhammad Danial
- Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ronald J Parchem
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patricia A Labosky
- Office of Strategic Coordination, Division of Program Coordination, Planning, and Strategic Initiatives, and Office of Director, National Institute of Health, Bethesda, MD 20892, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA.
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