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Zhang H, Raymundo JR, Daly KE, Zhu W, Senapati B, Zhong H, Ahilan AR, Marneros AG. AP-2α/AP-2β Transcription Factors Are Key Regulators of Epidermal Homeostasis. J Invest Dermatol 2024; 144:1505-1521.e12. [PMID: 38237728 PMCID: PMC11193656 DOI: 10.1016/j.jid.2023.12.017] [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: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
AP-2 transcription factors regulate ectodermal development, but their roles in epidermal homeostasis in adult skin are unknown. We find that AP-2α is the predominant AP-2 family member in adult epidermis, followed by AP-2β. Through inactivation of AP-2α, AP-2β, or both in keratinocytes, we assessed the effects of a gradient of epidermal AP-2 activity on skin function. We find that (i) loss of AP-2β in keratinocytes is compensated for by AP-2α, (ii) loss of AP-2α impairs terminal keratinocyte differentiation and hair morphogenesis, and (iii) the combined loss of AP-2α/AP-2β results in more severe skin and hair abnormalities. Keratinocyte differentiation defects precede progressive neutrophilic skin inflammation. Inducible inactivation of AP-2α/AP-2β in the adult phenocopies these manifestations. Transcriptomic analyses of epidermis lacking AP-2α or AP-2α/AP-2β in keratinocytes demonstrate a terminal keratinocyte differentiation defect with upregulation of alarmin keratins and of several immune pathway regulators. Moreover, our analyses suggest a key role of reduced AP-2α-dependent gene expression of CXCL14 and the keratin 15 gene K15 as an early pathogenic event toward the manifestation of skin inflammation. Thus, AP-2α and AP-2β are critical regulators of epidermal homeostasis in adult skin.
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Affiliation(s)
- Hui Zhang
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Jackelyn R Raymundo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Kathleen E Daly
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Wenjuan Zhu
- Stanford Cardiovascular Institute, Stanford Univeristy, Stanford, California, USA
| | - Bill Senapati
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Hanyu Zhong
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Arjun R Ahilan
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Alexander G Marneros
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA.
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2
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Qin Y, Ren J, Yu H, He X, Cheng S, Chen W, Yang Z, Sun F, Wang C, Yuan S, Chen P, Wu D, Ren F, Huang A, Chen J. HOXA-AS2 Epigenetically Inhibits HBV Transcription by Recruiting the MTA1-HDAC1/2 Deacetylase Complex to cccDNA Minichromosome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306810. [PMID: 38647380 PMCID: PMC11200093 DOI: 10.1002/advs.202306810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers. Further experiments demonstrate that HBV DNA polymerase (DNA pol) induces HOXA-AS2 after establishing persistent high-level HBV replication. Functional studies reveal that HOXA-AS2 physically binds to cccDNA and significantly inhibits its transcription. Mechanistically, HOXA-AS2 recruits the MTA1-HDAC1/2 deacetylase complex to cccDNA minichromosome by physically interacting with metastasis associated 1 (MTA1) subunit, resulting in reduced acetylation of histone H3 at lysine 9 (H3K9ac) and lysine 27 (H3K27ac) associated with cccDNA and subsequently suppressing cccDNA transcription. Altogether, the study reveals a mechanism to self-limit HBV replication, wherein the upregulation of lncRNA HOXA-AS2, induced by HBV DNA pol, can epigenetically suppress cccDNA transcription.
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Affiliation(s)
- YiPing Qin
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing400030China
| | - JiHua Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - HaiBo Yu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Xin He
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - ShengTao Cheng
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - WeiXian Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Zhen Yang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - FengMing Sun
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)College of Laboratory MedicineChongqing Medical UniversityChongqing400016China
| | - ChunDuo Wang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - SiYu Yuan
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Peng Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - DaiQing Wu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Fang Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - AiLong Huang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Juan Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- State Key Laboratory of Ultrasound in Medicine and EngineeringCollege of Biomedical EngineeringChongqing Medical UniversityChongqing400016China
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3
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Musolf AM, Justice CM, Erdogan-Yildirim Z, Goovaerts S, Cuellar A, Shaffer JR, Marazita ML, Claes P, Weinberg SM, Li J, Senders C, Zwienenberg M, Simeonov E, Kaneva R, Roscioli T, Di Pietro L, Barba M, Lattanzi W, Cunningham ML, Romitti PA, Boyadjiev SA. Whole genome sequencing identifies associations for nonsyndromic sagittal craniosynostosis with the intergenic region of BMP2 and noncoding RNA gene LINC01428. Sci Rep 2024; 14:8533. [PMID: 38609424 PMCID: PMC11014861 DOI: 10.1038/s41598-024-58343-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Craniosynostosis (CS) is a major birth defect resulting from premature fusion of cranial sutures. Nonsyndromic CS occurs more frequently than syndromic CS, with sagittal nonsyndromic craniosynostosis (sNCS) presenting as the most common CS phenotype. Previous genome-wide association and targeted sequencing analyses of sNCS have identified multiple associated loci, with the strongest association on chromosome 20. Herein, we report the first whole-genome sequencing study of sNCS using 63 proband-parent trios. Sequencing data for these trios were analyzed using the transmission disequilibrium test (TDT) and rare variant TDT (rvTDT) to identify high-risk rare gene variants. Sequencing data were also examined for copy number variants (CNVs) and de novo variants. TDT analysis identified a highly significant locus at 20p12.3, localized to the intergenic region between BMP2 and the noncoding RNA gene LINC01428. Three variants (rs6054763, rs6054764, rs932517) were identified as potential causal variants due to their probability of being transcription factor binding sites, deleterious combined annotation dependent depletion scores, and high minor allele enrichment in probands. Morphometric analysis of cranial vault shape in an unaffected cohort validated the effect of these three single nucleotide variants (SNVs) on dolichocephaly. No genome-wide significant rare variants, de novo loci, or CNVs were identified. Future efforts to identify risk variants for sNCS should include sequencing of larger and more diverse population samples and increased omics analyses, such as RNA-seq and ATAC-seq.
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Affiliation(s)
- Anthony M Musolf
- Statistical Genetics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health (NIH), Baltimore, MD, 21224, USA
| | - Cristina M Justice
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Zeynep Erdogan-Yildirim
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Seppe Goovaerts
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT-PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Araceli Cuellar
- Department of Pediatrics, University of California Davis, Sacramento, CA, 95817, USA
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT-PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jae Li
- Bioinformatics Core, Genome Center, University of California Davis, Davis, CA, 95618, USA
| | - Craig Senders
- Department of Otolaryngology, Head and Neck Surgery, University of California Davis, Sacramento, CA, 95817, USA
| | - Marike Zwienenberg
- Department of Neurosurgery, University of California Davis, Sacramento, CA, 95817, USA
| | - Emil Simeonov
- Pediatric Clinic, Alexandrovska University Hospital, Medical University of Sofia, 1431, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 1431, Sofia, Bulgaria
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, Australia
| | - Lorena Di Pietro
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | - Marta Barba
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | - Wanda Lattanzi
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | - Michael L Cunningham
- Seattle Children's Craniofacial Center, Center of Developmental Biology and Regenerative Medicine and Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98105, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Simeon A Boyadjiev
- Department of Pediatrics, University of California Davis, Sacramento, CA, 95817, USA
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4
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王 蕊, 安 可, 谢 静, 邹 淑. [Role of Fibroblast Growth Factor 7 in Craniomaxillofacial Development]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:469-474. [PMID: 38645865 PMCID: PMC11026893 DOI: 10.12182/20240360505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Indexed: 04/23/2024]
Abstract
Craniomaxillofacial development involves a series of highly ordered temporal-spatial cellular differentiation processes in which a variety of cell signaling factors, such as fibroblast growth factors, play important regulatory roles. As a classic fibroblast growth factor, fibroblast growth factor 7 (FGF7) serves a wide range of regulatory functions. Previous studies have demonstrated that FGF7 regulates the proliferation and migration of epithelial cells, protects them, and promotes their repair. Furthermore, recent findings indicate that epithelial cells are not the only ones subjected to the broad and powerful regulatory capacity of FGF7. It has potential effects on skeletal system development as well. In addition, FGF7 plays an important role in the development of craniomaxillofacial organs, such as the palate, the eyes, and the teeth. Nonetheless, the role of FGF7 in oral craniomaxillofacial development needs to be further elucidated. In this paper, we summarized the published research on the role of FGF7 in oral craniomaxillofacial development to demonstrate the overall understanding of FGF7 and its potential functions in oral craniomaxillofacial development.
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Affiliation(s)
- 蕊欣 王
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 可 安
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 静 谢
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 淑娟 邹
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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5
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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Dynamic enhancer landscapes in human craniofacial development. Nat Commun 2024; 15:2030. [PMID: 38448444 PMCID: PMC10917818 DOI: 10.1038/s41467-024-46396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Laura E Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Cailyn H Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, 3010, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Lucile Packard Children's Hospital, Stanford University, Stanford, CA, 94304, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA, 94110, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Octant Inc., Emeryville, CA, 94608, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, CA, USA.
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6
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Sekulovski N, Wettstein JC, Carleton AE, Juga LN, Taniguchi LE, Ma X, Rao S, Schmidt JK, Golos TG, Lin CW, Taniguchi K. Temporally resolved early BMP-driven transcriptional cascade during human amnion specification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.19.545574. [PMID: 38496419 PMCID: PMC10942271 DOI: 10.1101/2023.06.19.545574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Amniogenesis, a process critical for continuation of healthy pregnancy, is triggered in a collection of pluripotent epiblast cells as the human embryo implants. Previous studies have established that BMP signaling is a major driver of this lineage specifying process, but the downstream BMP-dependent transcriptional networks that lead to successful amniogenesis remain to be identified. This is, in part, due to the current lack of a robust and reproducible model system that enables mechanistic investigations exclusively into amniogenesis. Here, we developed an improved model of early amnion specification, using a human pluripotent stem cell-based platform in which the activation of BMP signaling is controlled and synchronous. Uniform amniogenesis is seen within 48 hours after BMP activation, and the resulting cells share transcriptomic characteristics with amnion cells of a gastrulating human embryo. Using detailed time-course transcriptomic analyses, we established a previously uncharacterized BMP-dependent amniotic transcriptional cascade, and identified markers that represent five distinct stages of amnion fate specification; the expression of selected markers was validated in early post-implantation macaque embryos. Moreover, a cohort of factors that could potentially control specific stages of amniogenesis was identified, including the transcription factor TFAP2A. Functionally, we determined that, once amniogenesis is triggered by the BMP pathway, TFAP2A controls the progression of amniogenesis. This work presents a temporally resolved transcriptomic resource for several previously uncharacterized amniogenesis states and demonstrates a critical intermediate role for TFAP2A during amnion fate specification.
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Affiliation(s)
- Nikola Sekulovski
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jenna C. Wettstein
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Amber E. Carleton
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Lauren N. Juga
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Linnea E. Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiaolong Ma
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Versiti Blood Research Institute, Milwaukee, WI 53226 USA
| | - Jenna K. Schmidt
- Wisconsin National Primate Research Center (WNPRC), Madison, WI, USA
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center (WNPRC), Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin - Madison School of Medicine and Public Health, Madison, WI USA
- Department of Comparative Biosciences, University of Wisconsin - Madison School of Veterinary Medicine, Madison, WI, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kenichiro Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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7
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Niu C, Wen H, Wang S, Shu G, Wang M, Yi H, Guo K, Pan Q, Yin G. Potential prognosis and immunotherapy predictor TFAP2A in pan-cancer. Aging (Albany NY) 2024; 16:1021-1048. [PMID: 38265973 PMCID: PMC10866441 DOI: 10.18632/aging.205225] [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: 08/02/2023] [Accepted: 10/12/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND TFAP2A is critical in regulating the expression of various genes, affecting various biological processes and driving tumorigenesis and tumor development. However, the significance of TFAP2A in carcinogenesis processes remains obscure. METHODS In our study, we explored multiple databases including TCGA, GTEx, HPA, cBioPortal, TCIA, and other well-established databases for further analysis to expound TFAP2A expression, genetic alternations, and their relationship with the prognosis and cellular signaling network alternations. GO term and KEGG pathway enrichment analysis as well as GSEA were conducted to examine the common functions of TFAP2A. RT-qPCR, Western Blot and Dual Luciferase Reporter assay were employed to perform experimental validation. RESULTS TFAP2A mRNA expression level was upregulated and its genetic alternations were frequently present in most cancer types. The enrichment analysis results prompted us to investigate the changes in the tumor immune microenvironment further. We discovered that the expression of TFAP2A was significantly associated with the expression of immune checkpoint genes, immune subtypes, ESTIMATE scores, tumor-infiltrating immune cells, and the possible role of TFAP2A in predicting immunotherapy efficacy. In addition, high TFAP2A expression significantly correlated with several ICP genes, and promoted the expression of PD-L1 on mRNA and protein levels through regulating its expression at the transcriptional level. TFAP2A protein level was upregulated in fresh colon tumor tissue samples compared to that in the adjacent normal tissues, which essentially positively correlated with the expression of PD-L1. CONCLUSIONS Our study suggests that targeting TFAP2A may provide a novel and effective strategy for cancer treatment.
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Affiliation(s)
- Chenxi Niu
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Haixuan Wen
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Shutong Wang
- Xiangya Medical School, Central South University, Changsha, China
| | - Guang Shu
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Maonan Wang
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Hanxi Yi
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ke Guo
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Qiong Pan
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
- China-Africa Research Center of Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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8
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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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9
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Shao F, Van Otterloo E, Cao H. Computational identification of key transcription factors for embryonic and postnatal Sox2+ dental epithelial stem cell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573158. [PMID: 38187542 PMCID: PMC10769342 DOI: 10.1101/2023.12.22.573158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
While many reptiles can replace their tooth throughout life, human loss the tooth replacement capability after formation of the permanent teeth. It was thought that the difference in tooth regeneration capability depends on the persistence of a specialized dental epithelial structure, the dental lamina that contains dental epithelial stem cells (DESC). Currently, we know very little about DESC such as what genes are expressed or its chromatin accessibility profile. Multiple markers of DESC have been proposed such as Sox2 and Lgr5 . Few single cell RNA-seq experiments have been performed previously, but no obvious DESC cluster was identified in these scRNA-seq datasets, possible due to that the expression level of DESC markers such as Sox2 and Lgr5 is too low or the percentage of DESC is too low in whole tooth. We utilize a mouse line Sox2-GFP to enrich Sox2+ DESC and use Smart-Seq2 protocol and ATAC-seq protocol to generate transcriptome profile and chromatin accessibility profile of P2 Sox2+ DESC. Additionally, we generate transcriptome profile and chromatin accessibility profile of E11.5 Sox2+ dental lamina cells. With transcriptome profile and chromatin accessibility profile, we systematically identify potential key transcription factors for E11.5 Sox2+ cells and P2 Sox2+ cells. We identified transcription factors including Pitx2, Id3, Pitx1, Tbx1, Trp63, Nkx2-3, Grhl3, Dlx2, Runx1, Nfix, Zfp536 , etc potentially formed the core transcriptional regulatory networks of Sox2+ DESC in both embryonic and postnatal stages.
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10
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Zhang H, Raymundo J, Daly KE, Zhu W, Senapati B, Marneros AG. AP-2α/AP-2β transcription factors are key regulators of epidermal homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.03.569763. [PMID: 38105942 PMCID: PMC10723278 DOI: 10.1101/2023.12.03.569763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
AP-2 transcription factors regulate ectodermal development but their roles for epidermal homeostasis in the adult skin are unknown. We find that AP-2α is the predominant AP-2 family member in adult epidermis, followed by AP-2β. Through inactivation of AP-2α, AP-2β, or both in keratinocytes we assessed the effects of a gradient of epidermal AP-2 activity on skin function. We find that (1) loss of AP-2β in keratinocytes is compensated for by AP-2α, (2) loss of AP-2α impairs terminal keratinocyte differentiation and hair morphogenesis, and (3) the combined loss of AP-2α/AP-2β results in more severe skin and hair abnormalities. Keratinocyte differentiation defects precede a progressive neutrophilic skin inflammation. Inducible inactivation of AP-2α/AP-2β in the adult phenocopies these manifestations. Transcriptomic analyses of epidermis lacking AP-2α or AP-2α/AP-2β in keratinocytes demonstrate a terminal keratinocyte differentiation defect with upregulation of alarmin keratins and of several immune pathway regulators. Moreover, our analyses suggest a key role of loss of AP-2α-dependent gene expression of CXCL14 and KRT15 as an early pathogenic event towards the manifestation of skin inflammation. Thus, AP-2α/AP-2β are critical regulators of epidermal homeostasis in the adult skin.
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Affiliation(s)
- Hui Zhang
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Jackelyn Raymundo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Kathleen E. Daly
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Wenjuan Zhu
- Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
| | - Bill Senapati
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Alexander G. Marneros
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
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11
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Selleri L, Rijli FM. Shaping faces: genetic and epigenetic control of craniofacial morphogenesis. Nat Rev Genet 2023; 24:610-626. [PMID: 37095271 DOI: 10.1038/s41576-023-00594-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Major differences in facial morphology distinguish vertebrate species. Variation of facial traits underlies the uniqueness of human individuals, and abnormal craniofacial morphogenesis during development leads to birth defects that significantly affect quality of life. Studies during the past 40 years have advanced our understanding of the molecular mechanisms that establish facial form during development, highlighting the crucial roles in this process of a multipotent cell type known as the cranial neural crest cell. In this Review, we discuss recent advances in multi-omics and single-cell technologies that enable genes, transcriptional regulatory networks and epigenetic landscapes to be closely linked to the establishment of facial patterning and its variation, with an emphasis on normal and abnormal craniofacial morphogenesis. Advancing our knowledge of these processes will support important developments in tissue engineering, as well as the repair and reconstruction of the abnormal craniofacial complex.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA.
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA.
| | - Filippo M Rijli
- Laboratory of Developmental Neuroepigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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12
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Liu K, Xiao Y, Gan L, Li W, Zhang J, Min J. Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors. Nucleic Acids Res 2023; 51:8270-8282. [PMID: 37409559 PMCID: PMC10450164 DOI: 10.1093/nar/gkad583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
The TFAP2 family regulates gene expression during differentiation, development, and organogenesis, and includes five homologs in humans. They all possess a highly conserved DNA binding domain (DBD) followed by a helix-span-helix (HSH) domain. The DBD-HSH tandem domain specifically binds to a GCC(N3)GGC consensus sequence, but the precise recognition mechanisms remain unclear. Here, we found that TFAP2 preferred binding to the GCC(N3)GGC sequence, and the pseudo-palindromic GCC and GGC motifs and the length of the central spacer between the two motifs determined their binding specificity. Structural studies revealed that the two flat amphipathic α-helical HSH domains of TFAP2A stacked with each other to form a dimer via hydrophobic interactions, while the stabilized loops from both DBD domains inserted into two neighboring major grooves of the DNA duplex to form base-specific interactions. This specific DNA binding mechanism controlled the length of the central spacer and determined the DNA sequence specificity of TFAP2. Mutations of the TFAP2 proteins are implicated in various diseases. We illustrated that reduction or disruption of the DNA binding ability of the TFAP2 proteins is the primary cause of TFAP2 mutation-associated diseases. Thus, our findings also offer valuable insights into the pathogenesis of disease-associated mutations in TFAP2 proteins.
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Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yuqing Xiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Linyao Gan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Weifang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jin Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
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13
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Hu S, Chen S, Zeng H, Ruan X, Lin X, Vlashi R, Zhou C, Wang H, Chen G. Ap-2β regulates cranial osteogenic potential via the activation of Wnt/β-catenin signaling pathway. Dev Biol 2023; 501:S0012-1606(23)00114-8. [PMID: 37355029 DOI: 10.1016/j.ydbio.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
The skull is a fundamental bone that protects the development of brain and consists of several bony elements, such as the frontal and parietal bones. Frontal bone exhibited superior in osteogenic potential and regeneration of cranial defects compared to parietal bone. However, how this regional difference is regulated remains largely unknown. In this study, we identified an Ap-2β transcriptional factor with a higher expression in frontal bone, but its molecular function in osteoblasts needs to be elucidated. We found that Ap-2β knockdown in preosteoblasts leads to reduced proliferation, increased cell death and impaired differentiation. Through RNA-seq analysis, we found that Ap-2β influences multiple signaling pathways including the Wnt pathway, and overexpression of Ap-2β showed increased nuclear β-catenin and its target genes expressions in osteoblasts. Pharmacological activation of Wnt/β-catenin signaling using LiCl treatment cannot rescue the reduced luciferase activities of the β-catenin/TCF/LEF reporter in Ap-2β knockdown preosteoblasts. Besides, transient expression of Ap-2β via the lentivirus system could sufficiently rescue the inferior osteogenic potential in parietal osteoblasts, while Ap-2β knockdown in frontal osteoblasts resulted in reduced osteoblast activity, reduced active β-catenin and target genes expressions. Taken together, our data demonstrated that Ap-2β modulates osteoblast proliferation and differentiation through the regulation of Wnt/β-catenin signaling pathway and plays an important role in regulating regional osteogenic potential in frontal and parietal bone.
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Affiliation(s)
- Sujie Hu
- Department of Biopharmacy, College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Sisi Chen
- Department of Biopharmacy, College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Haozu Zeng
- Department of Biopharmacy, College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xinyi Ruan
- Department of Biopharmacy, College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xinyi Lin
- Department of Biopharmacy, College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Rexhina Vlashi
- Department of Biopharmacy, College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Chenhe Zhou
- Department of Orthopedic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China
| | - Haidong Wang
- Department of Orthopedics, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314001, China.
| | - Guiqian Chen
- Department of Biopharmacy, College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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14
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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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15
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Zbasnik N, Fish JL. Fgf8 regulates first pharyngeal arch segmentation through pouch-cleft interactions. Front Cell Dev Biol 2023; 11:1186526. [PMID: 37287454 PMCID: PMC10242020 DOI: 10.3389/fcell.2023.1186526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Introduction: The pharyngeal arches are transient developmental structures that, in vertebrates, give rise to tissues of the head and neck. A critical process underlying the specification of distinct arch derivatives is segmentation of the arches along the anterior-posterior axis. Formation of ectodermal-endodermal interfaces is a key mediator of this process, and although it is essential, mechanisms regulating the establishment of these interfaces vary between pouches and between taxa. Methods: Here, we focus on the patterning and morphogenesis of epithelia associated with the first pharyngeal arch, the first pharyngeal pouch (pp1) and the first pharyngeal cleft (pc1), and the role of Fgf8 dosage in these processes in the mouse model system. Results: We find that severe reductions of Fgf8 levels disrupt both pp1 and pc1 development. Notably, out-pocketing of pp1 is largely robust to Fgf8 reductions, however, pp1 extension along the proximal-distal axis fails when Fgf8 is low. Our data indicate that Fgf8 is required for specification of regional identity in both pp1 and pc1, for localized changes in cell polarity, and for elongation and extension of both pp1 and pc1. Discussion: Based on Fgf8-mediated changes in tissue relationships between pp1 and pc1, we hypothesize that extension of pp1 requires physical interaction with pc1. Overall, our data indicate a critical role for the lateral surface ectoderm in segmentation of the first pharyngeal arch that has previously been under-appreciated.
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16
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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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17
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Zbasnik N, Fish JL. Fgf8 regulates first pharyngeal arch segmentation through pouch-cleft interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532781. [PMID: 36993764 PMCID: PMC10055162 DOI: 10.1101/2023.03.15.532781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The pharyngeal arches are transient developmental structures that, in vertebrates, give rise to tissues of the head and neck. A critical process underlying the specification of distinct arch derivatives is segmentation of the arches along the anterior-posterior axis. Out-pocketing of the pharyngeal endoderm between the arches is a key mediator of this process, and although it is essential, mechanisms regulating out-pocketing vary between pouches and between taxa. Here, we focus on the patterning and morphogenesis of epithelia associated with the first pharyngeal arch, the first pharyngeal pouch (pp1) and the first pharyngeal cleft (pc1), and the role of Fgf8 dosage in these processes. We find that severe reductions of Fgf8 levels disrupt both pp1 and pc1 development. Notably, out-pocketing of pp1 is largely robust to Fgf8 reductions, however, pp1 extension along the proximal-distal axis fails when Fgf8 is low. Our data indicate that extension of pp1 requires physical interaction with pc1, and that multiple aspects of pc1 morphogenesis require Fgf8 . In particular, Fgf8 is required for specification of regional identity in both pp1 and pc1, for localized changes in cell polarity, and for elongation and extension of both pp1 and pc1. Overall, our data indicate a critical role for the lateral surface ectoderm in segmentation of the first pharyngeal arch that has previously been under-appreciated.
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Ye Q, Bhojwani A, Hu JK. Understanding the development of oral epithelial organs through single cell transcriptomic analysis. Development 2022; 149:dev200539. [PMID: 35831953 PMCID: PMC9481975 DOI: 10.1242/dev.200539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/07/2022] [Indexed: 01/29/2023]
Abstract
During craniofacial development, the oral epithelium begins as a morphologically homogeneous tissue that gives rise to locally complex structures, including the teeth, salivary glands and taste buds. How the epithelium is initially patterned and specified to generate diverse cell types remains largely unknown. To elucidate the genetic programs that direct the formation of distinct oral epithelial populations, we mapped the transcriptional landscape of embryonic day 12 mouse mandibular epithelia at single cell resolution. Our analysis identified key transcription factors and gene regulatory networks that define different epithelial cell types. By examining the spatiotemporal patterning process along the oral-aboral axis, our results propose a model in which the dental field is progressively confined to its position by the formation of the aboral epithelium anteriorly and the non-dental oral epithelium posteriorly. Using our data, we also identified Ntrk2 as a proliferation driver in the forming incisor, contributing to its invagination. Together, our results provide a detailed transcriptional atlas of the embryonic mandibular epithelium, and unveil new genetic markers and regulators that are present during the specification of various oral epithelial structures.
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Affiliation(s)
- Qianlin Ye
- School of Dentistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Arshia Bhojwani
- School of Dentistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jimmy K. Hu
- School of Dentistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
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Huang H, Liu J, Li M, Guo H, Zhu J, Zhu L, Wu S, Mo K, Huang Y, Tan J, Chen C, Wang B, Yu Y, Wang L, Liu Y, Ouyang H. Cis-regulatory chromatin loops analysis identifies GRHL3 as a master regulator of surface epithelium commitment. SCIENCE ADVANCES 2022; 8:eabo5668. [PMID: 35857527 PMCID: PMC9278850 DOI: 10.1126/sciadv.abo5668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Understanding the regulatory network of cell fate acquisition remains a major challenge. Using the induction of surface epithelium (SE) from human embryonic stem cells as a paradigm, we show that the dynamic changes in morphology-related genes (MRGs) closely correspond to SE fate transitions. The marked remodeling of cytoskeleton indicates the initiation of SE differentiation. By integrating promoter interactions, epigenomic features, and transcriptome, we delineate an SE-specific cis-regulatory network and identify grainyhead-like 3 (GRHL3) as an initiation factor sufficient to drive SE commitment. Mechanically, GRHL3 primes the SE chromatin accessibility landscape and activates SE-initiating gene expression. In addition, the evaluation of GRHL3-mediated promoter interactions unveils a positive feedback loop of GRHL3 and bone morphogenetic protein 4 on SE fate decisions. Our work proposes a concept that MRGs could be used to identify cell fate transitions and provides insights into regulatory principles of SE lineage development and stem cell-based regenerative medicine.
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Affiliation(s)
- Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jin Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Liqiong Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Ying Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Chaoqun Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Bofeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yankun Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510060, China
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