1
|
Li J, Chen S, Xiao J, Ji J, Huang C, Shu G. FOXC1 transcriptionally suppresses ABHD5 to inhibit the progression of renal cell carcinoma through AMPK/mTOR pathway. Cell Biol Toxicol 2024; 40:62. [PMID: 39093497 PMCID: PMC11297099 DOI: 10.1007/s10565-024-09899-w] [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: 02/29/2024] [Accepted: 07/04/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Increased activity of the transcription factor FOXC1 leads to elevated transcription of target genes, ultimately facilitating the progression of various cancer types. However, there are currently no literature reports on the role of FOXC1 in renal cell carcinoma. METHODS By using RT-qPCR, immunohistochemistry and Western blotting, FOXC1 mRNA and protein expression was evaluated. Gain of function experiments were utilized to assess the proliferation and metastasis ability of cells. A nude mouse model was created for transplanting tumors and establishing a lung metastasis model to observe cell proliferation and spread in a living organism. Various techniques including biological analysis, CHIP assay, luciferase assay, RT-qRCR and Western blotting experiments were utilized to investigate how FOXC1 contributes to the transcription of ABHD5 on a molecular level. FOXC1 was assessed by Western blot for its impact on AMPK/mTOR signaling pathway. RESULTS FOXC1 is down-regulated in RCC, causing unfavorable prognosis of patients with RCC. Further experiments showed that forced FOXC1 expression significantly restrains RCC cell growth and cell metastasis. Mechanically, FOXC1 promotes the transcription of ABHD5 to activate AMPK signal pathway to inhibit mTOR signal pathway. Finally, knockdown of ABHD5 recovered the inhibitory role of FOXC1 overexpression induced cell growth and metastasis suppression. CONCLUSION In general, our study demonstrates that FOXC1 exerts its tumor suppressor role by promoting ABHD5 transcription to regulating AMPK/mTOR signal pathway. FOXC1 could serve as both a diagnostic indicator and potential treatment focus for RCC.
Collapse
Affiliation(s)
- Jianfa Li
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuangchen Chen
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Jing Xiao
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jiayuan Ji
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chenchen Huang
- Department of Urology, Peking University First Hospital, Beijing, China.
| | - Ge Shu
- Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China.
| |
Collapse
|
2
|
Wang X, Ma C, Zhang X, Yuan P, Wang Y, Fu M, Zhang Z, Shi R, Wei N, Wang J, Wu W. Mussel inspired 3D elastomer enabled rapid calvarial bone regeneration through recruiting more osteoprogenitors from the dura mater. Regen Biomater 2024; 11:rbae059. [PMID: 38911700 PMCID: PMC11193312 DOI: 10.1093/rb/rbae059] [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: 01/14/2024] [Revised: 04/17/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Currently, the successful healing of critical-sized calvarial bone defects remains a considerable challenge. The immune response plays a key role in regulating bone regeneration after material grafting. Previous studies mainly focused on the relationship between macrophages and bone marrow mesenchymal stem cells (BMSCs), while dural cells were recently found to play a vital role in the calvarial bone healing. In this study, a series of 3D elastomers with different proportions of polycaprolactone (PCL) and poly(glycerol sebacate) (PGS) were fabricated, which were further supplemented with polydopamine (PDA) coating. The physicochemical properties of the PCL/PGS and PCL/PGS/PDA grafts were measured, and then they were implanted as filling materials for 8 mm calvarial bone defects. The results showed that a matched and effective PDA interface formed on a well-proportioned elastomer, which effectively modulated the polarization of M2 macrophages and promoted the recruitment of dural cells to achieve full-thickness bone repair through both intramembranous and endochondral ossification. Single-cell RNA sequencing analysis revealed the predominance of dural cells during bone healing and their close relationship with macrophages. The findings illustrated that the crosstalk between dural cells and macrophages determined the vertical full-thickness bone repair for the first time, which may be the new target for designing bone grafts for calvarial bone healing.
Collapse
Affiliation(s)
- Xuqiao Wang
- The College of Life Sciences, Northwest University, Xi'an, 710127, PR China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Clinical Research Center for Oral Diseases, Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| | - Chaoqun Ma
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Clinical Research Center for Oral Diseases, Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| | - Xinchi Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| | - Pingping Yuan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Clinical Research Center for Oral Diseases, Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| | - Yujiao Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Clinical Research Center for Oral Diseases, Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| | - Mingdi Fu
- The College of Life Sciences, Northwest University, Xi'an, 710127, PR China
| | - Zheqian Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Clinical Research Center for Oral Diseases, Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| | - Ruiying Shi
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Clinical Research Center for Oral Diseases, Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| | - Na Wei
- The College of Life Sciences, Northwest University, Xi'an, 710127, PR China
| | - Juncheng Wang
- Institute of Stomatology, First Medical Center, Chinese PLA General Hospital, Beijing, 100853, PR China
| | - Wei Wu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Clinical Research Center for Oral Diseases, Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, PR China
| |
Collapse
|
3
|
Wang W, Yang N, Wang L, Zhu Y, Chu X, Xu W, Li Y, Xu Y, Gao L, Zhang B, Zhang G, Sun Q, Wang W, Wang Q, Zhang W, Chen D. The TET-Sall4-BMP regulatory axis controls craniofacial cartilage development. Cell Rep 2024; 43:113873. [PMID: 38427557 DOI: 10.1016/j.celrep.2024.113873] [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: 04/23/2023] [Revised: 07/25/2023] [Accepted: 02/12/2024] [Indexed: 03/03/2024] Open
Abstract
Craniofacial microsomia (CFM) is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However, the molecular basis of CFM pathogenesis is largely unknown. Here, we employ the zebrafish model to investigate mechanisms of CFM pathogenesis. In early embryos, tet2 and tet3 are essential for pharyngeal cartilage development. Single-cell RNA sequencing reveals that loss of Tet2/3 impairs chondrocyte differentiation due to insufficient BMP signaling. Moreover, biochemical and genetic evidence reveals that the sequence-specific 5mC/5hmC-binding protein, Sall4, binds the promoter of bmp4 to activate bmp4 expression and control pharyngeal cartilage development. Mechanistically, Sall4 directs co-phase separation of Tet2/3 with Sall4 to form condensates that mediate 5mC oxidation on the bmp4 promoter, thereby promoting bmp4 expression and enabling sufficient BMP signaling. These findings suggest the TET-BMP-Sall4 regulatory axis is critical for pharyngeal cartilage development. Collectively, our study provides insights into understanding craniofacial development and CFM pathogenesis.
Collapse
Affiliation(s)
- Weigang Wang
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Na Yang
- Institute of Biomedical Research, Yunnan University, Kunming, China; Department of Ultrasound, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Liangliang Wang
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Xiao Chu
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Weijie Xu
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Yawei Li
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Yihai Xu
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Lina Gao
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Beibei Zhang
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Guoqiang Zhang
- Institute of Biomedical Research, Yunnan University, Kunming, China
| | - Qinmiao Sun
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Weihong Wang
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Kunming Medical University, Kunming, China.
| | - Qiang Wang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China.
| | - Wenxin Zhang
- Institute of Biomedical Research, Yunnan University, Kunming, China.
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming, China; Southwest United Graduate School, Kunming, China.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Hojo H, Ohba S. Runt-related Transcription Factors and Gene Regulatory Mechanisms in Skeletal Development and Diseases. Curr Osteoporos Rep 2023; 21:485-492. [PMID: 37436583 PMCID: PMC10543954 DOI: 10.1007/s11914-023-00808-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
PURPOSE OF REVIEW Runt-related transcription factors (RUNX) play critical roles in skeletal development, metabolism, and diseases. In mammals, three RUNX members, namely RUNX1, RUNX2, and RUNX3, play distinct and redundant roles, although RUNX2 is a dominant factor in skeletal development and several skeletal diseases. This review is to provide an overview of the current understanding of RUNX-mediated transcriptional regulation in different skeletal cell types. RECENT FINDINGS Advances in chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) have revealed genome-wide RUNX-mediated gene regulatory mechanisms, including their association with cis-regulatory elements and putative target genes. Further studies with genome-wide analysis and biochemical assays have shed light on RUNX-mediated pioneering action and involvements of RUNX2 in lipid-lipid phase separation. Emerging multi-layered mechanisms of RUNX-mediated gene regulations help us better understanding of skeletal development and diseases, which also provides clues to think how genome-wide studies can help develop therapeutic strategies for skeletal diseases.
Collapse
Affiliation(s)
- Hironori Hojo
- Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8655 Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita, Osaka 565-0871 Japan
| |
Collapse
|
7
|
Yeboah RL, Pira CU, Shankel M, Cooper AM, Haro E, Ly VD, Wysong K, Zhang M, Sandoval N, Oberg KC. Sox, Fox, and Lmx1b binding sites differentially regulate a Gdf5-Associated regulatory region during elbow development. Front Cell Dev Biol 2023; 11:1215406. [PMID: 37492222 PMCID: PMC10364121 DOI: 10.3389/fcell.2023.1215406] [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: 05/01/2023] [Accepted: 06/28/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction: The articulating ends of limb bones have precise morphology and asymmetry that ensures proper joint function. Growth differentiation factor 5 (Gdf5) is a secreted morphogen involved in cartilage and bone development that contributes to the architecture of developing joints. Dysregulation of Gdf5 results in joint dysmorphogenesis often leading to progressive joint degeneration or osteoarthritis (OA). The transcription factors and cis-regulatory modules (CRMs) that regulate Gdf5 expression are not well characterized. We previously identified a Gdf5-associated regulatory region (GARR) that contains predicted binding sites for Lmx1b, Osr2, Fox, and the Sox transcription factors. These transcription factors are recognized factors involved in joint morphogenesis and skeletal development. Methods: We used in situ hybridization to Gdf5, Col2A1, and the transcription factors of interest in developing chicken limbs to determine potential overlap in expression. We further analyzed scRNA-seq data derived from limbs and knees in published mouse and chicken datasets, identifying cells with coexpression of Gdf5 and the transcription factors of interest. We also performed site-directed mutatgenesis of the predicted transcription factor binding sites in a GARR-reporter construct and determined any change in activity using targeted regional electroporation (TREP) in micromass and embryonic chicken wing bioassays. Results: Gdf5 expression overlapped the expression of these transcription factors during joint development both by in situ hybridization (ISH) and scRNA-seq analyses. Within the GARR CRM, mutation of two binding sites common to Fox and Sox transcripstion factors reduced enhancer activity to background levels in micromass cultures and in ovo embryonic chicken wing bioassays, whereas mutation of two Sox-only binding sites caused a significant increase in activity. These results indicate that the Fox/Sox binding sites are required for activity, while the Sox-only sites are involved in repression of activity. Mutation of Lmx1b binding sites in GARR caused an overall reduction in enhancer activity in vitro and a dorsal reduction in ovo. Despite a recognized role for Osr2 in joint development, disruption of the predicted Osr2 site did not alter GARR activity. Conclusion: Taken together, our data indicates that GARR integrates positive, repressive, and asymmetrical inputs to fine-tune the expression of Gdf5 during elbow joint development.
Collapse
|
8
|
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. Cell Type- and Tissue-specific Enhancers in Craniofacial Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546603. [PMID: 37425964 PMCID: PMC10327103 DOI: 10.1101/2023.06.26.546603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development1-3. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined histone modification and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. We used transgenic mouse reporter assays to determine the in vivo activity patterns of human face enhancers predicted from these data. Across 16 in vivo validated human enhancers, we observed a rich diversity of craniofacial subregions in which these enhancers are active in vivo. To annotate the cell type specificities of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating these data across species, we find that the majority (56%) of human craniofacial enhancers are functionally conserved in mice, providing cell type- and embryonic stage-resolved predictions of their in vivo activity profiles. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we demonstrate the utility of these data for predicting the in vivo cell type specificity of enhancers. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
Collapse
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, University of Bern, 3008 Bern, 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
| | - 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
| | - 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
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- Newcastle University 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, Merced, California, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Wu T, Jin Y, Chen F, Xuan X, Cao J, Liang Y, Wang Y, Zhan J, Zhao M, Huang C. Identification and characterization of bone/cartilage-associated signatures in common fibrotic skin diseases. Front Genet 2023; 14:1121728. [PMID: 37082197 PMCID: PMC10111020 DOI: 10.3389/fgene.2023.1121728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Background: Fibrotic skin diseases are characterized by excessive accumulation of the extracellular matrix (ECM) and activation of fibroblasts, leading to a global healthcare burden. However, effective treatments of fibrotic skin diseases remain limited, and their pathological mechanisms require further investigation. This study aims to investigate the common biomarkers and therapeutic targets in two major fibrotic skin diseases, namely, keloid and systemic sclerosis (SSc), by bioinformatics analysis.Methods: The keloid (GSE92566) and SSc (GSE95065) datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, followed by functional enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We then constructed a protein–protein interaction (PPI) network for the identification of hub genes. We explored the possibility of further functional enrichment analysis of hub genes on the Metascape, GeneMANIA, and TissueNexus platforms. Transcription factor (TF)–hub gene and miRNA–hub gene networks were established using NetworkAnalyst. We fixed GSE90051 and GSE76855 as the external validation datasets. Student’s t-test and receiver operating characteristic (ROC) curve were used for candidate hub gene validation. Hub gene expression was assessed in vitro by quantitative real-time PCR.Results: A total of 157 overlapping DEGs (ODEGs) were retrieved from the GSE92566 and GSE95065 datasets, and five hub genes (COL11A1, COL5A2, ASPN, COL10A1, and COMP) were identified and validated. Functional studies revealed that hub genes were predominantly enriched in bone/cartilage-related and collagen-related processes. FOXC1 and miR-335-5p were predicted to be master regulators at both transcriptional and post‐transcriptional levels.Conclusion: COL11A1, COL5A2, ASPN, COL10A1, and COMP may help understand the pathological mechanism of the major fibrotic skin diseases; moreover, FOXC1 and miR-355-5p could build a regulatory network in keloid and SSc.
Collapse
Affiliation(s)
- Ting Wu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yifan Jin
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fangqi Chen
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiuyun Xuan
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juanmei Cao
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Liang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqing Wang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinshan Zhan
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengjie Zhao
- Department of Dermatology, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Mengjie Zhao, ; Changzheng Huang,
| | - Changzheng Huang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Mengjie Zhao, ; Changzheng Huang,
| |
Collapse
|
11
|
Hojo H. Emerging RUNX2-Mediated Gene Regulatory Mechanisms Consisting of Multi-Layered Regulatory Networks in Skeletal Development. Int J Mol Sci 2023; 24:ijms24032979. [PMID: 36769300 PMCID: PMC9917854 DOI: 10.3390/ijms24032979] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Skeletal development is tightly coordinated by chondrocytes and osteoblasts, which are derived from skeletal progenitors, and distinct cell-type gene regulatory programs underlie the specification and differentiation of cells. Runt-related transcription factor 2 (Runx2) is essential to chondrocyte hypertrophy and osteoblast differentiation. Genetic studies have revealed the biological functions of Runx2 and its involvement in skeletal genetic diseases. Meanwhile, molecular biology has provided a framework for our understanding of RUNX2-mediated transactivation at a limited number of cis-regulatory elements. Furthermore, studies using next-generation sequencing (NGS) have provided information on RUNX2-mediated gene regulation at the genome level and novel insights into the multiple layers of gene regulatory mechanisms, including the modes of action of RUNX2, chromatin accessibility, the concept of pioneer factors and phase separation, and three-dimensional chromatin organization. In this review, I summarize the emerging RUNX2-mediated regulatory mechanism from a multi-layer perspective and discuss future perspectives for applications in the treatment of skeletal diseases.
Collapse
Affiliation(s)
- Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| |
Collapse
|
12
|
Rowley AJ, Square TA, Miller CT. Site pleiotropy of a stickleback Bmp6 enhancer. Dev Biol 2022; 492:111-118. [PMID: 36198347 DOI: 10.1016/j.ydbio.2022.09.012] [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: 05/13/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/15/2022]
Abstract
Development and regeneration are orchestrated by gene regulatory networks that operate in part through transcriptional enhancers. Although many enhancers are pleiotropic and are active in multiple tissues, little is known about whether enhancer pleiotropy is due to 1) site pleiotropy, in which individual transcription factor binding sites (TFBS) are required for activity in multiple tissues, or 2) multiple distinct sites that regulate expression in different tissues. Here, we investigated the pleiotropy of an intronic enhancer of the stickleback Bone morphogenetic protein 6 (Bmp6) gene. This enhancer was previously shown to regulate evolved changes in tooth number and tooth regeneration, and is highly pleiotropic, with robust activity in both fins and teeth throughout embryonic, larval, and adult life, and in the heart and kidney in adult fish. We tested the hypothesis that the pleiotropy of this enhancer is due to site pleiotropy of an evolutionarily conserved predicted Foxc1 TFBS. Transgenic analysis and site-directed mutagenesis experiments both deleting and scrambling this predicted Foxc1 TFBS revealed that the binding site is required for enhancer activity in both teeth and fins throughout embryonic, larval, and adult development, and in the heart and kidney in adult fish. Collectively these data support a model where the pleiotropy of this Bmp6 enhancer is due to site pleiotropy and this putative binding site is required for enhancer activity in multiple anatomical sites from the embryo to the adult.
Collapse
Affiliation(s)
- Alyssa J Rowley
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Tyler A Square
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA.
| |
Collapse
|
13
|
Hojo H, Saito T, He X, Guo Q, Onodera S, Azuma T, Koebis M, Nakao K, Aiba A, Seki M, Suzuki Y, Okada H, Tanaka S, Chung UI, McMahon AP, Ohba S. Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages. Cell Rep 2022; 40:111315. [PMID: 36070691 PMCID: PMC9510047 DOI: 10.1016/j.celrep.2022.111315] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/31/2022] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator Runx2 (runt-related transcription factor 2) has essential but distinct roles in osteoblasts and chondrocytes in skeletal development. However, Runx2-mediated regulatory mechanisms underlying the distinctive programming of osteoblasts and chondrocytes are not well understood. Here, we perform an integrative analysis to investigate Runx2-DNA binding and chromatin accessibility ex vivo using neonatal osteoblasts and chondrocytes. We find that Runx2 engages with cell-type-distinct chromatin-accessible regions, potentially interacting with different combinations of transcriptional regulators, forming cell-type-specific hotspots, and potentiating chromatin accessibility. Genetic analysis and direct cellular reprogramming studies suggest that Runx2 is essential for establishment of chromatin accessibility in osteoblasts. Functional enhancer studies identify an Sp7 distal enhancer driven by Runx2-dependent binding and osteoblast-specific chromatin accessibility, contributing to normal osteoblast differentiation. Our findings provide a framework for understanding the regulatory landscape encompassing Runx2-mediated and cell-type-distinct enhancer networks that underlie the specification of osteoblasts. Hojo et al. investigate the gene-regulatory landscape underlying specification of skeletal cell types in neonatal mice. Runx2, an osteoblast determinant, engages with cell-type-distinct chromatin-accessible regions and is essential for establishment of chromatin accessibility in osteoblasts. The study provides insights into enhancer networks in skeletal development.
Collapse
Affiliation(s)
- Hironori Hojo
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Taku Saito
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Xinjun He
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shoko Onodera
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hiroyuki Okada
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Sakae Tanaka
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ung-Il Chung
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shinsuke Ohba
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan; Department of Oral Anatomy and Developmental Biology, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan.
| |
Collapse
|
14
|
Mutation of foxl1 Results in Reduced Cartilage Markers in a Zebrafish Model of Otosclerosis. Genes (Basel) 2022; 13:genes13071107. [PMID: 35885890 PMCID: PMC9319681 DOI: 10.3390/genes13071107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/08/2022] [Accepted: 06/11/2022] [Indexed: 02/05/2023] Open
Abstract
Bone diseases such as otosclerosis (conductive hearing loss) and osteoporosis (low bone mineral density) can result from the abnormal expression of genes that regulate cartilage and bone development. The forkhead box transcription factor FOXL1 has been identified as the causative gene in a family with autosomal dominant otosclerosis and has been reported as a candidate gene in GWAS meta-analyses for osteoporosis. This potentially indicates a novel role for foxl1 in chondrogenesis, osteogenesis, and bone remodelling. We created a foxl1 mutant zebrafish strain as a model for otosclerosis and osteoporosis and examined jaw bones that are homologous to the mammalian middle ear bones, and mineralization of the axial skeleton. We demonstrate that foxl1 regulates the expression of collagen genes such as collagen type 1 alpha 1a and collagen type 11 alpha 2, and results in a delay in jawbone mineralization, while the axial skeleton remains unchanged. foxl1 may also act with other forkhead genes such as foxc1a, as loss of foxl1 in a foxc1a mutant background increases the severity of jaw calcification phenotypes when compared to each mutant alone. Our zebrafish model demonstrates atypical cartilage formation and mineralization in the zebrafish craniofacial skeleton in foxl1 mutants and demonstrates that aberrant collagen expression may underlie the development of otosclerosis.
Collapse
|
15
|
FOXC1 Binds Enhancers and Promotes Cisplatin Resistance in Bladder Cancer. Cancers (Basel) 2022; 14:cancers14071717. [PMID: 35406487 PMCID: PMC8996937 DOI: 10.3390/cancers14071717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 01/25/2023] Open
Abstract
Simple Summary In bladder cancer, cisplatin remains the front-line therapy, but drug resistance is common. Previously, we showed that cancer cells can spontaneously convert to an aggressive drug-resistant phenotype without mutational events. In the current work, we explored the epigenetic mechanism behind the conversion to the drug-resistant phenotype. We discovered that drug-resistant cells have differentially accessible enhancers, which are bound by FOXC1, a transcription factor that is overexpressed in these cells. Accordingly, FOXC1 knockout significantly attenuates the emergence of the drug-resistant phenotype and reduces cell survival upon cisplatin treatment. These findings suggest that FOXC1 binding at accessible enhancers promotes cisplatin drug resistance in bladder cancer cells. Therefore, FOXC1 targeting may be a new therapeutic avenue to mitigate cisplatin resistance and improve treatment efficacy in bladder cancer. Abstract Chemotherapy resistance is traditionally attributed to DNA mutations that confer a survival advantage under drug selection pressure. However, in bladder cancer and other malignancies, we and others have previously reported that cancer cells can convert spontaneously to an aggressive drug-resistant phenotype without prior drug selection or mutational events. In the current work, we explored possible epigenetic mechanisms behind this phenotypic plasticity. Using Hoechst dye exclusion and flow cytometry, we isolated the aggressive drug-resistant cells and analyzed their chromatin accessibility at regulatory elements. Compared to the rest of the cancer cell population, the aggressive drug-resistant cells exhibited enhancer accessibility changes. In particular, we found that differentially accessible enhancers were enriched for the FOXC1 transcription factor motif, and that FOXC1 was the most significantly overexpressed gene in aggressive drug-resistant cells. ChIP-seq analysis revealed that differentially accessible enhancers in aggressive drug-resistant cells had a higher FOXC1 binding, which regulated the expression of adjacent cancer-relevant genes like ABCB1 and ID3. Accordingly, cisplatin treatment of bladder cancer cells led to an increased FOXC1 expression, which mediated cell survival and conversion to a drug-resistant phenotype. Collectively, these findings suggest that FOXC1 contributes to phenotypic plasticity by binding enhancers and promoting a mutation-independent shift towards cisplatin resistance in bladder cancer.
Collapse
|
16
|
Paudel S, Gjorcheska S, Bump P, Barske L. Patterning of cartilaginous condensations in the developing facial skeleton. Dev Biol 2022; 486:44-55. [DOI: 10.1016/j.ydbio.2022.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/14/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
|
17
|
Grimaldi A, Comai G, Mella S, Tajbakhsh S. Identification of bipotent progenitors that give rise to myogenic and connective tissues in mouse. eLife 2022; 11:70235. [PMID: 35225230 PMCID: PMC9020825 DOI: 10.7554/elife.70235] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
How distinct cell fates are manifested by direct lineage ancestry from bipotent progenitors, or by specification of individual cell types is a key question for understanding the emergence of tissues. The interplay between skeletal muscle progenitors and associated connective tissue cells provides a model for examining how muscle functional units are established. Most craniofacial structures originate from the vertebrate-specific neural crest cells except in the dorsal portion of the head, where they arise from cranial mesoderm. Here, using multiple lineage-tracing strategies combined with single cell RNAseq and in situ analyses, we identify bipotent progenitors expressing Myf5 (an upstream regulator of myogenic fate) that give rise to both muscle and juxtaposed connective tissue. Following this bifurcation, muscle and connective tissue cells retain complementary signalling features and maintain spatial proximity. Disrupting myogenic identity shifts muscle progenitors to a connective tissue fate. The emergence of Myf5-derived connective tissue is associated with the activity of several transcription factors, including Foxp2. Interestingly, this unexpected bifurcation in cell fate was not observed in craniofacial regions that are colonised by neural crest cells. Therefore, we propose that an ancestral bi-fated program gives rise to muscle and connective tissue cells in skeletal muscles that are deprived of neural crest cells.
Collapse
Affiliation(s)
| | - Glenda Comai
- UMR 3738, Department of Developmental and Stem Cell Biology, CNRS, Paris, France
| | - Sebastien Mella
- Cytometry and Biomarkers UTechS, Institut Pasteur, Paris, France
| | | |
Collapse
|
18
|
Fabian P, Tseng KC, Thiruppathy M, Arata C, Chen HJ, Smeeton J, Nelson N, Crump JG. Lifelong single-cell profiling of cranial neural crest diversification in zebrafish. Nat Commun 2022; 13:13. [PMID: 35013168 PMCID: PMC8748784 DOI: 10.1038/s41467-021-27594-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/30/2021] [Indexed: 01/13/2023] Open
Abstract
The cranial neural crest generates a huge diversity of derivatives, including the bulk of connective and skeletal tissues of the vertebrate head. How neural crest cells acquire such extraordinary lineage potential remains unresolved. By integrating single-cell transcriptome and chromatin accessibility profiles of cranial neural crest-derived cells across the zebrafish lifetime, we observe progressive and region-specific establishment of enhancer accessibility for distinct fates. Neural crest-derived cells rapidly diversify into specialized progenitors, including multipotent skeletal progenitors, stromal cells with a regenerative signature, fibroblasts with a unique metabolic signature linked to skeletal integrity, and gill-specific progenitors generating cell types for respiration. By retrogradely mapping the emergence of lineage-specific chromatin accessibility, we identify a wealth of candidate lineage-priming factors, including a Gata3 regulatory circuit for respiratory cell fates. Rather than multilineage potential being established during cranial neural crest specification, our findings support progressive and region-specific chromatin remodeling underlying acquisition of diverse potential.
Collapse
Affiliation(s)
- Peter Fabian
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Kuo-Chang Tseng
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Mathi Thiruppathy
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Claire Arata
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Hung-Jhen Chen
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Joanna Smeeton
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Nellie Nelson
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - J Gage Crump
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA.
| |
Collapse
|
19
|
Ruff GL, Murphy KE, Smith ZR, Vertino PM, Murphy PJ. Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation. BMC Cancer 2021; 21:1342. [PMID: 34922480 PMCID: PMC8684129 DOI: 10.1186/s12885-021-09077-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin state provides a clear decipherable blueprint for maintenance of transcriptional patterns, exemplifying a mitotically stable form of cellular programming in dividing cells. In this regard, genomic studies of chromatin states within cancerous tissues have the potential to uncover novel aspects of tumor biology and unique mechanisms associated with disease phenotypes and outcomes. The degree to which chromatin state differences occur in accordance with breast cancer features has not been established. METHODS We applied a series of unsupervised computational methods to identify chromatin and molecular differences associated with discrete physiologies across human breast cancer tumors. RESULTS Chromatin patterns alone are capable of stratifying tumors in association with cancer subtype and disease progression. Major differences occur at DNA motifs for the transcription factor FOXA1, in hormone receptor-positive tumors, and motifs for SOX9 in Basal-like tumors. We find that one potential driver of this effect, the histone chaperone ANP32E, is inversely correlated with tumor progression and relaxation of chromatin at FOXA1 binding sites. Tumors with high levels of ANP32E exhibit an immune response and proliferative gene expression signature, whereas tumors with low ANP32E levels appear programmed for differentiation. CONCLUSIONS Our results indicate that ANP32E may function through chromatin state regulation to control breast cancer differentiation and tumor plasticity. This study sets a precedent for future computational studies of chromatin changes in carcinogenesis.
Collapse
Affiliation(s)
- Garrett L Ruff
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Kristin E Murphy
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Zachary R Smith
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
- Wilmot Cancer Institute, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14624, USA
| | - Paula M Vertino
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
- Wilmot Cancer Institute, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14624, USA
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
- Wilmot Cancer Institute, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14624, USA.
| |
Collapse
|
20
|
Ohba S. Genome-scale actions of master regulators directing skeletal development. JAPANESE DENTAL SCIENCE REVIEW 2021; 57:217-223. [PMID: 34745394 PMCID: PMC8556520 DOI: 10.1016/j.jdsr.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/14/2021] [Accepted: 10/10/2021] [Indexed: 11/03/2022] Open
Abstract
The mammalian skeleton develops through two distinct modes of ossification: intramembranous ossification and endochondral ossification. During the process of skeletal development, SRY-box containing gene 9 (Sox9), runt-related transcription factor 2 (Runx2), and Sp7 work as master transcription factors (TFs) or transcriptional regulators, underlying cell fate specification of the two distinct populations: bone-forming osteoblasts and cartilage-forming chondrocytes. In the past two decades, core transcriptional circuits underlying skeletal development have been identified mainly through mouse genetics and biochemical approaches. Recently emerging next-generation sequencer (NGS)-based studies have provided genome-scale views on the gene regulatory landscape programmed by the master TFs/transcriptional regulators. With particular focus on Sox9, Runx2, and Sp7, this review aims to discuss the gene regulatory landscape in skeletal development, which has been identified by genome-scale data, and provide future perspectives in this field.
Collapse
Affiliation(s)
- Shinsuke Ohba
- Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| |
Collapse
|
21
|
French CR. Mechanistic Insights into Axenfeld-Rieger Syndrome from Zebrafish foxc1 and pitx2 Mutants. Int J Mol Sci 2021; 22:ijms221810001. [PMID: 34576164 PMCID: PMC8472202 DOI: 10.3390/ijms221810001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 12/11/2022] Open
Abstract
Axenfeld-Rieger syndrome (ARS) encompasses a group of developmental disorders that affect the anterior segment of the eye, as well as systemic developmental defects in some patients. Malformation of the ocular anterior segment often leads to secondary glaucoma, while some patients also present with cardiovascular malformations, craniofacial and dental abnormalities and additional periumbilical skin. Genes that encode two transcription factors, FOXC1 and PITX2, account for almost half of known cases, while the genetic lesions in the remaining cases remain unresolved. Given the genetic similarity between zebrafish and humans, as well as robust antisense inhibition and gene editing technologies available for use in these animals, loss of function zebrafish models for ARS have been created and shed light on the mechanism(s) whereby mutations in these two transcription factors cause such a wide array of developmental phenotypes. This review summarizes the published phenotypes in zebrafish foxc1 and pitx2 loss of function models and discusses possible mechanisms that may be used to target pharmaceutical development and therapeutic interventions.
Collapse
Affiliation(s)
- Curtis R French
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland and Labrador, St. John's, NL A1B 3V6, Canada
| |
Collapse
|
22
|
Sánchez N, Juárez-Balarezo J, Olhaberry M, González-Oneto H, Muzard A, Mardonez MJ, Franco P, Barrera F, Gaete M. Depression and Antidepressants During Pregnancy: Craniofacial Defects Due to Stem/Progenitor Cell Deregulation Mediated by Serotonin. Front Cell Dev Biol 2021; 9:632766. [PMID: 34476233 PMCID: PMC8406697 DOI: 10.3389/fcell.2021.632766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
Depression is a common and debilitating mood disorder that increases in prevalence during pregnancy. Worldwide, 7 to 12% of pregnant women experience depression, in which the associated risk factors include socio-demographic, psychological, and socioeconomic variables. Maternal depression could have psychological, anatomical, and physiological consequences in the newborn. Depression has been related to a downregulation in serotonin levels in the brain. Accordingly, the most commonly prescribed pharmacotherapy is based on selective serotonin reuptake inhibitors (SSRIs), which increase local serotonin concentration. Even though the use of SSRIs has few adverse effects compared with other antidepressants, altering serotonin levels has been associated with the advent of anatomical and physiological changes in utero, leading to defects in craniofacial development, including craniosynostosis, cleft palate, and dental defects. Migration and proliferation of neural crest cells, which contribute to the formation of bone, cartilage, palate, teeth, and salivary glands in the craniofacial region, are regulated by serotonin. Specifically, craniofacial progenitor cells are affected by serotonin levels, producing a misbalance between their proliferation and differentiation. Thus, it is possible to hypothesize that craniofacial development will be affected by the changes in serotonin levels, happening during maternal depression or after the use of SSRIs, which cross the placental barrier, increasing the risk of craniofacial defects. In this review, we provide a synthesis of the current research on depression and the use of SSRI during pregnancy, and how this could be related to craniofacial defects using an interdisciplinary perspective integrating psychological, clinical, and developmental biology perspectives. We discuss the mechanisms by which serotonin could influence craniofacial development and stem/progenitor cells, proposing some transcription factors as mediators of serotonin signaling, and craniofacial stem/progenitor cell biology. We finally highlight the importance of non-pharmacological therapies for depression on fertile and pregnant women, and provide an individual analysis of the risk-benefit balance for the use of antidepressants during pregnancy.
Collapse
Affiliation(s)
- Natalia Sánchez
- Department of Anatomy, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jesús Juárez-Balarezo
- Department of Anatomy, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcia Olhaberry
- Department of Psychology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute for Research in Depression and Personality (MIDAP), Santiago, Chile
| | - Humberto González-Oneto
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Antonia Muzard
- Department of Psychology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute for Research in Depression and Personality (MIDAP), Santiago, Chile
| | - María Jesús Mardonez
- Department of Psychology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute for Research in Depression and Personality (MIDAP), Santiago, Chile
| | - Pamela Franco
- Department of Psychology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute for Research in Depression and Personality (MIDAP), Santiago, Chile
| | - Felipe Barrera
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcia Gaete
- Department of Anatomy, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
23
|
Xu P, Yu HV, Tseng KC, Flath M, Fabian P, Segil N, Crump JG. Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation. eLife 2021; 10:63595. [PMID: 33501917 PMCID: PMC7891931 DOI: 10.7554/elife.63595] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/26/2021] [Indexed: 12/15/2022] Open
Abstract
The specification of cartilage requires Sox9, a transcription factor with broad roles for organogenesis outside the skeletal system. How Sox9 and other factors gain access to cartilage-specific cis-regulatory regions during skeletal development was unknown. By analyzing chromatin accessibility during the differentiation of neural crest cells into chondrocytes of the zebrafish head, we find that cartilage-associated chromatin accessibility is dynamically established. Cartilage-associated regions that become accessible after neural crest migration are co-enriched for Sox9 and Fox transcription factor binding motifs. In zebrafish lacking Foxc1 paralogs, we find a global decrease in chromatin accessibility in chondrocytes, consistent with a later loss of dorsal facial cartilages. Zebrafish transgenesis assays confirm that many of these Foxc1-dependent elements function as enhancers with region- and stage-specific activity in facial cartilages. These results show that Foxc1 promotes chondrogenesis in the face by establishing chromatin accessibility at a number of cartilage-associated gene enhancers.
Collapse
Affiliation(s)
- Pengfei Xu
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Haoze V Yu
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Kuo-Chang Tseng
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Mackenzie Flath
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Peter Fabian
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Neil Segil
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - J Gage Crump
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| |
Collapse
|
24
|
Xu J, Wang K, Zhang Z, Xue D, Li W, Pan Z. The Role of Forkhead Box Family in Bone Metabolism and Diseases. Front Pharmacol 2021; 12:772237. [PMID: 35153742 PMCID: PMC8832510 DOI: 10.3389/fphar.2021.772237] [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: 09/07/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022] Open
Abstract
Forkhead box (Fox) family, an evolutionarily conserved family of transcription factors carrying the "Forkhead" motif, plays an indispensable role in human health and disease. Fox family genes are involved in cell differentiation, proliferation and apoptosis, embryonic development, aging, glucose and lipid metabolism, and immune regulation. The regulatory role of the Fox family in the context of bone metabolism and orthopedic diseases is an emerging research hotspot. In this review, we highlight the major molecular mechanisms underlying the regulatory role of Fox factors in bone metabolism, bone development, bone homeostasis, and bone diseases associated with inhibition or upregulation of Fox factors. In addition, we discuss the emerging evidence in the realm of Fox factor-based therapeutics.
Collapse
Affiliation(s)
- Jianxiang Xu
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
| | - Kanbin Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
- Department of Orthopedic Surgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Zengjie Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
| | - Deting Xue
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
- *Correspondence: Deting Xue, ; Weixu Li, ; Zhijun Pan,
| | - Weixu Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
- *Correspondence: Deting Xue, ; Weixu Li, ; Zhijun Pan,
| | - Zhijun Pan
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Orthopedics Research Institute of Zhejiang University, Hangzhou, China
- Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou, China
- *Correspondence: Deting Xue, ; Weixu Li, ; Zhijun Pan,
| |
Collapse
|