1
|
Di Girolamo D, Di Iorio E, Missero C. Molecular and Cellular Function of p63 in Skin Development and Genetic Diseases. J Invest Dermatol 2024:S0022-202X(24)02076-1. [PMID: 39340489 DOI: 10.1016/j.jid.2024.08.011] [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: 05/07/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/30/2024]
Abstract
The transcription factor p63 is a master regulator of multiple ectodermal derivatives. During epidermal commitment, p63 interacts with several chromatin remodeling complexes to transactivate epidermal-specific genes and repress transcription of simple epithelial and nonepithelial genes. In the postnatal epidermis, p63 is required to control the proliferative potential of progenitor cells, maintain epidermal integrity, and contribute to epidermal differentiation. Autosomal dominant sequence variant in p63 cause a spectrum of syndromic disorders that affect several tissues, including or derived from stratified epithelia. In this review, we describe the recent studies that have provided novel insights into disease pathogenesis and potential therapeutic targets.
Collapse
Affiliation(s)
- Daniela Di Girolamo
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Biology Department, University of Naples Federico II, Naples, Italy
| | - Enzo Di Iorio
- Clinical Genetics Unit, University Hospital of Padua, Padua, Italy; Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Caterina Missero
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Biology Department, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
2
|
Neumayer G, Torkelson JL, Li S, McCarthy K, Zhen HH, Vangipuram M, Mader MM, Gebeyehu G, Jaouni TM, Jacków-Malinowska J, Rami A, Hansen C, Guo Z, Gaddam S, Tate KM, Pappalardo A, Li L, Chow GM, Roy KR, Nguyen TM, Tanabe K, McGrath PS, Cramer A, Bruckner A, Bilousova G, Roop D, Tang JY, Christiano A, Steinmetz LM, Wernig M, Oro AE. A scalable and cGMP-compatible autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa. Nat Commun 2024; 15:5834. [PMID: 38992003 PMCID: PMC11239819 DOI: 10.1038/s41467-024-49400-z] [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: 03/28/2023] [Accepted: 05/25/2024] [Indexed: 07/13/2024] Open
Abstract
We present Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a scalable platform producing autologous organotypic iPS cell-derived induced skin composite (iSC) grafts for definitive treatment. Clinical-grade manufacturing integrates CRISPR-mediated genetic correction with reprogramming into one step, accelerating derivation of COL7A1-edited iPS cells from patients. Differentiation into epidermal, dermal and melanocyte progenitors is followed by CD49f-enrichment, minimizing maturation heterogeneity. Mouse xenografting of iSCs from four patients with different mutations demonstrates disease modifying activity at 1 month. Next-generation sequencing, biodistribution and tumorigenicity assays establish a favorable safety profile at 1-9 months. Single cell transcriptomics reveals that iSCs are composed of the major skin cell lineages and include prominent holoclone stem cell-like signatures of keratinocytes, and the recently described Gibbin-dependent signature of fibroblasts. The latter correlates with enhanced graftability of iSCs. In conclusion, DEBCT overcomes manufacturing and safety roadblocks and establishes a reproducible, safe, and cGMP-compatible therapeutic approach to heal lesions of DEB patients.
Collapse
Affiliation(s)
- Gernot Neumayer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jessica L Torkelson
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Shengdi Li
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Kelly McCarthy
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Hanson H Zhen
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Madhuri Vangipuram
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Marius M Mader
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gulilat Gebeyehu
- Thermo Fisher Scientific, Life Sciences Solutions Group, Cell Biology, Research and Development, Frederick, MD, USA
| | - Taysir M Jaouni
- Thermo Fisher Scientific, Life Sciences Solutions Group, Cell Biology, Research and Development, Frederick, MD, USA
| | - Joanna Jacków-Malinowska
- Department of Dermatology, Columbia University, New York, NY, USA
- St. John's Institute of Dermatology, King's College London, London, UK
| | - Avina Rami
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Corey Hansen
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Zongyou Guo
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Sadhana Gaddam
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Keri M Tate
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Lingjie Li
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Grace M Chow
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Kevin R Roy
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Thuylinh Michelle Nguyen
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Patrick S McGrath
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Amber Cramer
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Anna Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Dennis Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Jean Y Tang
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA.
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA, USA.
| | - Anthony E Oro
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| |
Collapse
|
3
|
McCann AA, Baniulyte G, Woodstock DL, Sammons MA. Context dependent activity of p63-bound gene regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593326. [PMID: 38766006 PMCID: PMC11100809 DOI: 10.1101/2024.05.09.593326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The p53 family of transcription factors regulate numerous organismal processes including the development of skin and limbs, ciliogenesis, and preservation of genetic integrity and tumor suppression. p53 family members control these processes and gene expression networks through engagement with DNA sequences within gene regulatory elements. Whereas p53 binding to its cognate recognition sequence is strongly associated with transcriptional activation, p63 can mediate both activation and repression. How the DNA sequence of p63-bound gene regulatory elements is linked to these varied activities is not yet understood. Here, we use massively parallel reporter assays (MPRA) in a range of cellular and genetic contexts to investigate the influence of DNA sequence on p63-mediated transcription. Most regulatory elements with a p63 response element motif (p63RE) activate transcription, with those sites bound by p63 more frequently or adhering closer to canonical p53 family response element sequences driving higher transcriptional output. The most active regulatory elements are those also capable of binding p53. Elements uniquely bound by p63 have varied activity, with p63RE-mediated repression associated with lower overall GC content in flanking sequences. Comparison of activity across cell lines suggests differential activity of elements may be regulated by a combination of p63 abundance or context-specific cofactors. Finally, changes in p63 isoform expression dramatically alters regulatory element activity, primarily shifting inactive elements towards a strong p63-dependent activity. Our analysis of p63-bound gene regulatory elements provides new insight into how sequence, cellular context, and other transcription factors influence p63-dependent transcription. These studies provide a framework for understanding how p63 genomic binding locally regulates transcription. Additionally, these results can be extended to investigate the influence of sequence content, genomic context, chromatin structure on the interplay between p63 isoforms and p53 family paralogs.
Collapse
Affiliation(s)
- Abby A. McCann
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| | - Gabriele Baniulyte
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| | - Dana L. Woodstock
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| | - Morgan A. Sammons
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| |
Collapse
|
4
|
Gill JK, Rehsia SK, Verma E, Sareen N, Dhingra S. Stem cell therapy for cardiac regeneration: past, present, and future. Can J Physiol Pharmacol 2024; 102:161-179. [PMID: 38226807 DOI: 10.1139/cjpp-2023-0202] [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] [Indexed: 01/17/2024]
Abstract
Cardiac disorders remain the leading cause of mortality worldwide. Current clinical strategies, including drug therapy, surgical interventions, and organ transplantation offer limited benefits to patients without regenerating the damaged myocardium. Over the past decade, stem cell therapy has generated a keen interest owing to its unique self-renewal and immune privileged characteristics. Furthermore, the ability of stem cells to differentiate into specialized cell types, has made them a popular therapeutic tool against various diseases. This comprehensive review provides an overview of therapeutic potential of different types of stem cells in reference to cardiovascular diseases. Furthermore, it sheds light on the advantages and limitations associated with each cell type. An in-depth analysis of the challenges associated with stem cell research and the hurdles for its clinical translation and their possible solutions have also been elaborated upon. It examines the controversies surrounding embryonic stem cells and the emergence of alternative approaches, such as the use of induced pluripotent stem cells for cardiac therapeutic applications. Overall, this review serves as a valuable resource for researchers, clinicians, and policymakers involved in the field of regenerative medicine, guiding the development of safe and effective stem cell-based therapies to revolutionize patient care.
Collapse
Affiliation(s)
- Jaideep Kaur Gill
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre Regenerative Medicine Program, Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Biomedical Engineering Program, University of Manitoba, Winnipeg MB, R2H2A6, Canada
| | - Sargun Kaur Rehsia
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre Regenerative Medicine Program, Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Biomedical Engineering Program, University of Manitoba, Winnipeg MB, R2H2A6, Canada
| | - Elika Verma
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre Regenerative Medicine Program, Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Biomedical Engineering Program, University of Manitoba, Winnipeg MB, R2H2A6, Canada
| | - Niketa Sareen
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre Regenerative Medicine Program, Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Biomedical Engineering Program, University of Manitoba, Winnipeg MB, R2H2A6, Canada
| | - Sanjiv Dhingra
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre Regenerative Medicine Program, Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Biomedical Engineering Program, University of Manitoba, Winnipeg MB, R2H2A6, Canada
| |
Collapse
|
5
|
Abstract
Keratinocyte senescence contributes to skin ageing and epidermal dysfunction. According to the existing knowledge, the transcription factor ΔNp63α plays pivotal roles in differentiation and proliferation of keratinocytes. It is traditionally accepted that ΔNp63α exerts its functions via binding to promoter regions to activate or repress gene transcription. However, accumulating evidence demonstrates that ΔNp63α can bind to elements away from promoter regions of its target genes, mediating epigenetic regulation. On the other hand, several epigenetic alterations, including DNA methylation, histone modification and variation, chromatin remodelling, as well as enhancer-promoter looping, are found to be related to cell senescence. To systematically elucidate how ΔNp63α affects keratinocyte senescence via epigenetic regulation, we comprehensively compiled the literatures on the roles of ΔNp63α in keratinocyte senescence, epigenetics in cellular senescence, and the relation between ΔNp63α-mediated epigenetic regulation and keratinocyte senescence. Based on the published data, we conclude that ΔNp63α mediates epigenetic regulation via multiple mechanisms: recruiting epigenetic enzymes to modify DNA or histones, coordinating chromatin remodelling complexes (CRCs) or regulating their expression, and mediating enhancer-promoter looping. Consequently, the expression of genes related to cell cycle is modulated, and proliferation of keratinocytes and renewal of stem cells are maintained, by ΔNp63α. During skin inflammaging, the decline of ΔNp63α may lead to epigenetic dysregulation, resultantly deteriorating keratinocyte senescence.
Collapse
Affiliation(s)
- Linghan Kuang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - Chenghua Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| |
Collapse
|
6
|
Dudgeon C, Casabianca A, Harris C, Ogier C, Bellina M, Fiore S, Bernet A, Ducarouge B, Goldschneider D, Su X, Pitarresi J, Hezel A, De S, Narrow W, Soliman F, Shields C, Vendramini-Costa DB, Prela O, Wang L, Astsaturov I, Mehlen P, Carpizo DR. Netrin-1 feedforward mechanism promotes pancreatic cancer liver metastasis via hepatic stellate cell activation, retinoid, and ELF3 signaling. Cell Rep 2023; 42:113369. [PMID: 37922311 DOI: 10.1016/j.celrep.2023.113369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 09/04/2023] [Accepted: 10/18/2023] [Indexed: 11/05/2023] Open
Abstract
The biology of metastatic pancreatic ductal adenocarcinoma (PDAC) is distinct from that of the primary tumor due to changes in cell plasticity governed by a distinct transcriptome. Therapeutic strategies that target this distinct biology are needed. We detect an upregulation of the neuronal axon guidance molecule Netrin-1 in PDAC liver metastases that signals through its dependence receptor (DR), uncoordinated-5b (Unc5b), to facilitate metastasis in vitro and in vivo. The mechanism of Netrin-1 induction involves a feedforward loop whereby Netrin-1 on the surface of PDAC-secreted extracellular vesicles prepares the metastatic niche by inducing hepatic stellate cell activation and retinoic acid secretion that in turn upregulates Netrin-1 in disseminated tumor cells via RAR/RXR and Elf3 signaling. While this mechanism promotes PDAC liver metastasis, it also identifies a therapeutic vulnerability, as it can be targeted using anti-Netrin-1 therapy to inhibit metastasis using the Unc5b DR cell death mechanism.
Collapse
Affiliation(s)
- Crissy Dudgeon
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Anthony Casabianca
- Department of Surgery, Division of Surgical Oncology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA; Wilmot Cancer Center, University of Rochester, Rochester, NY, USA
| | - Chris Harris
- Department of Surgery, Division of Surgical Oncology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA; Wilmot Cancer Center, University of Rochester, Rochester, NY, USA
| | - Charline Ogier
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Mélanie Bellina
- Apoptosis, Cancer and Development Laboratory - Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence PLAsCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, 69008 Lyon, France; Netris Pharma, 69008 Lyon, France
| | - Stephany Fiore
- Apoptosis, Cancer and Development Laboratory - Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence PLAsCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, 69008 Lyon, France
| | - Agnes Bernet
- Apoptosis, Cancer and Development Laboratory - Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence PLAsCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, 69008 Lyon, France; Netris Pharma, 69008 Lyon, France
| | | | | | - Xiaoyang Su
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Jason Pitarresi
- Department of Medicine, Division of Hematology/Oncology, University of Massachusetts, Worcester, MA, USA
| | - Aram Hezel
- Department of Medicine, Division of Medical Oncology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Wade Narrow
- Department of Surgery, Division of Surgical Oncology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA; Wilmot Cancer Center, University of Rochester, Rochester, NY, USA
| | - Fady Soliman
- Rutgers Robert Wood-Johnson Medical School, New Brunswick, NJ, USA
| | - Cory Shields
- Wilmot Cancer Center, University of Rochester, Rochester, NY, USA
| | | | - Orjola Prela
- Department of Surgery, Division of Surgical Oncology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Lan Wang
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Igor Astsaturov
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory - Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence PLAsCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, 69008 Lyon, France; Netris Pharma, 69008 Lyon, France
| | - Darren R Carpizo
- Department of Surgery, Division of Surgical Oncology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA; Wilmot Cancer Center, University of Rochester, Rochester, NY, USA.
| |
Collapse
|
7
|
Li X, Xie R, Luo Y, Shi R, Ling Y, Zhao X, Xu X, Chu W, Wang X. Cooperation of TGF-β and FGF signalling pathways in skin development. Cell Prolif 2023; 56:e13489. [PMID: 37150846 PMCID: PMC10623945 DOI: 10.1111/cpr.13489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Abstract
The skin is a multi-layered structure composed of the epidermis, dermis and hypodermis. The epidermis originates entirely from the ectoderm, whereas the dermis originates from various germ layers depending on its anatomical location; thus, there are different developmental patterns of the skin. Although the regulatory mechanisms of epidermal formation are well understood, mechanisms regulating dermis development are not clear owing to the complex origin. It has been shown that several morphogenetic pathways regulate dermis development. Of these, transforming growth factor-β (TGF-β) and fibroblast growth factor (FGF) signalling pathways are the main modulators regulating skin cell induction, fate decision, migration and differentiation. Recently, the successful generation of human skin by modulating TGF-β and FGF signals further demonstrated the irreplaceable roles of these pathways in skin regeneration. This review provides evidence of the role of TGF-β and FGF signalling pathways in the development of different skin layers, especially the disparate dermis of different body regions. This review also provides new perspectives on the distinct developmental patterns of skin and explores new ideas for clinical applications in the future.
Collapse
Affiliation(s)
- Xinxin Li
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Rongfang Xie
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Yilin Luo
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Runlu Shi
- Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Yuanqiang Ling
- Guangzhou Wishing Tree Hair Medical Technology Limited CompanyGuangzhouChina
| | - Xiaojing Zhao
- Guangzhou Wishing Tree Hair Medical Technology Limited CompanyGuangzhouChina
| | - Xuejuan Xu
- Department of EndocrinologyThe First People's Hospital of FoshanFoshanChina
| | - Weiwei Chu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| |
Collapse
|
8
|
Yang Y, McCullough CG, Seninge L, Guo L, Kwon WJ, Zhang Y, Li NY, Gaddam S, Pan C, Zhen H, Torkelson J, Glass IA, Charville G, Que J, Stuart J, Ding H, Oro A. A Spatiotemporal and Machine-Learning Platform Accelerates the Manufacturing of hPSC-derived Esophageal Mucosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563664. [PMID: 37961271 PMCID: PMC10634774 DOI: 10.1101/2023.10.24.563664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Human pluripotent stem cell-derived tissue engineering offers great promise in designer cell-based personalized therapeutics. To harness such potential, a broader approach requires a deeper understanding of tissue-level interactions. We previously developed a manufacturing system for the ectoderm-derived skin epithelium for cell replacement therapy. However, it remains challenging to manufacture the endoderm-derived esophageal epithelium, despite both possessing similar stratified structure. Here we employ single cell and spatial technologies to generate a spatiotemporal multi-omics cell atlas for human esophageal development. We illuminate the cellular diversity, dynamics and signal communications for the developing esophageal epithelium and stroma. Using the machine-learning based Manatee, we prioritize the combinations of candidate human developmental signals for in vitro derivation of esophageal basal cells. Functional validation of the Manatee predictions leads to a clinically-compatible system for manufacturing human esophageal mucosa. Our approach creates a versatile platform to accelerate human tissue manufacturing for future cell replacement therapies to treat human genetic defects and wounds.
Collapse
|
9
|
Zhang Y, Karagiannis D, Liu H, Lin M, Fang Y, Jiang M, Chen X, Suresh S, Huang H, She J, Shi F, Yang P, El-Rifai W, Zaika A, Oro AE, Rustgi AK, Wang TC, Lu C, Que J. Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.556982. [PMID: 37745439 PMCID: PMC10515764 DOI: 10.1101/2023.09.09.556982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
While cell fate determination and maintenance are important in establishing and preserving tissue identity and function during development, aberrant cell fate transition leads to cancer cell heterogeneity and resistance to treatment. Here, we report an unexpected role for the transcription factor p63 (Trp63/TP63) in the fate choice of squamous versus neuroendocrine lineage in esophageal development and malignancy. Deletion of p63 results in extensive neuroendocrine differentiation in the developing mouse esophagus and esophageal progenitors derived from human embryonic stem cells. In human esophageal neuroendocrine carcinoma (eNEC) cells, p63 is transcriptionally silenced by EZH2-mediated H3K27 trimethylation (H3K27me3). Upregulation of the major p63 isoform ΔNp63α, through either ectopic expression or EZH2 inhibition, promotes squamous transdifferentiation of eNEC cells. Together these findings uncover p63 as a rheostat in coordinating the transition between squamous and neuroendocrine cell fates during esophageal development and tumor progression.
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Neumayer G, Torkelson JL, Li S, McCarthy K, Zhen HH, Vangipuram M, Jackow J, Rami A, Hansen C, Guo Z, Gaddam S, Pappalardo A, Li L, Cramer A, Roy KR, Nguyen TM, Tanabe K, McGrath PS, Bruckner A, Bilousova G, Roop D, Bailey I, Tang JY, Christiano A, Steinmetz LM, Wernig M, Oro AE. A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.529447. [PMID: 36909618 PMCID: PMC10002612 DOI: 10.1101/2023.02.28.529447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Background Gene editing in induced pluripotent stem (iPS) cells has been hailed to enable new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa (DEB). However, manufacturing, efficacy and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. Methods We developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a new generation GMP-compatible (cGMP), reproducible, and scalable platform to produce autologous clinical-grade iPS cell-derived organotypic induced skin composite (iSC) grafts to treat incurable wounds of patients lacking type VII collagen (C7). DEBCT uses a combined high-efficiency reprogramming and CRISPR-based genetic correction single step to generate genome scar-free, COL7A1 corrected clonal iPS cells from primary patient fibroblasts. Validated iPS cells are converted into epidermal, dermal and melanocyte progenitors with a novel 2D organoid differentiation protocol, followed by CD49f enrichment and expansion to minimize maturation heterogeneity. iSC product characterization by single cell transcriptomics was followed by mouse xenografting for disease correcting activity at 1 month and toxicology analysis at 1-6 months. Culture-acquired mutations, potential CRISPR-off targets, and cancer-driver variants were evaluated by targeted and whole genome sequencing. Findings iPS cell-derived iSC grafts were reproducibly generated from four recessive DEB patients with different pathogenic mutations. Organotypic iSC grafts onto immune-compromised mice developed into stable stratified skin with functional C7 restoration. Single cell transcriptomic characterization of iSCs revealed prominent holoclone stem cell signatures in keratinocytes and the recently described Gibbin-dependent signature in dermal fibroblasts. The latter correlated with enhanced graftability. Multiple orthogonal sequencing and subsequent computational approaches identified random and non-oncogenic mutations introduced by the manufacturing process. Toxicology revealed no detectable tumors after 3-6 months in DEBCT-treated mice. Interpretation DEBCT successfully overcomes previous roadblocks and represents a robust, scalable, and safe cGMP manufacturing platform for production of a CRISPR-corrected autologous organotypic skin graft to heal DEB patient wounds.
Collapse
Affiliation(s)
- Gernot Neumayer
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, and Department of Chemical and Systems Biology
| | - Jessica L. Torkelson
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Shengdi Li
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Kelly McCarthy
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Hanson H. Zhen
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Madhuri Vangipuram
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, and Department of Chemical and Systems Biology
| | - Joanna Jackow
- Department of Dermatology, Columbia University, New York, NY 10032
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Avina Rami
- Department of Dermatology, Columbia University, New York, NY 10032
| | - Corey Hansen
- Department of Dermatology, Columbia University, New York, NY 10032
| | - Zongyou Guo
- Department of Dermatology, Columbia University, New York, NY 10032
| | - Sadhana Gaddam
- Program in Epithelial Biology and Department of Dermatology
| | | | - Lingjie Li
- Program in Epithelial Biology and Department of Dermatology
| | - Amber Cramer
- Program in Epithelial Biology and Department of Dermatology
| | - Kevin R. Roy
- Department of Genetics and Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thuylinh Michelle Nguyen
- Department of Genetics and Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Patrick S. McGrath
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anna Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dennis Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Irene Bailey
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Jean Y. Tang
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | | | - Lars M. Steinmetz
- Department of Genetics and Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA 94305, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, and Department of Chemical and Systems Biology
| | - Anthony E. Oro
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| |
Collapse
|
12
|
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: 4] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
13
|
Collier A, Liu A, Torkelson J, Pattison J, Gaddam S, Zhen H, Patel T, McCarthy K, Ghanim H, Oro AE. Gibbin mesodermal regulation patterns epithelial development. Nature 2022; 606:188-196. [PMID: 35585237 PMCID: PMC9202145 DOI: 10.1038/s41586-022-04727-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/05/2022] [Indexed: 02/04/2023]
Abstract
Proper ectodermal patterning during human development requires previously identified transcription factors such as GATA3 and p63, as well as positional signalling from regional mesoderm1-6. However, the mechanism by which ectoderm and mesoderm factors act to stably pattern gene expression and lineage commitment remains unclear. Here we identify the protein Gibbin, encoded by the Xia-Gibbs AT-hook DNA-binding-motif-containing 1 (AHDC1) disease gene7-9, as a key regulator of early epithelial morphogenesis. We find that enhancer- or promoter-bound Gibbin interacts with dozens of sequence-specific zinc-finger transcription factors and methyl-CpG-binding proteins to regulate the expression of mesoderm genes. The loss of Gibbin causes an increase in DNA methylation at GATA3-dependent mesodermal genes, resulting in a loss of signalling between developing dermal and epidermal cell types. Notably, Gibbin-mutant human embryonic stem-cell-derived skin organoids lack dermal maturation, resulting in p63-expressing basal cells that possess defective keratinocyte stratification. In vivo chimeric CRISPR mouse mutants reveal a spectrum of Gibbin-dependent developmental patterning defects affecting craniofacial structure, abdominal wall closure and epidermal stratification that mirror patient phenotypes. Our results indicate that the patterning phenotypes seen in Xia-Gibbs and related syndromes derive from abnormal mesoderm maturation as a result of gene-specific DNA methylation decisions.
Collapse
Affiliation(s)
- Ann Collier
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Angela Liu
- Stem Cell Biology and Regenerative Medicine Program, Stanford University, Stanford, CA, USA
| | - Jessica Torkelson
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Jillian Pattison
- 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
| | - Tiffany Patel
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Kelly McCarthy
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Hana Ghanim
- Stem Cell Biology and Regenerative Medicine Program, Stanford University, Stanford, CA, USA
| | - Anthony E Oro
- Stem Cell Biology and Regenerative Medicine Program, Stanford University, Stanford, CA, USA.
| |
Collapse
|
14
|
Soares E, Zhou H. Pluripotent Stem Cell Differentiation Toward Functional Basal Stratified Epithelial Cells. Methods Mol Biol 2022; 2454:297-304. [PMID: 32833130 DOI: 10.1007/7651_2020_301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this chapter, an efficient feeder-free protocol of differentiating human pluripotent stem cells (hPSCs) toward the epidermal lineage to generate induced epidermal keratinocytes (iKCs) is described. The iKCs are able to terminally differentiate supra-basally. This hPSC-to-iKC differentiation can serve as a useful model to study epidermal development and disease as well as for therapeutic applications.
Collapse
Affiliation(s)
- Eduardo Soares
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| |
Collapse
|
15
|
Zhang W, Li Y, Wang L, Xin T, Zhang C. Generation of a DKK2 homozygous knockout human embryonic stem cell line using the CRISPR/Cas9 system. Stem Cell Res 2021; 57:102611. [PMID: 34856466 DOI: 10.1016/j.scr.2021.102611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/19/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022] Open
Abstract
Dickkopf-2 (DKK2) is an antagonist of canonical Wnt signaling, which is involved invarious biological processes of development, such as epidermal appendage formation andeye development. To identify underlying effects of DKK2 during embryonic development, we generated a DKK2 homozygous knockout human embryonic stem cell (hESC) line through the CRISPR/Cas9 genome-editing technology. This cell line, which maintains normal stem cell morphology and stably expresses pluripotent markers, could provide an ideal platform for exploring the role of DKK2 in embryonic development. In addition, Zeocin selection combined with tiny clone picking might be a highly efficient way to generate gene-knockout hESC lines.
Collapse
Affiliation(s)
- Wang Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yuming Li
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan 250014, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Tao Xin
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan 250014, China.
| | - Canwei Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Department of Ophthalmology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China.
| |
Collapse
|
16
|
Piekos SN, Gaddam S, Bhardwaj P, Radhakrishnan P, Guha RV, Oro AE. Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes. PLoS Comput Biol 2021; 17:e1009382. [PMID: 34543288 PMCID: PMC8483327 DOI: 10.1371/journal.pcbi.1009382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 09/30/2021] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
The repurposing of biomedical data is inhibited by its fragmented and multi-formatted nature that requires redundant investment of time and resources by data scientists. This is particularly true for Type 1 Diabetes (T1D), one of the most intensely studied common childhood diseases. Intense investigation of the contribution of pancreatic β-islet and T-lymphocytes in T1D has been made. However, genetic contributions from B-lymphocytes, which are known to play a role in a subset of T1D patients, remain relatively understudied. We have addressed this issue through the creation of Biomedical Data Commons (BMDC), a knowledge graph that integrates data from multiple sources into a single queryable format. This increases the speed of analysis by multiple orders of magnitude. We develop a pipeline using B-lymphocyte multi-dimensional epigenome and connectome data and deploy BMDC to assess genetic variants in the context of Type 1 Diabetes (T1D). Pipeline-identified variants are primarily common, non-coding, poorly conserved, and are of unknown clinical significance. While variants and their chromatin connectivity are cell-type specific, they are associated with well-studied disease genes in T-lymphocytes. Candidates include established variants in the HLA-DQB1 and HLA-DRB1 and IL2RA loci that have previously been demonstrated to protect against T1D in humans and mice providing validation for this method. Others are included in the well-established T1D GRS2 genetic risk scoring method. More intriguingly, other prioritized variants are completely novel and form the basis for future mechanistic and clinical validation studies The BMDC community-based platform can be expanded and repurposed to increase the accessibility, reproducibility, and productivity of biomedical information for diverse applications including the prioritization of cell type-specific disease alleles from complex phenotypes.
Collapse
Affiliation(s)
- Samantha N. Piekos
- Program in Epithelial Biology, Stanford University, Stanford, California, United States of America
- Google Data Commons, Mountain View, California, United States of America
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University, Stanford, California, United States of America
| | - Pranav Bhardwaj
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | | | - Ramanathan V. Guha
- Google Data Commons, Mountain View, California, United States of America
| | - Anthony E. Oro
- Program in Epithelial Biology, Stanford University, Stanford, California, United States of America
| |
Collapse
|
17
|
Liu C, Lee MK, Naqvi S, Hoskens H, Liu D, White JD, Indencleef K, Matthews H, Eller RJ, Li J, Mohammed J, Swigut T, Richmond S, Manyama M, Hallgrímsson B, Spritz RA, Feingold E, Marazita ML, Wysocka J, Walsh S, Shriver MD, Claes P, Weinberg SM, Shaffer JR. Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations. PLoS Genet 2021; 17:e1009695. [PMID: 34411106 PMCID: PMC8375984 DOI: 10.1371/journal.pgen.1009695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 07/02/2021] [Indexed: 12/16/2022] Open
Abstract
Facial morphology is highly variable, both within and among human populations, and a sizable portion of this variation is attributable to genetics. Previous genome scans have revealed more than 100 genetic loci associated with different aspects of normal-range facial variation. Most of these loci have been detected in Europeans, with few studies focusing on other ancestral groups. Consequently, the degree to which facial traits share a common genetic basis across diverse sets of humans remains largely unknown. We therefore investigated the genetic basis of facial morphology in an East African cohort. We applied an open-ended data-driven phenotyping approach to a sample of 2,595 3D facial images collected on Tanzanian children. This approach segments the face into hierarchically arranged, multivariate features that capture the shape variation after adjusting for age, sex, height, weight, facial size and population stratification. Genome scans of these multivariate shape phenotypes revealed significant (p < 2.5 × 10−8) signals at 20 loci, which were enriched for active chromatin elements in human cranial neural crest cells and embryonic craniofacial tissue, consistent with an early developmental origin of the facial variation. Two of these associations were in highly conserved regions showing craniofacial-specific enhancer activity during embryological development (5q31.1 and 12q21.31). Six of the 20 loci surpassed a stricter threshold accounting for multiple phenotypes with study-wide significance (p < 6.25 × 10−10). Cross-population comparisons indicated 10 association signals were shared with Europeans (seven sharing the same associated SNP), and facilitated fine-mapping of causal variants at previously reported loci. Taken together, these results may point to both shared and population-specific components to the genetic architecture of facial variation. Genetic factors play an important role in shaping human facial features. Over the last decade, studies have identified numerous genes associated with various facial traits. The vast majority of these studies have focused on European or Asian populations, while African populations have been underrepresented. Increasing the diversity of these analyses can reveal novel associations and cross-population analyses can help deepen our understanding of known genetic associations. We therefore performed a genome scan of 3D facial features in African children from Tanzania and then compared our results to Europeans. We found 20 regions of the genome associated with facial shape in Tanzanian children, 10 of which were also present in Europeans, indicating evidence for a partly shared genetic basis for human facial shape across populations. In addition, about half of the genetic associations observed in Tanzanians were not present in Europeans, and some of the shared signals differed between populations in the specific genetic variants associated or specific facial traits affected. These results shed light on the shared and population-specific genetic contributors to normal-range facial variation.
Collapse
Affiliation(s)
- Chenxing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Myoung Keun Lee
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hanne Hoskens
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Dongjing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Julie D. White
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Karlijne Indencleef
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Harold Matthews
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Ryan J. Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Jiarui Li
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Mange Manyama
- Anatomy in Radiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Benedikt Hallgrímsson
- Department of Anatomy and Cell Biology, Alberta Children´s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Richard A. Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mary L. Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Mark D. Shriver
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Peter Claes
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Seth M. Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SMW); (JRS)
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SMW); (JRS)
| |
Collapse
|
18
|
Affiliation(s)
- Bogi Andersen
- Departments of Medicine and Biological Chemistry, University of California, Irvine
| | - Sarah Millar
- Black Family Stem Cell Institute, Departments of Cell, Developmental and Regenerative Biology and Dermatology, Icahn School of Medicine at Mount Sinai
| |
Collapse
|
19
|
Li LY, Yang Q, Jiang YY, Yang W, Jiang Y, Li X, Hazawa M, Zhou B, Huang GW, Xu XE, Gery S, Zhang Y, Ding LW, Ho AS, Zumsteg ZS, Wang MR, Fullwood MJ, Freedland SJ, Meltzer SJ, Xu LY, Li EM, Koeffler HP, Lin DC. Interplay and cooperation between SREBF1 and master transcription factors regulate lipid metabolism and tumor-promoting pathways in squamous cancer. Nat Commun 2021; 12:4362. [PMID: 34272396 PMCID: PMC8285542 DOI: 10.1038/s41467-021-24656-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/29/2021] [Indexed: 02/05/2023] Open
Abstract
Squamous cell carcinomas (SCCs) comprise one of the most common histologic types of human cancer. Transcriptional dysregulation of SCC cells is orchestrated by tumor protein p63 (TP63), a master transcription factor (TF) and a well-researched SCC-specific oncogene. In the present study, both Gene Set Enrichment Analysis (GSEA) of SCC patient samples and in vitro loss-of-function assays establish fatty-acid metabolism as a key pathway downstream of TP63. Further studies identify sterol regulatory element binding transcription factor 1 (SREBF1) as a central mediator linking TP63 with fatty-acid metabolism, which regulates the biosynthesis of fatty-acids, sphingolipids (SL), and glycerophospholipids (GPL), as revealed by liquid chromatography tandem mass spectrometry (LC-MS/MS)-based lipidomics. Moreover, a feedback co-regulatory loop consisting of SREBF1/TP63/Kruppel like factor 5 (KLF5) is identified, which promotes overexpression of all three TFs in SCCs. Downstream of SREBF1, a non-canonical, SCC-specific function is elucidated: SREBF1 cooperates with TP63/KLF5 to regulate hundreds of cis-regulatory elements across the SCC epigenome, which converge on activating cancer-promoting pathways. Indeed, SREBF1 is essential for SCC viability and migration, and its overexpression is associated with poor survival in SCC patients. Taken together, these data shed light on mechanisms of transcriptional dysregulation in cancer, identify specific epigenetic regulators of lipid metabolism, and uncover SREBF1 as a potential therapeutic target and prognostic marker in SCC.
Collapse
Affiliation(s)
- Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Qian Yang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yan-Yi Jiang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yuan Jiang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiang Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Bo Zhou
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Guo-Wei Huang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiu-E Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Sigal Gery
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Allen S Ho
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zachary S Zumsteg
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Stephen J Freedland
- Division of Urology, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, USA and the Durham VA Medical Center, Durham, NC, USA
| | - Stephen J Meltzer
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - De-Chen Lin
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| |
Collapse
|
20
|
Woodstock DL, Sammons MA, Fischer M. p63 and p53: Collaborative Partners or Dueling Rivals? Front Cell Dev Biol 2021; 9:701986. [PMID: 34291055 PMCID: PMC8287303 DOI: 10.3389/fcell.2021.701986] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022] Open
Abstract
The tumor suppressor p53 and its oncogenic sibling p63 (ΔNp63) direct opposing fates in tumor development. These paralog proteins are transcription factors that elicit their tumor suppressive and oncogenic capacity through the regulation of both shared and unique target genes. Both proteins predominantly function as activators of transcription, leading to a paradigm shift away from ΔNp63 as a dominant negative to p53 activity. The discovery of p53 and p63 as pioneer transcription factors regulating chromatin structure revealed new insights into how these paralogs can both positively and negatively influence each other to direct cell fate. The previous view of a strict rivalry between the siblings needs to be revisited, as p53 and p63 can also work together toward a common goal.
Collapse
Affiliation(s)
- Dana L Woodstock
- Department of Biological Sciences, The State University of New York at Albany, Albany, NY, United States
| | - Morgan A Sammons
- Department of Biological Sciences, The State University of New York at Albany, Albany, NY, United States
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| |
Collapse
|
21
|
Oss-Ronen L, Cohen I. Epigenetic regulation and signalling pathways in Merkel cell development. Exp Dermatol 2021; 30:1051-1064. [PMID: 34152646 DOI: 10.1111/exd.14415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
Merkel cells are specialized epithelial cells connected to afferent nerve endings responsible for light-touch sensations, formed at specific locations in touch-sensitive regions of the mammalian skin. Although Merkel cells are descendants of the epidermal lineage, little is known about the mechanisms responsible for the development of these unique mechanosensory cells. Recent studies have highlighted that the Polycomb group (PcG) of proteins play a significant role in spatiotemporal regulation of Merkel cell formation. In addition, several of the major signalling pathways involved in skin development have been shown to regulate Merkel cell development as well. Here, we summarize the current understandings of the role of developmental regulators in Merkel cell formation, including the interplay between the epigenetic machinery and key signalling pathways, and the lineage-specific transcription factors involved in the regulation of Merkel cell development.
Collapse
Affiliation(s)
- Liat Oss-Ronen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
22
|
Abstract
In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.
Collapse
Affiliation(s)
- Namyoung Jung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Yonsei University, Seoul 03722, Korea
| |
Collapse
|
23
|
Hoskens H, Liu D, Naqvi S, Lee MK, Eller RJ, Indencleef K, White JD, Li J, Larmuseau MHD, Hens G, Wysocka J, Walsh S, Richmond S, Shriver MD, Shaffer JR, Peeters H, Weinberg SM, Claes P. 3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies. PLoS Genet 2021; 17:e1009528. [PMID: 33983923 PMCID: PMC8118281 DOI: 10.1371/journal.pgen.1009528] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17-0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.
Collapse
Affiliation(s)
- Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Dongjing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Myoung Keun Lee
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ryan J. Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Karlijne Indencleef
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Otorhinolaryngology, KU Leuven, Leuven, Belgium
| | - Julie D. White
- Department of Anthropology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Jiarui Li
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Maarten H. D. Larmuseau
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
- Histories vzw, Mechelen, Belgium
| | - Greet Hens
- Department of Otorhinolaryngology, KU Leuven, Leuven, Belgium
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Mark D. Shriver
- Department of Anthropology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| |
Collapse
|
24
|
Pokorná Z, Vysloužil J, Hrabal V, Vojtěšek B, Coates PJ. The foggy world(s) of p63 isoform regulation in normal cells and cancer. J Pathol 2021; 254:454-473. [PMID: 33638205 DOI: 10.1002/path.5656] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/24/2021] [Indexed: 12/19/2022]
Abstract
The p53 family member p63 exists as two major protein variants (TAp63 and ΔNp63) with distinct expression patterns and functional properties. Whilst downstream target genes of p63 have been studied intensively, how p63 variants are themselves controlled has been relatively neglected. Here, we review advances in understanding ΔNp63 and TAp63 regulation, highlighting their distinct pathways. TAp63 has roles in senescence and metabolism, and in germ cell genome maintenance, where it is activated post-transcriptionally by phosphorylation cascades after DNA damage. The function and regulation of TAp63 in mesenchymal and haematopoietic cells is less clear but may involve epigenetic control through DNA methylation. ΔNp63 functions to maintain stem/progenitor cells in various epithelia and is overexpressed in squamous and certain other cancers. ΔNp63 is transcriptionally regulated through multiple enhancers in concert with chromatin modifying proteins. Many signalling pathways including growth factors, morphogens, inflammation, and the extracellular matrix influence ΔNp63 levels, with inconsistent results reported. There is also evidence for reciprocal regulation, including ΔNp63 activating its own transcription. ΔNp63 is downregulated during cell differentiation through transcriptional regulation, while post-transcriptional events cause proteasomal degradation. Throughout the review, we identify knowledge gaps and highlight discordances, providing potential explanations including cell-context and cell-matrix interactions. Identifying individual p63 variants has roles in differential diagnosis and prognosis, and understanding their regulation suggests clinically approved agents for targeting p63 that may be useful combination therapies for selected cancer patients. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Zuzana Pokorná
- Research Centre of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Jan Vysloužil
- Research Centre of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Václav Hrabal
- Research Centre of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Borˇivoj Vojtěšek
- Research Centre of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Philip J Coates
- Research Centre of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| |
Collapse
|
25
|
Haensel D, Jin S, Sun P, Cinco R, Dragan M, Nguyen Q, Cang Z, Gong Y, Vu R, MacLean AL, Kessenbrock K, Gratton E, Nie Q, Dai X. Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics. Cell Rep 2021; 30:3932-3947.e6. [PMID: 32187560 PMCID: PMC7218802 DOI: 10.1016/j.celrep.2020.02.091] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 01/07/2020] [Accepted: 02/25/2020] [Indexed: 01/17/2023] Open
Abstract
Our knowledge of transcriptional heterogeneities in epithelial stem and progenitor cell compartments is limited. Epidermal basal cells sustain cutaneous tissue maintenance and drive wound healing. Previous studies have probed basal cell heterogeneity in stem and progenitor potential, but a comprehensive dissection of basal cell dynamics during differentiation is lacking. Using single-cell RNA sequencing coupled with RNAScope and fluorescence lifetime imaging, we identify three non-proliferative and one proliferative basal cell state in homeostatic skin that differ in metabolic preference and become spatially partitioned during wound re-epithelialization. Pseudotemporal trajectory and RNA velocity analyses predict a quasi-linear differentiation hierarchy where basal cells progress from Col17a1Hi/Trp63Hi state to early-response state, proliferate at the juncture of these two states, or become growth arrested before differentiating into spinous cells. Wound healing induces plasticity manifested by dynamic basal-spinous interconversions at multiple basal transcriptional states. Our study provides a systematic view of epidermal cellular dynamics, supporting a revised “hierarchical-lineage” model of homeostasis. Haensel et al. performed a comprehensive dissection of the cellular makeup of skin during homeostasis and wound healing and the molecular heterogeneity and cellular dynamics within its stem-cell-containing epidermal basal layer. Their work provides insights and stimulates further investigation into the mechanism of skin maintenance and repair.
Collapse
Affiliation(s)
- Daniel Haensel
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- These authors contributed equally
| | - Suoqin Jin
- Department of Mathematics, University of California, Irvine, CA 92697, USA
- These authors contributed equally
| | - Peng Sun
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Rachel Cinco
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Morgan Dragan
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Zixuan Cang
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- Department of Mathematics, University of California, Irvine, CA 92697, USA
| | - Yanwen Gong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Remy Vu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
| | - Adam L. MacLean
- Department of Mathematics, University of California, Irvine, CA 92697, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Qing Nie
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- Department of Mathematics, University of California, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Correspondence: (Q.N.), (X.D.)
| | - Xing Dai
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- Lead Contact
- Correspondence: (Q.N.), (X.D.)
| |
Collapse
|
26
|
Cao H, Huang H, Tang H. Zbtb7a and Zbtb7b: Opening naïve loci to reprogram ESCs. Biosci Trends 2021; 15:58-60. [PMID: 33627571 DOI: 10.5582/bst.2020.03429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Bone morphogenetic protein 4 (BMP4) was recently reported to confer reprogramming capability to embryonic stem cells (ESCs) by reactivating naïve pluripotency genes via Zbtb7a and Zbtb7b. A visual reporting system was developed to first identify BMP4 as a driver for the primed-to-naïve transition (PNT). In addition, two specific inhibitors were identified as significantly improving the efficiency of PNT (~80% transition) within 8 days. The Zbtb7 family members were first introduced in the context of PNT and stem cell fate decision-making. These findings provide valuable information on acquiring naïve pluripotent stem cells for regenerative medicine.
Collapse
Affiliation(s)
- Hua Cao
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Hong Huang
- Institute of Cardiovascular Disease, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China.,Institute of Clinical Medicine, The First Affiliated Hospital of University of South China, Hengyang, Hunan Province, China
| | - Huifang Tang
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China.,Institute of Cardiovascular Disease, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| |
Collapse
|
27
|
Goh KJ, Tan EK, Lu H, Roy S, Dunn NR. An NKX2-1 GFP and TP63 tdTomato dual fluorescent reporter for the investigation of human lung basal cell biology. Sci Rep 2021; 11:4712. [PMID: 33633173 PMCID: PMC7907081 DOI: 10.1038/s41598-021-83825-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/08/2021] [Indexed: 11/09/2022] Open
Abstract
Basal cells are multipotent stem cells responsible for the repair and regeneration of all the epithelial cell types present in the proximal lung. In mice, the elusive origins of basal cells and their contribution to lung development were recently revealed by high-resolution, lineage tracing studies. It however remains unclear if human basal cells originate and participate in lung development in a similar fashion, particularly with mounting evidence for significant species-specific differences in this process. To address this outstanding question, in the last several years differentiation protocols incorporating human pluripotent stem cells (hPSC) have been developed to produce human basal cells in vitro with varying efficiencies. To facilitate this endeavour, we introduced tdTomato into the human TP63 gene, whose expression specifically labels basal cells, in the background of a previously described hPSC line harbouring an NKX2-1GFP reporter allele. The functionality and specificity of the NKX2-1GFP;TP63tdTomato hPSC line was validated by directed differentiation into lung progenitors as well as more specialised lung epithelial subtypes using an organoid platform. This dual fluorescent reporter hPSC line will be useful for tracking, isolating and expanding basal cells from heterogenous differentiation cultures for further study.
Collapse
Affiliation(s)
- Kim Jee Goh
- Institute of Medical Biology, Agency for Science Technology and Research (A∗STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore
- Skin Research Institute of Singapore, 11 Mandalay Road #17-01 Clinical Sciences Building, Singapore, 308232, Singapore
| | - Ee Kim Tan
- Institute of Medical Biology, Agency for Science Technology and Research (A∗STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Hao Lu
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore, 119288, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - N Ray Dunn
- Institute of Medical Biology, Agency for Science Technology and Research (A∗STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore.
- Skin Research Institute of Singapore, 11 Mandalay Road #17-01 Clinical Sciences Building, Singapore, 308232, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore.
| |
Collapse
|
28
|
Sun C, Wang H, Ma Q, Chen C, Yue J, Li B, Zhang X. Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells. Cell Biosci 2021; 11:24. [PMID: 33485387 PMCID: PMC7824938 DOI: 10.1186/s13578-021-00541-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human pluripotent stem cell-derived limbal stem cells (hPSC-derived LSCs) provide a promising cell source for corneal transplants and ocular surface reconstruction. Although recent efforts in the identification of LSC markers have increased our understanding of the biology of LSCs, much more remains to be characterized in the developmental origin, cell fate determination, and identity of human LSCs. The lack of knowledge hindered the establishment of efficient differentiation protocols for generating hPSC-derived LSCs and held back their clinical application. RESULTS Here, we performed a time-course single-cell RNA-seq to investigate transcriptional heterogeneity and expression changes of LSCs derived from human embryonic stem cells (hESCs). Based on current protocol, expression heterogeneity of reported LSC markers were identified in subpopulations of differentiated cells. EMT has been shown to occur during differentiation process, which could possibly result in generation of untargeted cells. Pseudotime trajectory analysis revealed transcriptional changes and signatures of commitment of hESCs-derived LSCs and their progeny-the transit amplifying cells. CONCLUSION Single-cell RNA-seq revealed time-course expression changes and significant transcriptional heterogeneity during hESC-derived LSC differentiation in vitro. Our results demonstrated candidate developmental trajectory and several new candidate markers for LSCs, which could facilitate elucidating the identity and developmental origin of human LSCs in vivo.
Collapse
Affiliation(s)
- Changbin Sun
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Hailun Wang
- Department of Radiation Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Qiwang Ma
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Chao Chen
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China
| | - Jianhui Yue
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.,Section of Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.
| | - Xi Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518082, China.
| |
Collapse
|
29
|
White JD, Indencleef K, Naqvi S, Eller RJ, Hoskens H, Roosenboom J, Lee MK, Li J, Mohammed J, Richmond S, Quillen EE, Norton HL, Feingold E, Swigut T, Marazita ML, Peeters H, Hens G, Shaffer JR, Wysocka J, Walsh S, Weinberg SM, Shriver MD, Claes P. Insights into the genetic architecture of the human face. Nat Genet 2021; 53:45-53. [PMID: 33288918 PMCID: PMC7796995 DOI: 10.1038/s41588-020-00741-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/23/2020] [Indexed: 01/28/2023]
Abstract
The human face is complex and multipartite, and characterization of its genetic architecture remains challenging. Using a multivariate genome-wide association study meta-analysis of 8,246 European individuals, we identified 203 genome-wide-significant signals (120 also study-wide significant) associated with normal-range facial variation. Follow-up analyses indicate that the regions surrounding these signals are enriched for enhancer activity in cranial neural crest cells and craniofacial tissues, several regions harbor multiple signals with associations to different facial phenotypes, and there is evidence for potential coordinated actions of variants. In summary, our analyses provide insights into the understanding of how complex morphological traits are shaped by both individual and coordinated genetic actions.
Collapse
Affiliation(s)
- Julie D White
- Department of Anthropology, Pennsylvania State University, State College, PA, USA.
| | - Karlijne Indencleef
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan J Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hanne Hoskens
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jasmien Roosenboom
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Myoung Keun Lee
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiarui Li
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, UK
| | - Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Greet Hens
- Department of Neurosciences, Experimental Oto-Rhino-Laryngology, KU Leuven, Leuven, Belgium
| | - John R Shaffer
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
| |
Collapse
|
30
|
Zhang C, Yu Y, Li F, Lan X, Wang L. Generating an MEIS1 homozygous knockout human embryonic stem cell line using the CRISPR/Cas9 system. Stem Cell Res 2020; 49:102069. [PMID: 33157390 DOI: 10.1016/j.scr.2020.102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/18/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022] Open
Abstract
Myeloid ecotropic viral integration site 1 (MEIS1) plays an essential role in the development of several embryonic organs, such as the central nervous system and eyes. To further investigate the role of MEIS1 in embryonic development, herein, we generated a MEIS1 homozygous knockout human embryonic stem cell (hESC) line using the CRISPR/Cas9 genome-editing technology. We believe that this cell line will be a good resource for exploring the function of the MEIS1 gene in embryonic development in vitro. Furthermore, the gene-knockout method reported in this study is efficient and labor-saving, which may provide an effective strategy for hESC gene deletion.
Collapse
Affiliation(s)
- Canwei Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Yankun Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Fuxi Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Xihong Lan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China.
| |
Collapse
|
31
|
Yi M, Tan Y, Wang L, Cai J, Li X, Zeng Z, Xiong W, Li G, Li X, Tan P, Xiang B. TP63 links chromatin remodeling and enhancer reprogramming to epidermal differentiation and squamous cell carcinoma development. Cell Mol Life Sci 2020; 77:4325-4346. [PMID: 32447427 PMCID: PMC7588389 DOI: 10.1007/s00018-020-03539-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/21/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022]
Abstract
Squamous cell carcinoma (SCC) is an aggressive malignancy that can originate from various organs. TP63 is a master regulator that plays an essential role in epidermal differentiation. It is also a lineage-dependent oncogene in SCC. ΔNp63α is the prominent isoform of TP63 expressed in epidermal cells and SCC, and overexpression promotes SCC development through a variety of mechanisms. Recently, ΔNp63α was highlighted to act as an epidermal-specific pioneer factor that binds closed chromatin and enhances chromatin accessibility at epidermal enhancers. ΔNp63α coordinates chromatin-remodeling enzymes to orchestrate the tissue-specific enhancer landscape and three-dimensional high-order architecture of chromatin. Moreover, ΔNp63α establishes squamous-like enhancer landscapes to drive oncogenic target expression during SCC development. Importantly, ΔNp63α acts as an upstream regulator of super enhancers to activate a number of oncogenic transcripts linked to poor prognosis in SCC. Mechanistically, ΔNp63α activates genes transcription through physically interacting with a number of epigenetic modulators to establish enhancers and enhance chromatin accessibility. In contrast, ΔNp63α also represses gene transcription via interacting with repressive epigenetic regulators. ΔNp63α expression is regulated at multiple levels, including transcriptional, post-transcriptional, and post-translational levels. In this review, we summarize recent advances of p63 in epigenomic and transcriptional control, as well as the mechanistic regulation of p63.
Collapse
Affiliation(s)
- Mei Yi
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yixin Tan
- Department of Dermatology, The Second Xiangya Hospital, The Central South University, Changsha, 410011, Hunan, China
| | - Li Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Cai
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| | - Pingqing Tan
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Department of Head and Neck Surgery, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China.
| |
Collapse
|
32
|
Brauweiler AM, Leung DYM, Goleva E. The Transcription Factor p63 Is a Direct Effector of IL-4- and IL-13-Mediated Repression of Keratinocyte Differentiation. J Invest Dermatol 2020; 141:770-778. [PMID: 33038352 DOI: 10.1016/j.jid.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Atopic Dermatitis is an inflammatory skin disease associated with broad defects in skin barrier function caused by increased levels of type-2 cytokines (IL-4 and IL-13) that repress keratinocyte (KC) differentiation. Although crucial in mediating allergic disease, the mechanisms for gene repression induced by type-2 cytokines remain unclear. In this study, we determined that gene repression requires the master regulator of the epidermal differentiation program, p63. We found that type-2 cytokine-mediated inhibition of the expression of genes involved in early KC differentiation, including keratin 1, keratin 10, and DSC-1, is reversed by p63 blockade. Type-2 cytokines, through p63, also regulate additional genes involved in KC differentiation, including CHAC-1, STC2, and CALML5. The regulation of the expression of these genes is ablated by p63 small interfering RNA as well. In addition, we found that IL-4 and IL-13 and Staphylococcus aureus lipoteichoic acid work in combination through p63 to further suppress the early KC differentiation program. Finally, we found that IL-4 and IL-13 also inhibit the activity of Notch, a transcription factor required to induce early KC differentiation. In conclusion, type-2 cytokine-mediated gene repression and blockade of KC differentiation are multifactorial, involving pathways that converge on transcription factors critical for epidermal development, p63 and Notch.
Collapse
Affiliation(s)
- Anne M Brauweiler
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Donald Y M Leung
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA; Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
| | - Elena Goleva
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.
| |
Collapse
|
33
|
Sammons MA, Nguyen TAT, McDade SS, Fischer M. Tumor suppressor p53: from engaging DNA to target gene regulation. Nucleic Acids Res 2020; 48:8848-8869. [PMID: 32797160 PMCID: PMC7498329 DOI: 10.1093/nar/gkaa666] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
The p53 transcription factor confers its potent tumor suppressor functions primarily through the regulation of a large network of target genes. The recent explosion of next generation sequencing protocols has enabled the study of the p53 gene regulatory network (GRN) and underlying mechanisms at an unprecedented depth and scale, helping us to understand precisely how p53 controls gene regulation. Here, we discuss our current understanding of where and how p53 binds to DNA and chromatin, its pioneer-like role, and how this affects gene regulation. We provide an overview of the p53 GRN and the direct and indirect mechanisms through which p53 affects gene regulation. In particular, we focus on delineating the ubiquitous and cell type-specific network of regulatory elements that p53 engages; reviewing our understanding of how, where, and when p53 binds to DNA and the mechanisms through which these events regulate transcription. Finally, we discuss the evolution of the p53 GRN and how recent work has revealed remarkable differences between vertebrates, which are of particular importance to cancer researchers using mouse models.
Collapse
Affiliation(s)
- Morgan A Sammons
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Thuy-Ai T Nguyen
- Genome Integrity & Structural Biology Laboratory and Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| |
Collapse
|
34
|
Abstract
p63 (also known as TP63) is a transcription factor of the p53 family, along with p73. Multiple isoforms of p63 have been discovered and these have diverse functions encompassing a wide array of cell biology. p63 isoforms are implicated in lineage specification, proliferative potential, differentiation, cell death and survival, DNA damage response and metabolism. Furthermore, p63 is linked to human disease states including cancer. p63 is critical to many aspects of cell signaling, and in this Cell science at a glance article and the accompanying poster, we focus on the signaling cascades regulating TAp63 and ΔNp63 isoforms and those that are regulated by TAp63 and ΔNp63, as well the role of p63 in disease.
Collapse
Affiliation(s)
- Matthew L Fisher
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Seamus Balinth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Stony Brook University, Department of Molecular and Cell Biology, Stony Brook, NY, 11794, USA
| | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| |
Collapse
|
35
|
The Transcriptional Cofactor VGLL1 Drives Transcription of Human Papillomavirus Early Genes via TEAD1. J Virol 2020; 94:JVI.01945-19. [PMID: 32132238 DOI: 10.1128/jvi.01945-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
The TEAD family of transcription factors requires associating cofactors to induce gene expression. TEAD1 is known to activate the early promoter of human papillomavirus (HPV), but the precise mechanisms of TEAD1-mediated transactivation of the HPV promoter, including its relevant cofactors, remain unexplored. Here, we reveal that VGLL1, a TEAD-interacting cofactor, contributes to HPV early gene expression. Knockdown of VGLL1 and/or TEAD1 led to a decrease in viral early gene expression in human cervical keratinocytes and cervical cancer cell lines. We identified 11 TEAD1 target sites in the HPV16 long control region (LCR) by in vitro DNA pulldown assays; 8 of these sites contributed to the transcriptional activation of the early promoter in luciferase reporter assays. VGLL1 bound to the HPV16 LCR via its interaction with TEAD1 both in vitro and in vivo Furthermore, introducing HPV16 and HPV18 whole genomes into primary human keratinocytes led to increased levels of VGLL1, due in part to the upregulation of TEADs. These results suggest that multiple VGLL1/TEAD1 complexes are recruited to the LCR to support the efficient transcription of HPV early genes.IMPORTANCE Although a number of transcription factors have been reported to be involved in HPV gene expression, little is known about the cofactors that support HPV transcription. In this study, we demonstrate that the transcriptional cofactor VGLL1 plays a prominent role in HPV early gene expression, dependent on its association with the transcription factor TEAD1. Whereas TEAD1 is ubiquitously expressed in a variety of tissues, VGLL1 displays tissue-specific expression and is implicated in the development and differentiation of epithelial lineage tissues, where HPV gene expression occurs. Our results suggest that VGLL1 may contribute to the epithelial specificity of HPV gene expression, providing new insights into the mechanisms that regulate HPV infection. Further, VGLL1 is also critical for the growth of cervical cancer cells and may represent a novel therapeutic target for HPV-associated cancers.
Collapse
|
36
|
Epidermal Stem Cells in Wound Healing and Regeneration. Stem Cells Int 2020; 2020:9148310. [PMID: 32399054 PMCID: PMC7204129 DOI: 10.1155/2020/9148310] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/06/2020] [Indexed: 12/24/2022] Open
Abstract
Skin stem cells distributed in the basal layer of the epidermis and hair follicles are important cell sources for skin development, metabolism, and injury repair. At present, great progress has been made in the study of epidermal stem cells at the cellular and molecular levels. Stem cell transplantation is reported to promote skin healing, endothelial cell transformation, and vascular formation. Local stem cells can also be transformed into keratinocytes, sebaceous gland, and other skin-associated tissues. However, the mechanism of action of epidermal stem cells on wound healing and regeneration is not completely clear. This review is aimed at briefly summarizing the biological characteristics of epidermal stem cells and their clinical application in wound healing and tissue regeneration. It further discussed the mechanism of action and the development direction in the future.
Collapse
|
37
|
Liu N, Yin Y, Wang H, Zhou Z, Sheng X, Fu H, Guo R, Wang H, Yang J, Gong P, Ning W, Ju Z, Liu Y, Liu L. Telomere dysfunction impairs epidermal stem cell specification and differentiation by disrupting BMP/pSmad/P63 signaling. PLoS Genet 2019; 15:e1008368. [PMID: 31518356 PMCID: PMC6760834 DOI: 10.1371/journal.pgen.1008368] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/25/2019] [Accepted: 08/12/2019] [Indexed: 11/19/2022] Open
Abstract
Telomere shortening is associated with aging and age-associated diseases. Additionally, telomere dysfunction resulting from telomerase gene mutation can lead to premature aging, such as apparent skin atrophy and hair loss. However, the molecular signaling linking telomere dysfunction to skin atrophy remains elusive. Here we show that dysfunctional telomere disrupts BMP/pSmad/P63 signaling, impairing epidermal stem cell specification and differentiation of skin and hair follicles. We find that telomere shortening mediated by Terc loss up-regulates Follistatin (Fst), inhibiting pSmad signaling and down-regulating P63 and epidermal keratins in an ESC differentiation model as well as in adult development of telomere-shortened mice. Mechanistically, short telomeres disrupt PRC2/H3K27me3-mediated repression of Fst. Our findings reveal that skin atrophy due to telomere dysfunction is caused by a previously unappreciated link with Fst and BMP signaling that could be explored in the development of therapies.
Collapse
Affiliation(s)
- Na Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Key Laboratory of Bioactive Materials, Ministry of Education, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
- School of Medicine, Nankai University, Tianjin, China
| | - Yu Yin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Yunnan Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Haiying Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Zhongcheng Zhou
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Xiaoyan Sheng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Haifeng Fu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Hua Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Peng Gong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Wen Ning
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Yifei Liu
- Yale Fertility Center and Department of OB/GYN, Yale University School of Medicine, New Haven, CT, United States of America
- * E-mail: (YL); (LL)
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Key Laboratory of Bioactive Materials, Ministry of Education, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
- * E-mail: (YL); (LL)
| |
Collapse
|
38
|
Haller M, Ma L. Temporal, spatial, and genetic regulation of external genitalia development. Differentiation 2019; 110:1-7. [PMID: 31521888 DOI: 10.1016/j.diff.2019.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 12/26/2022]
Abstract
Fertilization requires the physical combination of gametes, and terrestrial mammals necessitated the evolution of genitalia capable of successfully completing the fertilization process in a non-aqueous environment. Thus, the male mammalian external genitalia evolved as an outgrowth from the body, an appendage sufficient to fertilize eggs housed deep inside the female. In this way, sexual dimorphism of mammalian genitalia became highly pronounced. This highly complex evolutionary divergence both from aqueous fertilization, as well as divergence between the sexes of terrestrial mammals, required exquisitely coordinated, novel patterns of gene expression to regulate the spatial and temporal events governing external genitalia development. Recent studies delineating the genetic regulation of external genitalia development, largely focusing on development of the murine genital tubercle, have vastly enlightened the field of reproductive developmental biology. Murine homologs of human genes have been selectively deleted in the mouse, either in the whole body or using tissue-specific and temporally-specific genetic drivers. The defects in outgrowth and urethral tubularization subsequent to the deletion of specific genes in the developing murine external genitalia delineates which genes are required in which compartments and at what times. This review details how these murine genetic models have created a somewhat modest but rapidly growing library of knowledge detailing the spatial-temporal genetic regulation of external genitalia development.
Collapse
Affiliation(s)
- Meade Haller
- Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Liang Ma
- Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.
| |
Collapse
|
39
|
Single-cell RNA-seq identifies a reversible mesodermal activation in abnormally specified epithelia of p63 EEC syndrome. Proc Natl Acad Sci U S A 2019; 116:17361-17370. [PMID: 31413199 DOI: 10.1073/pnas.1908180116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mutations in transcription factor p63 are associated with developmental disorders that manifest defects in stratified epithelia including the epidermis. The underlying cellular and molecular mechanism is however not yet understood. We established an epidermal commitment model using human induced pluripotent stem cells (iPSCs) and characterized differentiation defects of iPSCs derived from ectrodactyly, ectodermal dysplasia, and cleft lip/palate (EEC) syndrome patients carrying p63 mutations. Transcriptome analyses revealed stepwise cell fate transitions during epidermal commitment: Specification from multipotent simple epithelium to basal stratified epithelia and ultimately to the mature epidermal fate. Differentiation defects of EEC iPSCs caused by p63 mutations occurred during the specification switch from the simple epithelium to the basal-stratified epithelial fate. Single-cell transcriptome and pseudotime analyses of cell states identified mesodermal activation that was associated with the deviated commitment route of EEC iPSCs. Integrated analyses of differentially regulated genes and p63-dependent dynamic genomic enhancers during epidermal commitment suggest that p63 directly controls epidermal gene activation at the specification switch and has an indirect effect on mesodermal gene repression. Importantly, inhibitors of mesodermal induction enhanced epidermal commitment of EEC iPSCs. Our findings demonstrate that p63 is required for specification of stratified epithelia, and that epidermal commitment defects caused by p63 mutations can be reversed by repressing mesodermal induction. This study provides insights into disease mechanisms underlying stratified epithelial defects caused by p63 mutations and suggests potential therapeutic strategies for the disease.
Collapse
|
40
|
Santos-Pereira JM, Gallardo-Fuentes L, Neto A, Acemel RD, Tena JJ. Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification. Nat Commun 2019; 10:3049. [PMID: 31296872 PMCID: PMC6624255 DOI: 10.1038/s41467-019-11121-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/20/2019] [Indexed: 12/14/2022] Open
Abstract
The transcription factor p63 is a master regulator of ectoderm development. Although previous studies show that p63 triggers epidermal differentiation in vitro, the roles of p63 in developing embryos remain poorly understood. Here, we use zebrafish embryos to analyze in vivo how p63 regulates gene expression during development. We generate tp63-knock-out mutants that recapitulate human phenotypes and show down-regulated epidermal gene expression. Following p63-binding dynamics, we find two distinct functions clearly separated in space and time. During early development, p63 binds enhancers associated to neural genes, limiting Sox3 binding and reducing neural gene expression. Indeed, we show that p63 and Sox3 are co-expressed in the neural plate border. On the other hand, p63 acts as a pioneer factor by binding non-accessible chromatin at epidermal enhancers, promoting their opening and epidermal gene expression in later developmental stages. Therefore, our results suggest that p63 regulates cell fate decisions during vertebrate ectoderm specification.
Collapse
Affiliation(s)
- José M Santos-Pereira
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Ana Neto
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013, Seville, Spain.
| |
Collapse
|
41
|
Karsli Uzunbas G, Ahmed F, Sammons MA. Control of p53-dependent transcription and enhancer activity by the p53 family member p63. J Biol Chem 2019; 294:10720-10736. [PMID: 31113863 DOI: 10.1074/jbc.ra119.007965] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/15/2019] [Indexed: 01/20/2023] Open
Abstract
Transcriptional activation by p53 provides powerful, organism-wide tumor suppression. We hypothesized that the local chromatin environment, including differential enhancer activities, contributes to various p53-dependent transcriptional activities in different cell types during stress-induced signaling. In this work, using ChIP-sequencing, immunoblotting, quantitative PCR, and computational analyses across various mammalian cell lines, we demonstrate that the p53-induced transcriptome varies by cell type, reflects cell type-specific activities, and is considerably broader than previously anticipated. We found that these molecular events are strongly influenced by p53's engagement with differentially active cell type-specific enhancers and promoters. We also observed that p53 activity depends on the p53 family member tumor protein p63 in epithelial cell types. Notably, we demonstrate that p63 is required for epithelial enhancer identity, including enhancers used by p53 during stress-dependent signaling. Loss of p63, but not p53, caused site-specific depletion of enhancer-associated chromatin modifications, suggesting that p63 functions as an enhancer maintenance factor in epithelial cells. Additionally, a subset of epithelial-specific enhancers depends on the activity of p63 providing a direct link between lineage determination and enhancer structure. These results suggest that a broad, cell-intrinsic mechanism controls p53-dependent cellular stress response through differential regulation of cis-regulatory elements.
Collapse
Affiliation(s)
- Gizem Karsli Uzunbas
- From the Department of Biological Sciences, State University of New York at Albany, Albany, New York 12222
| | - Faraz Ahmed
- From the Department of Biological Sciences, State University of New York at Albany, Albany, New York 12222
| | - Morgan A Sammons
- From the Department of Biological Sciences, State University of New York at Albany, Albany, New York 12222
| |
Collapse
|
42
|
Miroshnikova YA, Cohen I, Ezhkova E, Wickström SA. Epigenetic gene regulation, chromatin structure, and force-induced chromatin remodelling in epidermal development and homeostasis. Curr Opin Genet Dev 2019; 55:46-51. [PMID: 31112907 DOI: 10.1016/j.gde.2019.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/05/2019] [Accepted: 04/15/2019] [Indexed: 01/14/2023]
Abstract
The skin epidermis is a constantly renewing stratified epithelium that provides essential protective barrier functions throughout life. Epidermal stratification is governed by a step-wise differentiation program that requires precise spatiotemporal control of gene expression. How epidermal self-renewal and differentiation are regulated remains a fundamental open question. Cell-intrinsic and cell-extrinsic mechanisms that modify chromatin structure and interactions have been identified as key regulators of epidermal differentiation and stratification. Here, we will review the recent advances in our understanding of how chromatin modifiers, tissue-specific transcription factors, and force-induced nuclear remodeling processes function to shape chromatin and to control epidermal tissue development and homeostasis.
Collapse
Affiliation(s)
- Yekaterina A Miroshnikova
- Helsinki Institute of Life Science, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, 00290, Finland; Wihuri Research Institute, University of Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland; Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Idan Cohen
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA.
| | - Sara A Wickström
- Helsinki Institute of Life Science, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, 00290, Finland; Wihuri Research Institute, University of Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland; Max Planck Institute for Biology of Ageing, Cologne, Germany.
| |
Collapse
|
43
|
TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment. Cell Stem Cell 2019; 24:271-284.e8. [PMID: 30686763 DOI: 10.1016/j.stem.2018.12.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 10/04/2018] [Accepted: 12/17/2018] [Indexed: 11/22/2022]
Abstract
Tissue development results from lineage-specific transcription factors (TFs) programming a dynamic chromatin landscape through progressive cell fate transitions. Here, we define epigenomic landscape during epidermal differentiation of human pluripotent stem cells (PSCs) and create inference networks that integrate gene expression, chromatin accessibility, and TF binding to define regulatory mechanisms during keratinocyte specification. We found two critical chromatin networks during surface ectoderm initiation and keratinocyte maturation, which are driven by TFAP2C and p63, respectively. Consistently, TFAP2C, but not p63, is sufficient to initiate surface ectoderm differentiation, and TFAP2C-initiated progenitor cells are capable of maturing into functional keratinocytes. Mechanistically, TFAP2C primes the surface ectoderm chromatin landscape and induces p63 expression and binding sites, thus allowing maturation factor p63 to positively autoregulate its own expression and close a subset of the TFAP2C-initiated surface ectoderm program. Our work provides a general framework to infer TF networks controlling chromatin transitions that will facilitate future regenerative medicine advances.
Collapse
|