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Osterburg C, Ferniani M, Antonini D, Frombach AS, D'Auria L, Osterburg S, Lotz R, Löhr F, Kehrloesser S, Zhou H, Missero C, Dötsch V. Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree. Cell Death Dis 2023; 14:274. [PMID: 37072394 PMCID: PMC10113246 DOI: 10.1038/s41419-023-05796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023]
Abstract
The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. Mutations in the DNA binding domain (DBD) of p53 have been studied in great detail, enabling a general mechanism-based classification. In this study we provide a detailed investigation of all currently known mutations in the p63 DBD, which are associated with developmental syndromes, by measuring their impact on transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes. Here we propose a classification of the p63 DBD mutations based on the four different mechanisms of DNA binding impairment which we identified: direct DNA contact, zinc finger region, H2 region, and dimer interface mutations. The data also demonstrate that, in contrast to p53 cancer mutations, no p63 mutation induces global unfolding and subsequent aggregation of the domain. The dimer interface mutations that affect the DNA binding affinity by disturbing the interaction between the individual DBDs retain partial DNA binding capacity which correlates with a milder patient phenotype.
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Affiliation(s)
- Christian Osterburg
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Marco Ferniani
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Dario Antonini
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Ann-Sophie Frombach
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Ludovica D'Auria
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Susanne Osterburg
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Rebecca Lotz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Sebastian Kehrloesser
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Huiqing Zhou
- Departments of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
- Departments of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Caterina Missero
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80145, Naples, Italy.
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany.
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A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms. Int J Mol Sci 2023; 24:ijms24065603. [PMID: 36982676 PMCID: PMC10052683 DOI: 10.3390/ijms24065603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Keratins are a family of intermediate filament-forming proteins highly specific to epithelial cells. A combination of expressed keratin genes is a defining property of the epithelium belonging to a certain type, organ/tissue, cell differentiation potential, and at normal or pathological conditions. In a variety of processes such as differentiation and maturation, as well as during acute or chronic injury and malignant transformation, keratin expression undergoes switching: an initial keratin profile changes accordingly to changed cell functions and location within a tissue as well as other parameters of cellular phenotype and physiology. Tight control of keratin expression implies the presence of complex regulatory landscapes within the keratin gene loci. Here, we highlight patterns of keratin expression in different biological conditions and summarize disparate data on mechanisms controlling keratin expression at the level of genomic regulatory elements, transcription factors (TFs), and chromatin spatial structure.
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3
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Oceguera-Yanez F, Avila-Robinson A, Woltjen K. Differentiation of pluripotent stem cells for modeling human skin development and potential applications. Front Cell Dev Biol 2022; 10:1030339. [PMID: 36506084 PMCID: PMC9728031 DOI: 10.3389/fcell.2022.1030339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
The skin of mammals is a multilayered and multicellular tissue that forms an environmental barrier with key functions in protection, regulation, and sensation. While animal models have long served to study the basic functions of the skin in vivo, new insights are expected from in vitro models of human skin development. Human pluripotent stem cells (PSCs) have proven to be invaluable tools for studying human development in vitro. To understand the mechanisms regulating human skin homeostasis and injury repair at the molecular level, recent efforts aim to differentiate PSCs towards skin epidermal keratinocytes, dermal fibroblasts, and skin appendages such as hair follicles and sebaceous glands. Here, we present an overview of the literature describing strategies for human PSC differentiation towards the components of skin, with a particular focus on keratinocytes. We highlight fundamental advances in the field employing patient-derived human induced PSCs (iPSCs) and skin organoid generation. Importantly, PSCs allow researchers to model inherited skin diseases in the search for potential treatments. Skin differentiation from human PSCs holds the potential to clarify human skin biology.
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Affiliation(s)
- Fabian Oceguera-Yanez
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan,*Correspondence: Fabian Oceguera-Yanez, ; Knut Woltjen,
| | | | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan,*Correspondence: Fabian Oceguera-Yanez, ; Knut Woltjen,
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4
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Bai Y, Yang Z, Xu X, Ding W, Qi J, Liu F, Wang X, Zhou B, Zhang W, Zhuang X, Li G, Zhao Y. Direct chemical induction of hepatocyte-like cells with capacity for liver repopulation. Hepatology 2022; 77:1550-1565. [PMID: 35881538 DOI: 10.1002/hep.32686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND AIMS Cell fate can be directly reprogrammed from accessible cell types (e.g., fibroblasts) into functional cell types by exposure to small molecule stimuli. However, no chemical reprogramming method has been reported to date that successfully generates functional hepatocyte-like cells that can repopulate liver tissue, casting doubt over the feasibility of chemical reprogramming approaches to obtain desirable cell types for therapeutic applications. APPROACH AND RESULTS Here, through chemical induction of phenotypic plasticity, we provide a proof-of-concept demonstration of the direct chemical reprogramming of mouse fibroblasts into functional hepatocyte-like cells using exposure to small molecule cocktails in culture medium to successively stimulate endogenous expression of master transcription factors associated with hepatocyte development, such as hepatocyte nuclear factor 4a, nuclear receptor subfamily 1, group I, member 2, and nuclear receptor subfamily 1, group H, member 4. RNA sequencing analysis, metabolic assays, and in vivo physiological experiments show that chemically induced hepatocytes (CiHeps) exhibit comparable activity and function to primary hepatocytes, especially in liver repopulation to rescue liver failure in fumarylacetoacetate hydrolase-/- recombination activating gene 2-/- interleukin 2 receptor, gamma chain-/- mice in vivo. Single-cell RNA-seq further revealed that gastrointestinal-like and keratinocyte-like cells were induced along with CiHeps, resembling the activation of an intestinal program within hepatic reprogramming as described in transgenic approaches. CONCLUSIONS Our findings show that direct chemical reprogramming can generate hepatocyte-like cells with high-quality physiological properties, providing a paradigm for establishing hepatocyte identity in fibroblasts and demonstrating the potential for chemical reprogramming in organ/tissue repair and regeneration therapies.
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Affiliation(s)
- Yunfei Bai
- State Key Laboratory of Natural and Biomimetic Drugs, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Zhenghao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | | | - Wanqiu Ding
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Juntian Qi
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Feng Liu
- National Clinical Research Center for Infectious Disease, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Peking University People's Hospital, Beijing, China
| | - Xiaoxiao Wang
- National Clinical Research Center for Infectious Disease, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Peking University People's Hospital, Beijing, China
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenpeng Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xiaomei Zhuang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Guanglu Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
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Leon A, Subirana L, Magre K, Cases I, Tena JJ, Irimia M, Gomez-Skarmeta JL, Escriva H, Bertrand S. Gene regulatory networks of epidermal and neural fate choice in a chordate. Mol Biol Evol 2022; 39:6547258. [PMID: 35276009 PMCID: PMC9004418 DOI: 10.1093/molbev/msac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Neurons are a highly specialized cell type only found in metazoans. They can be scattered throughout the body or grouped together, forming ganglia or nerve cords. During embryogenesis, centralized nervous systems develop from the ectoderm, which also forms the epidermis. How pluripotent ectodermal cells are directed toward neural or epidermal fates, and to which extent this process is shared among different animal lineages, are still open questions. Here, by using micromere explants, we were able to define in silico the putative gene regulatory networks (GRNs) underlying the first steps of the epidermis and the central nervous system formation in the cephalochordate amphioxus. We propose that although the signal triggering neural induction in amphioxus (i.e., Nodal) is different from vertebrates, the main transcription factors implicated in this process are conserved. Moreover, our data reveal that transcription factors of the neural program seem to not only activate neural genes but also to potentially have direct inputs into the epidermal GRN, suggesting that the Nodal signal might also contribute to neural fate commitment by repressing the epidermal program. Our functional data on whole embryos support this result and highlight the complex interactions among the transcription factors activated by the signaling pathways that drive ectodermal cell fate choice in chordates.
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Affiliation(s)
- Anthony Leon
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Kevin Magre
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
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Liu LP, Zheng DX, Xu ZF, Zhou HC, Wang YC, Zhou H, Ge JY, Sako D, Li M, Akimoto K, Li YM, Zheng YW. Transcriptomic and Functional Evidence Show Similarities between Human Amniotic Epithelial Stem Cells and Keratinocytes. Cells 2021; 11:70. [PMID: 35011631 PMCID: PMC8750621 DOI: 10.3390/cells11010070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 01/06/2023] Open
Abstract
Amniotic epithelial stem cells (AESCs) are considered as potential alternatives to keratinocytes (KCs) in tissue-engineered skin substitutes used for treating skin damage. However, their clinical application is limited since similarities and distinctions between AESCs and KCs remain unclear. Herein, a transcriptomics analysis and functional evaluation were used to understand the commonalities and differences between AESCs and KCs. RNA-sequencing revealed that AESCs are involved in multiple epidermis-associated biological processes shared by KCs and show more similarity to early stage immature KCs than to adult KCs. However, AESCs were observed to be heterogeneous, and some possessed hybrid mesenchymal and epithelial features distinct from KCs. A functional evaluation revealed that AESCs can phagocytose melanosomes transported by melanocytes in both 2D and 3D co-culture systems similar to KCs, which may help reconstitute pigmented skin. The overexpression of TP63 and activation of NOTCH signaling could promote AESC stemness and improve their differentiation features, respectively, bridging the gap between AESCs and KCs. These changes induced the convergence of AESC cell fate with KCs. In future, modified reprogramming strategies, such as the use of small molecules, may facilitate the further modulation human AESCs for use in skin regeneration.
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Affiliation(s)
- Li-Ping Liu
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China; (L.-P.L.); (H.-C.Z.); (Y.-C.W.); (H.Z.); (M.L.)
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan; (D.-X.Z.); (J.-Y.G.); (D.S.)
| | - Dong-Xu Zheng
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan; (D.-X.Z.); (J.-Y.G.); (D.S.)
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Zheng-Fang Xu
- Department of Obstetrics and Gynaecology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China;
| | - Hu-Cheng Zhou
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China; (L.-P.L.); (H.-C.Z.); (Y.-C.W.); (H.Z.); (M.L.)
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Yun-Cong Wang
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China; (L.-P.L.); (H.-C.Z.); (Y.-C.W.); (H.Z.); (M.L.)
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Hang Zhou
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China; (L.-P.L.); (H.-C.Z.); (Y.-C.W.); (H.Z.); (M.L.)
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Jian-Yun Ge
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan; (D.-X.Z.); (J.-Y.G.); (D.S.)
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
| | - Daisuke Sako
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan; (D.-X.Z.); (J.-Y.G.); (D.S.)
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510, Japan;
| | - Mi Li
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China; (L.-P.L.); (H.-C.Z.); (Y.-C.W.); (H.Z.); (M.L.)
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Kazunori Akimoto
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510, Japan;
| | - Yu-Mei Li
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China; (L.-P.L.); (H.-C.Z.); (Y.-C.W.); (H.Z.); (M.L.)
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Yun-Wen Zheng
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China; (L.-P.L.); (H.-C.Z.); (Y.-C.W.); (H.Z.); (M.L.)
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan; (D.-X.Z.); (J.-Y.G.); (D.S.)
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
- School of Medicine, Yokohama City University, Yokohama 236-0004, Kanagawa, Japan
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7
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Sun H, Zhang YX, Li YM. Generation of Skin Organoids: Potential Opportunities and Challenges. Front Cell Dev Biol 2021; 9:709824. [PMID: 34805138 PMCID: PMC8600117 DOI: 10.3389/fcell.2021.709824] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/21/2021] [Indexed: 12/03/2022] Open
Abstract
Although several types of human skin substitutes are currently available, they usually do not include important skin appendages such as hair follicles and sweat glands, or various skin-related cells, such as dermal adipocytes and sensory neurons. This highlights the need to improve the in vitro human skin generation model for use as a tool for investigating skin diseases and as a source of cells or tissues for skin regeneration. Skin organoids are generated from stem cells and are expected to possess the complexity and function of natural skin. Here, we summarize the current literatures relating to the "niches" of the local skin stem cell microenvironment and the formation of skin organoids, and then discuss the opportunities and challenges associated with multifunctional skin organoids.
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Affiliation(s)
- Hui Sun
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yi-Xuan Zhang
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yu-Mei Li
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
- School of Medicine, Jiangsu University, Zhenjiang, China
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8
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Xu Q, Georgiou G, Frölich S, van der Sande M, Veenstra G, Zhou H, van Heeringen S. ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination. Nucleic Acids Res 2021; 49:7966-7985. [PMID: 34244796 PMCID: PMC8373078 DOI: 10.1093/nar/gkab598] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Proper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors. However, experimental elucidation of key transcription factors that drive cellular identity is currently often intractable. Here, we present ANANSE (ANalysis Algorithm for Networks Specified by Enhancers), a network-based method that exploits enhancer-encoded regulatory information to identify the key transcription factors in cell fate determination. As cell type-specific transcription factors predominantly bind to enhancers, we use regulatory networks based on enhancer properties to prioritize transcription factors. First, we predict genome-wide binding profiles of transcription factors in various cell types using enhancer activity and transcription factor binding motifs. Subsequently, applying these inferred binding profiles, we construct cell type-specific gene regulatory networks, and then predict key transcription factors controlling cell fate transitions using differential networks between cell types. This method outperforms existing approaches in correctly predicting major transcription factors previously identified to be sufficient for trans-differentiation. Finally, we apply ANANSE to define an atlas of key transcription factors in 18 normal human tissues. In conclusion, we present a ready-to-implement computational tool for efficient prediction of transcription factors in cell fate determination and to study transcription factor-mediated regulatory mechanisms. ANANSE is freely available at https://github.com/vanheeringen-lab/ANANSE.
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Affiliation(s)
- Quan Xu
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Georgios Georgiou
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Siebren Frölich
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Maarten van der Sande
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Huiqing Zhou
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
- Radboud University Medical Center, Department of Human Genetics, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Simon J van Heeringen
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
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9
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Isoform-Specific Roles of Mutant p63 in Human Diseases. Cancers (Basel) 2021; 13:cancers13030536. [PMID: 33572532 PMCID: PMC7866788 DOI: 10.3390/cancers13030536] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary The protein p63 belongs to the family of the p53 tumor suppressor. Mouse models have, however, shown that it is not a classical tumor suppressor but instead involved in developmental processes. Mutations in the p63 gene cause several developmental defects in human patients characterized by limb deformation, cleft lip/palate, and ectodermal dysplasia due to p63’s role as a master regulator of epidermal development. In addition, p63 plays a key role as a quality control factor in oocytes and p63 mutations can result either in compromised genetic quality control or premature cell death of all oocytes. Abstract The p63 gene encodes a master regulator of epidermal commitment, development, and differentiation. Heterozygous mutations in the DNA binding domain cause Ectrodactyly, Ectodermal Dysplasia, characterized by limb deformation, cleft lip/palate, and ectodermal dysplasia while mutations in in the C-terminal domain of the α-isoform cause Ankyloblepharon-Ectodermal defects-Cleft lip/palate (AEC) syndrome, a life-threatening disorder characterized by skin fragility, severe, long-lasting skin erosions, and cleft lip/palate. The molecular disease mechanisms of these syndromes have recently become elucidated and have enhanced our understanding of the role of p63 in epidermal development. Here we review the molecular cause and functional consequences of these p63-mutations for skin development and discuss the consequences of p63 mutations for female fertility.
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10
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Sah SK, Kanaujiya JK, Chen IP, Reichenberger EJ. Generation of Keratinocytes from Human Induced Pluripotent Stem Cells Under Defined Culture Conditions. Cell Reprogram 2020; 23:1-13. [PMID: 33373529 DOI: 10.1089/cell.2020.0046] [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] [Indexed: 11/12/2022] Open
Abstract
Differentiation of keratinocytes from human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) has become an important tool for wound healing research and for studying skin diseases in instances where patient cells are not available. Several keratinocyte differentiation protocols using hiPSC colony fragments or embryoid bodies have been published with some requiring prolonged time for differentiation or extended use of reagent cocktails. In this study, we present a simplified method to efficiently generate large numbers of uniformly differentiated keratinocytes in less than 4 weeks from singularized hiPSCs with differentiation factors, retinoic acid and bone morphogenetic protein 4 (BMP4). Low seeding density of singularized iPSCs results in keratinocyte cultures with minimum cell death during differentiation and up to 96% homogeneity for keratin 14-positive cells and low percentage of keratinocyte maturation markers, comparable to early passage primary keratinocytes. hiPSC-derived keratinocytes remain in a proliferative state, can be maintained for prolonged periods of time, and can be terminally differentiated under high calcium conditions in the same way as primary human keratinocytes. Moreover, coculturing hiPSC-derived fibroblasts and keratinocytes consistently formed organotypic 3D skin equivalents. Therefore, keratinocytes generated by this method are a viable source of cells for downstream applications.
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Affiliation(s)
- Shyam Kishor Sah
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health, Farmington, Connecticut, USA
| | - Jitendra K Kanaujiya
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health, Farmington, Connecticut, USA
| | - I-Ping Chen
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health, Farmington, Connecticut, USA
| | - Ernst J Reichenberger
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health, Farmington, Connecticut, USA
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11
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Distinct p63 and p73 Protein Interactions Predict Specific Functions in mRNA Splicing and Polyploidy Control in Epithelia. Cells 2020; 10:cells10010025. [PMID: 33375680 PMCID: PMC7824480 DOI: 10.3390/cells10010025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022] Open
Abstract
Epithelial organs are the first barrier against microorganisms and genotoxic stress, in which the p53 family members p63 and p73 have both overlapping and distinct functions. Intriguingly, p73 displays a very specific localization to basal epithelial cells in human tissues, while p63 is expressed in both basal and differentiated cells. Here, we analyse systematically the literature describing p63 and p73 protein-protein interactions to reveal distinct functions underlying the aforementioned distribution. We have found that p73 and p63 cooperate in the genome stability surveillance in proliferating cells; p73 specific interactors contribute to the transcriptional repression, anaphase promoting complex and spindle assembly checkpoint, whereas p63 specific interactors play roles in the regulation of mRNA processing and splicing in both proliferating and differentiated cells. Our analysis reveals the diversification of the RNA and DNA specific functions within the p53 family.
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12
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Saxena K, Srikrishnan S, Celia-Terrassa T, Jolly MK. OVOL1/2: Drivers of Epithelial Differentiation in Development, Disease, and Reprogramming. Cells Tissues Organs 2020; 211:183-192. [PMID: 32932250 DOI: 10.1159/000511383] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/26/2020] [Indexed: 11/19/2022] Open
Abstract
OVOL proteins (OVOL1 and OVOL2), vertebrate homologs of Drosophila OVO, are critical regulators of epithelial lineage determination and differentiation during embryonic development in tissues such as kidney, skin, mammary epithelia, and testis. OVOL can inhibit epithelial-mesenchymal transition and/or can promote mesenchymal-epithelial transition. Moreover, they can regulate the stemness of cancer cells, thus playing an important role during cancer cell metastasis. Due to their central role in differentiation and maintenance of epithelial lineage, OVOL overexpression has been shown to be capable of reprogramming fibroblasts to epithelial cells. Here, we review the roles of OVOL-mediated epithelial differentiation across multiple contexts, including embryonic development, cancer progression, and cellular reprogramming.
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Affiliation(s)
- Kritika Saxena
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | | | - Toni Celia-Terrassa
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Mohit Kumar Jolly
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India,
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13
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Zhang Y, Hu W, Ma K, Zhang C, Fu X. Reprogramming of Keratinocytes as Donor or Target Cells Holds Great Promise for Cell Therapy and Regenerative Medicine. Stem Cell Rev Rep 2020; 15:680-689. [PMID: 31197578 DOI: 10.1007/s12015-019-09900-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
One of the most crucial branches of regenerative medicine is cell therapy, in which cellular material is injected into the patient to initiate the regenerative process. Cells obtained by reprogramming of the patient's own cells offer ethical and clinical advantages could provide a new source of material for therapeutic applications. Studies to date have shown that only a subset of differentiated cell types can be reprogrammed. Among these, keratinocytes, which are the most abundant proliferating cell type in the epidermis, have gained increasing attention as both donor and target cells for reprogramming and have become a new focus of regenerative medicine. As target cells for the treatment of skin defects, keratinocytes can be differentiated or reprogrammed from embryonic stem cells, induced pluripotent stem cells, fibroblasts, adipose tissue stem cells, and mesenchymal cells. As donor cells, keratinocytes can be reprogrammed or direct reprogrammed into a number of cell types, including induced pluripotent stem cells, neural cells, and Schwann cells. In this review, we discuss recent advances in keratinocyte reprogramming, focusing on the induction methods, potential molecular mechanisms, conversion efficiency, and safety for clinical applications. Graphical Abstract KCs as target cells can be reprogrammed or differentiated from fibroblasts, iPSCs, ATSCs, and mesenchymal cells. And as donor cells, KCs can be reprogrammed or directly reprogrammded into iPSCs, neural cells, Schwann cells, and epidermal stem cells.
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Affiliation(s)
- Yuehou Zhang
- School of Medicine, NanKai University, 94 Wei Jin Road, NanKai District, Tianjin, 300071, People's Republic of China.,Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Wenzhi Hu
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Kui Ma
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Cuiping Zhang
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China.
| | - Xiaobing Fu
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China.
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14
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Jones J, Chen Y, Tiwari M, Li J, Ling J, Sen GL. KLF3 Mediates Epidermal Differentiation through the Epigenomic Writer CBP. iScience 2020; 23:101320. [PMID: 32659720 PMCID: PMC7358749 DOI: 10.1016/j.isci.2020.101320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Impairments in the differentiation process can lead to skin diseases that can afflict ∼20% of the population. Thus, it is of utmost importance to understand the factors that promote the differentiation process. Here we identify the transcription factor KLF3 as a regulator of epidermal differentiation. Knockdown of KLF3 results in reduced differentiation gene expression and increased cell cycle gene expression. Over half of KLF3's genomic binding sites occur at active enhancers. KLF3 binds to active enhancers proximal to differentiation genes that are dependent upon KLF3 for expression. KLF3's genomic binding sites also highly overlaps with CBP, a histone acetyltransferase necessary for activating enhancers. Depletion of KLF3 causes reduced CBP localization at enhancers proximal to differentiation gene clusters, which leads to loss of enhancer activation but not priming. Our results suggest that KLF3 is necessary to recruit CBP to activate enhancers and drive epidermal differentiation gene expression.
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Affiliation(s)
- Jackson Jones
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Ji Ling
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA.
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15
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Zheng J, Yun W, Park J, Kang PJ, Lee G, Song G, Kim IY, You S. Long-term expansion of directly reprogrammed keratinocyte-like cells and in vitro reconstitution of human skin. J Biomed Sci 2020; 27:56. [PMID: 32312260 PMCID: PMC7171822 DOI: 10.1186/s12929-020-00642-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/26/2020] [Indexed: 11/29/2022] Open
Abstract
Background Human keratinocytes and derived products are crucial for skin repair and regeneration. Despite substantial advances in engineered skin equivalents, their poor availability and immunorejection remain major challenges in skin grafting. Methods Induced keratinocyte-like cells (iKCs) were directly reprogrammed from human urine cells by retroviral transduction of two lineage-specific transcription factors BMI1 and △NP63α (BN). Expression of keratinocyte stem cell or their differentiation markers were assessed by PCR, immunofluorescence and RNA-Sequencing. Regeneration capacity of iKCs were assessed by reconstitution of a human skin equivalent under air-interface condition. Results BN-driven iKCs were similar to primary keratinocytes (pKCs) in terms of their morphology, protein expression, differentiation potential, and global gene expression. Moreover, BN-iKCs self-assembled to form stratified skin equivalents in vitro. Conclusions This study demonstrated an approach to generate human iKCs that could be directly reprogrammed from human somatic cells and extensively expanded in serum- and feeder cell-free systems, which will facilitate their broad applicability in an efficient and patient-specific manner.
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Affiliation(s)
- Jie Zheng
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Wonjin Yun
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Junghyun Park
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Phil Jun Kang
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Gilju Lee
- Department of Pathology, College of Medicine, Korea University Guro Hospital, Seoul, 08308, Republic of Korea
| | - Gwonhwa Song
- Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - In Yong Kim
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - Seungkwon You
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea. .,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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16
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Omori H, Nishio M, Masuda M, Miyachi Y, Ueda F, Nakano T, Sato K, Mimori K, Taguchi K, Hikasa H, Nishina H, Tashiro H, Kiyono T, Mak TW, Nakao K, Nakagawa T, Maehama T, Suzuki A. YAP1 is a potent driver of the onset and progression of oral squamous cell carcinoma. SCIENCE ADVANCES 2020; 6:eaay3324. [PMID: 32206709 PMCID: PMC7080500 DOI: 10.1126/sciadv.aay3324] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/18/2019] [Indexed: 05/23/2023]
Abstract
Head-and-neck squamous cell carcinoma (HNSCC) is the sixth most common group of cancers in the world, and patients have a poor prognosis. Here, we present data indicating that YAP1 may be a strong driver of the onset and progression of oral SCC (OSCC), a major subtype of HNSCC. Mice with tongue-specific deletion of Mob1a/b and thus endogenous YAP1 hyperactivation underwent surprisingly rapid and highly reproducible tumorigenesis, developing tongue carcinoma in situ within 2 weeks and invasive SCC within 4 weeks. In humans, precancerous tongue dysplasia displays YAP1 activation correlating with reduced patient survival. Combinations of molecules mutated in OSCC may increase and sustain YAP1 activation to the point of oncogenicity. Strikingly, siRNA or pharmacological inhibition of YAP1 blocks murine OSCC onset in vitro and in vivo. Our work justifies targeting YAP1 as therapy for OSCC and perhaps HNSCC, and our mouse model represents a powerful tool for evaluating these agents.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Biomarkers, Tumor
- Carcinoma, Squamous Cell/etiology
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Disease Models, Animal
- Disease Progression
- Disease Susceptibility
- Gene Expression
- Humans
- Immunohistochemistry
- Intracellular Signaling Peptides and Proteins/deficiency
- Mice
- Mice, Knockout
- Mouth Neoplasms/etiology
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/mortality
- Mouth Neoplasms/pathology
- Oncogene Proteins
- Prognosis
- Transcription Factors/genetics
- Transcription Factors/metabolism
- YAP-Signaling Proteins
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Affiliation(s)
- Hirofumi Omori
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Miki Nishio
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Muneyuki Masuda
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Yosuke Miyachi
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Fumihito Ueda
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Takafumi Nakano
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Kuniaki Sato
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Kenichi Taguchi
- Department of Pathology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Hiroki Hikasa
- Department of Biochemistry, School of Medicine, University of Occupational and Environmental Health, Fukuoka, Japan
| | - Hiroshi Nishina
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hironori Tashiro
- Department of Women’s Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tohru Kiyono
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tokyo, Japan
| | - Tak Wah Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kazuwa Nakao
- Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Nakagawa
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomohiko Maehama
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Akira Suzuki
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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17
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Li D, Kishta MS, Wang J. Regulation of pluripotency and reprogramming by RNA binding proteins. Curr Top Dev Biol 2020; 138:113-138. [PMID: 32220295 DOI: 10.1016/bs.ctdb.2020.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Embryonic stem cells have the capacities of self-renewal and pluripotency. Pluripotency establishment (somatic cell reprogramming), maintenance, and execution (differentiation) require orchestrated regulatory mechanisms of a cell's molecular machinery, including signaling pathways, epigenetics, transcription, translation, and protein degradation. RNA binding proteins (RBPs) take part in every process of RNA regulation and recent studies began to address their important functions in the regulation of pluripotency and reprogramming. Here, we discuss the roles of RBPs in key regulatory steps in the control of pluripotency and reprogramming. Among RNA binding proteins are a group of RNA helicases that are responsible for RNA structure remodeling with important functional implications. We highlight the largest family of RNA helicases, DDX (DEAD-box) helicase family and our current understanding of their functions specifically in the regulation of pluripotency and reprogramming.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mohamed S Kishta
- Hormones Department, Medical Research Division, National Research Centre, Cairo, Egypt; Stem Cell Lab., Center of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States.
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18
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Zhao A, Yang Y, Pan X, Pan Y, Cai S. Generation of keratinocyte stem-like cells from human fibroblasts via a direct reprogramming approach. Biotechnol Prog 2020; 36:e2961. [PMID: 31930712 DOI: 10.1002/btpr.2961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/29/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
Skin repair and reconstruction are important after severe wound and trauma. Keratinocyte stem cells (KSCs) in the basal layer of the epidermis can regrow the stratified epidermis but are almost depleted after skin injury. Thus, generating enough KSCs is indispensable for skin regeneration. Pluripotent stem cells such as ESC and iPSC can differentiate into KSCs, but their applications are challenged by ethical issues and risks of tumor formation. Lineage reprogramming from one cell type into another one makes it feasible to generate the desired cell type. Here, we develop a method to convert human fibroblasts into induced keratinocyte stem-like cells (iKSC) by coupling transient expression of reprogramming factors with a chemically defined culture medium, without the formation of iPSC. iKSC resemble normal KSC in the morphological and phenotypic features and can differentiate in vitro and regenerate stratified epidermis after transplantation in vivo. Therefore, iKSC may provide abundant cellular sources for skin repair and regeneration.
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Affiliation(s)
- Andong Zhao
- Health Science Center, Shenzhen University, Shenzhen, China
| | - Yi Yang
- Health Science Center, Shenzhen University, Shenzhen, China
| | - Xiaohua Pan
- Department of Trauma and Orthopedics, The Affiliated Baoan Hospital of Southern Medical University, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yu Pan
- Department of Trauma and Orthopedics, The Affiliated Baoan Hospital of Southern Medical University, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Sa Cai
- Health Science Center, Shenzhen University, Shenzhen, China
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19
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Bioactive Molecules for Skin Repair and Regeneration: Progress and Perspectives. Stem Cells Int 2019; 2019:6789823. [PMID: 32082386 PMCID: PMC7012201 DOI: 10.1155/2019/6789823] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022] Open
Abstract
Skin regeneration is a vexing problem in the field of regenerative medicine. A bioactive molecule-based strategy has been frequently used in skin wound healing in recent years. Bioactive molecules are practical tools for regulating cellular processes and have been applied to control cellular differentiation, dedifferentiation, and reprogramming. In this review, we focus on recent progress in the use of bioactive molecules in skin regenerative medicine, by which desired cell types can be generated in vitro for cell therapy and conventional therapeutics can be developed to repair and regenerate skin in vivo through activation of the endogenous repairing potential. We further prospect that the bioactive molecule-base method might be one of the promising strategies to achieve in situ skin regeneration in the future.
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20
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Zhang F, Zhang D, Cheng K, Zhou Z, Liu S, Chen L, Hu Y, Mao C, Liu S. Spontaneous evolution of human skin fibroblasts into wound-healing keratinocyte-like cells. Theranostics 2019; 9:5200-5213. [PMID: 31410210 PMCID: PMC6691578 DOI: 10.7150/thno.31526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/28/2019] [Indexed: 12/17/2022] Open
Abstract
Producing keratinocyte cells (KCs) in large scale is difficult due to their slow proliferation, disabling their use as seed cells for skin regeneration and wound healing. Cell reprogramming is a promising inducer-based approach to KC production but only reaches very low cellular conversion. Here we reported a unique cellular conversion phenomenon, where human skin fibroblasts (FBs) were spontaneously converted into keratinocyte-like cells (KLCs) over the time without using any inducers. Methods: FBs were routinely cultured for more than 120 days in regular culture medium. Characteristics of KLCs were checked at the molecular and cellular level. Then the functionality and safety of the KLCs were verified by wound healing and tumorigenicity assay, respectively. To identify the mechanism of the cell conversion phenomenon, high-throughput RNA sequencing was also performed. Results: The global conversion started on day 90 and reached 90% on day 110. The KLCs were as functional and effective as KCs in wound healing without causing oncogenicity. The conversion was regulated via a PI3K-AKT signaling pathway mediated by a long non-coding RNA, LINC00672. Modulating the pathway could shorten the conversion time to 14 days. Conclusion: The discovered FBs-KLCs conversion in the study might open a new avenue to the scalable production of cell sources needed for regenerating skins and healing large-area wounds.
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21
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Kurita M, Izpisua Belmonte JC, Suzuki K, Okazaki M. Development of de novo epithelialization method for treatment of cutaneous ulcers. J Dermatol Sci 2019; 95:8-12. [PMID: 31255469 DOI: 10.1016/j.jdermsci.2019.06.006] [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: 06/01/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 11/29/2022]
Abstract
Cutaneous ulcers are a common cause of morbidity. We have developed a de novo epithelialization method for treating cutaneous ulcers by means of reprogramming wound-resident mesenchymal cells in vivo into cells able to form a stratified epithelium: induced stratified epithelial progenitors (iSEPs). Administration of 4 transcription factors (DNP63A, GRHL2, TFAP2A, and cMYC) expressed via adeno-associated viral vectors enabled generation of epithelial cells and tissues, thereby acheiving de novo epithelialization from the surfaces of cutaneous ulcers in a mouse model. Generated epithelia, having barrier functions equivalent to the original epidermis, were maintained for more than 6 months. Our findings constitute a proof of concept for future development towards innovative therapies for cutaneous ulcers via de novo epithelialization.
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Affiliation(s)
- Masakazu Kurita
- Department of Plastic and Aesthetic Surgery, The University of Tokyo Hospital, Japan.
| | | | - Keiichiro Suzuki
- Institute for Advanced Co-Creation Studies, Osaka University, Japan; Graduate School of Engineering Science, Osaka University, Japan
| | - Mutsumi Okazaki
- Department of Plastic and Aesthetic Surgery, The University of Tokyo Hospital, Japan
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22
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p73 regulates epidermal wound healing and induced keratinocyte programming. PLoS One 2019; 14:e0218458. [PMID: 31216312 PMCID: PMC6583996 DOI: 10.1371/journal.pone.0218458] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/03/2019] [Indexed: 12/19/2022] Open
Abstract
p63 is a transcriptional regulator of ectodermal development that is required for basal cell proliferation and stem cell maintenance. p73 is a closely related p53 family member that is expressed in select p63-positive basal cells and can heterodimerize with p63. p73-/- mice lack multiciliated cells and have reduced numbers of basal epithelial cells in select tissues; however, the role of p73 in basal epithelial cells is unknown. Herein, we show that p73-deficient mice exhibit delayed wound healing despite morphologically normal-appearing skin. The delay in wound healing is accompanied by decreased proliferation and increased levels of biomarkers of the DNA damage response in basal keratinocytes at the epidermal wound edge. In wild-type mice, this same cell population exhibited increased p73 expression after wounding. Analyzing single-cell transcriptomic data, we found that p73 was expressed by epidermal and hair follicle stem cells, cell types required for wound healing. Moreover, we discovered that p73 isoforms expressed in the skin (ΔNp73) enhance p63-mediated expression of keratinocyte genes during cellular reprogramming from a mesenchymal to basal keratinocyte-like cell. We identified a set of 44 genes directly or indirectly regulated by ΔNp73 that are involved in skin development, cell junctions, cornification, proliferation, and wound healing. Our results establish a role for p73 in cutaneous wound healing through regulation of basal keratinocyte function.
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23
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Advanced drug delivery systems and artificial skin grafts for skin wound healing. Adv Drug Deliv Rev 2019; 146:209-239. [PMID: 30605737 DOI: 10.1016/j.addr.2018.12.014] [Citation(s) in RCA: 289] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/27/2018] [Accepted: 12/27/2018] [Indexed: 12/14/2022]
Abstract
Cutaneous injuries, especially chronic wounds, burns, and skin wound infection, require painstakingly long-term treatment with an immense financial burden to healthcare systems worldwide. However, clinical management of chronic wounds remains unsatisfactory in many cases. Various strategies including growth factor and gene delivery as well as cell therapy have been used to enhance the healing of non-healing wounds. Drug delivery systems across the nano, micro, and macroscales can extend half-life, improve bioavailability, optimize pharmacokinetics, and decrease dosing frequency of drugs and genes. Replacement of the damaged skin tissue with substitutes comprising cell-laden scaffold can also restore the barrier and regulatory functions of skin at the wound site. This review covers comprehensively the advanced treatment strategies to improve the quality of wound healing.
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24
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Lin-Shiao E, Lan Y, Welzenbach J, Alexander KA, Zhang Z, Knapp M, Mangold E, Sammons M, Ludwig KU, Berger SL. p63 establishes epithelial enhancers at critical craniofacial development genes. SCIENCE ADVANCES 2019; 5:eaaw0946. [PMID: 31049400 PMCID: PMC6494499 DOI: 10.1126/sciadv.aaw0946] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/19/2019] [Indexed: 05/15/2023]
Abstract
The transcription factor p63 is a key mediator of epidermal development. Point mutations in p63 in patients lead to developmental defects, including orofacial clefting. To date, knowledge on how pivotal the role of p63 is in human craniofacial development is limited. Using an inducible transdifferentiation model, combined with epigenomic sequencing and multicohort meta-analysis of genome-wide association studies data, we show that p63 establishes enhancers at craniofacial development genes to modulate their transcription. Disease-specific substitution mutation in the DNA binding domain or sterile alpha motif protein interaction domain of p63, respectively, eliminates or reduces establishment of these enhancers. We show that enhancers established by p63 are highly enriched for single-nucleotide polymorphisms associated with nonsyndromic cleft lip ± cleft palate (CL/P). These orthogonal approaches indicate a strong molecular link between p63 enhancer function and CL/P, illuminating molecular mechanisms underlying this developmental defect and revealing vital regulatory elements and new candidate causative genes.
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Affiliation(s)
- Enrique Lin-Shiao
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics, Biomedical Sciences Graduate Program, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Julia Welzenbach
- Institute of Human Genetics, University Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Katherine A Alexander
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Zhen Zhang
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Morgan Sammons
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Kerstin U Ludwig
- Institute of Human Genetics, University Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Shelley L Berger
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
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Watanabe K, Liu Y, Noguchi S, Murray M, Chang JC, Kishima M, Nishimura H, Hashimoto K, Minoda A, Suzuki H. OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages. Sci Rep 2019; 9:6490. [PMID: 31019211 PMCID: PMC6482152 DOI: 10.1038/s41598-019-43021-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/08/2019] [Indexed: 01/12/2023] Open
Abstract
Mesenchymal-to-epithelial transition (MET) is an important step in cell reprogramming from fibroblasts (a cell type frequently used for this purpose) to various epithelial cell types. However, the mechanism underlying MET induction in fibroblasts remains to be understood. The present study aimed to identify the transcription factors (TFs) that efficiently induce MET in dermal fibroblasts. OVOL2 was identified as a potent inducer of key epithelial genes, and OVOL2 cooperatively enhanced MET induced by HNF1A, TP63, and KLF4, which are known reprogramming TFs to epithelial lineages. In TP63/KLF4-induced keratinocyte-like cell-state reprogramming, OVOL2 greatly facilitated the activation of epithelial and keratinocyte-specific genes. This was accompanied by enhanced changes in chromatin accessibility across the genome. Mechanistically, motif enrichment analysis revealed that the target loci of KLF4 and TP63 become accessible upon induction of TFs, whereas the OVOL2 target loci become inaccessible. This indicates that KLF4 and TP63 positively regulate keratinocyte-associated genes whereas OVOL2 suppresses fibroblast-associated genes. The exogenous expression of OVOL2 therefore disrupts fibroblast lineage identity and facilitates fibroblast cell reprogramming into epithelial lineages cooperatively with tissue-specific reprogramming factors. Identification of OVOL2 as an MET inducer and an epithelial reprogramming enhancer in fibroblasts provides new insights into cellular reprogramming improvement for future applications.
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Affiliation(s)
- Kazuhide Watanabe
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ye Liu
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Madeleine Murray
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mami Kishima
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hajime Nishimura
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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26
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Soares E, Zhou H. Master regulatory role of p63 in epidermal development and disease. Cell Mol Life Sci 2018; 75:1179-1190. [PMID: 29103147 PMCID: PMC5843667 DOI: 10.1007/s00018-017-2701-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/16/2017] [Accepted: 10/26/2017] [Indexed: 01/19/2023]
Abstract
The transcription factor p63 is a master regulator of epidermal development. Mutations in p63 give rise to human developmental diseases that often manifest epidermal defects. In this review, we summarize major p63 isoforms identified so far and p63 mutation-associated human diseases that show epidermal defects. We discuss key roles of p63 in epidermal keratinocyte proliferation and differentiation, emphasizing its master regulatory control of the gene expression pattern and epigenetic landscape that define epidermal fate. We subsequently review the essential function of p63 during epidermal commitment and transdifferentiation towards epithelial lineages, highlighting the notion that p63 is the guardian of the epithelial lineage. Finally, we discuss current therapeutic development strategies for p63 mutation-associated diseases. Our review proposes future directions for dissecting p63-controlled mechanisms in normal and diseased epidermal development and for developing therapeutic options.
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Affiliation(s)
- Eduardo Soares
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 274, Postbus 9101, 6500HB, Nijmegen, The Netherlands
- 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, 274, Postbus 9101, 6500HB, Nijmegen, The Netherlands.
- Department of Human Genetics, Radboud University Medical Center, 855, Postbus 9101, 6500HB, Nijmegen, The Netherlands.
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27
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Protein aggregation of the p63 transcription factor underlies severe skin fragility in AEC syndrome. Proc Natl Acad Sci U S A 2018; 115:E906-E915. [PMID: 29339502 PMCID: PMC5798343 DOI: 10.1073/pnas.1713773115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The p63 gene encodes a master regulator of epidermal development and function. Specific mutations in p63 are causative of a life-threatening disorder mainly characterized by severe skin erosions and cleft palate. Little is known about the mechanisms underlying disease pathology and possible treatments. Based on biochemical studies, genetic mouse models, and functional assays, we demonstrate that these mutations cause p63 protein misfolding and aggregation. Protein aggregation lead to reduced DNA binding and impaired transcriptional activity. Importantly, genetic modifications of p63 that abolish aggregation of the mutant proteins rescue its function, revealing that ankyloblepharon-ectodermal defects-cleft lip/palate syndrome is a protein aggregation disorder and opening avenues for therapeutic intervention. The p63 gene encodes a master regulator of epidermal commitment, development, and differentiation. Heterozygous mutations in the C-terminal domain of the p63 gene can cause ankyloblepharon-ectodermal defects-cleft lip/palate (AEC) syndrome, a life-threatening disorder characterized by skin fragility and severe, long-lasting skin erosions. Despite deep knowledge of p63 functions, little is known about mechanisms underlying disease pathology and possible treatments. Here, we show that multiple AEC-associated p63 mutations, but not those causative of other diseases, lead to thermodynamic protein destabilization, misfolding, and aggregation, similar to the known p53 gain-of-function mutants found in cancer. AEC mutant proteins exhibit impaired DNA binding and transcriptional activity, leading to dominant negative effects due to coaggregation with wild-type p63 and p73. Importantly, p63 aggregation occurs also in a conditional knock-in mouse model for the disorder, in which the misfolded p63 mutant protein leads to severe epidermal defects. Variants of p63 that abolish aggregation of the mutant proteins are able to rescue p63’s transcriptional function in reporter assays as well as in a human fibroblast-to-keratinocyte conversion assay. Our studies reveal that AEC syndrome is a protein aggregation disorder and opens avenues for therapeutic intervention.
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28
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Abstract
Somatic cells can be reprogrammed to pluripotent stem cells or transdifferentiate to another lineage cell type. Much efforts have been made to unravel the epigenetic mechanisms underlying the cell fate conversion. Histone modifications as the major epigenetic regulator are implicated in various aspects of reprogramming and transdifferentiation. Here, we discuss the roles of histone modifications on reprogramming and transdifferentiation and hopefully provide new insights into induction and promotion of the cell fate conversion by modulating histone modifications.
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29
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Wessels D, Lusche DF, Voss E, Kuhl S, Buchele EC, Klemme MR, Russell KB, Ambrose J, Soll BA, Bossler A, Milhem M, Goldman C, Soll DR. Melanoma cells undergo aggressive coalescence in a 3D Matrigel model that is repressed by anti-CD44. PLoS One 2017; 12:e0173400. [PMID: 28264026 PMCID: PMC5338862 DOI: 10.1371/journal.pone.0173400] [Citation(s) in RCA: 16] [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: 12/08/2016] [Accepted: 02/20/2017] [Indexed: 12/29/2022] Open
Abstract
Using unique computer-assisted 3D reconstruction software, it was previously demonstrated that tumorigenic cell lines derived from breast tumors, when seeded in a 3D Matrigel model, grew as clonal aggregates which, after approximately 100 hours, underwent coalescence mediated by specialized cells, eventually forming a highly structured large spheroid. Non-tumorigenic cells did not undergo coalescence. Because histological sections of melanomas forming in patients suggest that melanoma cells migrate and coalesce to form tumors, we tested whether they also underwent coalescence in a 3D Matrigel model. Melanoma cells exiting fragments of three independent melanomas or from secondary cultures derived from them, and cells from the melanoma line HTB-66, all underwent coalescence mediated by specialized cells in the 3D model. Normal melanocytes did not. However, coalescence of melanoma cells differed from that of breast-derived tumorigenic cell lines in that they 1) coalesced immediately, 2) underwent coalescence as individual cells as well as aggregates, 3) underwent coalescence far faster and 4) ultimately formed long, flat, fenestrated aggregates that were extremely dynamic. A screen of 51 purified monoclonal antibodies (mAbs) targeting cell surface-associated molecules revealed that two mAbs, anti-beta 1 integrin/(CD29) and anti-CD44, blocked melanoma cell coalescence. They also blocked coalescence of tumorigenic cells derived from a breast tumor. These results add weight to the commonality of coalescence as a characteristic of tumorigenic cells, as well as the usefulness of the 3D Matrigel model and software for both investigating the mechanisms regulating tumorigenesis and screening for potential anti-tumorigenesis mAbs.
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Affiliation(s)
- Deborah Wessels
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Daniel F. Lusche
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Edward Voss
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Spencer Kuhl
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Emma C. Buchele
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Michael R. Klemme
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Kanoe B. Russell
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Joseph Ambrose
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Benjamin A. Soll
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
| | - Aaron Bossler
- Department of Molecular Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA United States of America
| | - Mohammed Milhem
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA United States of America
| | - Charles Goldman
- Mercy Hospital System of Des Moines, Des Moines, IA United States of America
| | - David R. Soll
- Developmental Studies Hybridoma Bank, Department of Biology, University of Iowa, Iowa City, IA United States of America
- * E-mail:
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30
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Varga N, Mózes J, Keegan H, White C, Kelly L, Pilkington L, Benczik M, Zsuzsanna S, Sobel G, Koiss R, Babarczi E, Nyíri M, Kovács L, Attila S, Kaltenecker B, Géresi A, Kocsis A, O'Leary J, Martin CM, Jeney C. The Value of a Novel Panel of Cervical Cancer Biomarkers for Triage of HPV Positive Patients and for Detecting Disease Progression. Pathol Oncol Res 2016; 23:295-305. [PMID: 27497597 DOI: 10.1007/s12253-016-0094-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/14/2016] [Indexed: 01/12/2023]
Abstract
In the era of primary vaccination against HPV and at the beginning of the low prevalence of cervical lesions, introduction of screening methods that can distinguish between low- and high-grade lesions is necessary in order to maintain the positive predictive value of screening. This case-control study included 562 women who attended cervical screening or were referred for colposcopy and 140 disease free controls, confirmed by histology and/or cytology. The cases were stratified by age. Using routine exfoliated liquid based cytological samples RT-PCR measurements of biomarker genes, high-risk HPV testing and liquid based cytology were performed and used to evaluate different testing protocols including sets of genes/tests with different test cut-offs for the diagnostic panels. Three new panels of cellular biomarkers for improved triage of hrHPV positive women (diagnostic panel) and for prognostic assessment of CIN lesions were proposed. The diagnostic panel (PIK3AP1, TP63 and DSG3) has the potential to distinguish cytologically normal hrHPV+ women from hrHPV+ women with CIN2+. The prognostic gene panels (KRT78, MUC5AC, BPIFB1 and CXCL13, TP63, DSG3) have the ability to differentiate hrHPV+ CIN1 and carcinoma cases. The diagnostic triage panel showed good likelihood ratios for all age groups. The panel showed age-unrelated performance and even better diagnostic value under age 30, a unique feature among the established cervical triage tests. The prognostic gene-panels demonstrated good discriminatory power and oncogenic, anti-oncogenic grouping of genes. The study highlights the potential for the gene expression panels to be used for diagnostic triage and lesion prognostics in cervical cancer screening.
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Affiliation(s)
- Norbert Varga
- CellCall Ltd, Röppentyű utca 48, Budapest, 1134, Hungary
| | - Johanna Mózes
- CellCall Ltd, Röppentyű utca 48, Budapest, 1134, Hungary
| | - Helen Keegan
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Laboratory, Department of Pathology, Coombe Women and Infants University Hospital, Dublin, 8, Ireland
| | - Christine White
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Laboratory, Department of Pathology, Coombe Women and Infants University Hospital, Dublin, 8, Ireland
| | - Lynne Kelly
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Laboratory, Department of Pathology, Coombe Women and Infants University Hospital, Dublin, 8, Ireland
| | - Loretto Pilkington
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Laboratory, Department of Pathology, Coombe Women and Infants University Hospital, Dublin, 8, Ireland
| | - Márta Benczik
- CellCall Ltd, Röppentyű utca 48, Budapest, 1134, Hungary
| | - Schaff Zsuzsanna
- 2nd Department of Pathology, Semmelweis University, Üllöi út 93, Budapest, 1091, Hungary
| | - Gábor Sobel
- 2nd Department of Obstetrics and Gynecology, Semmelweis University, Üllői út 78/a, Budapest, 1082, Hungary
| | - Róbert Koiss
- Department of Gynecology-Oncology, United Hospital of St. Stephan and Laszlo, Nagyvárad tér 1, Budapest, 1087, Hungary
| | - Edit Babarczi
- Department of Gynecology-Oncology, United Hospital of St. Stephan and Laszlo, Nagyvárad tér 1, Budapest, 1087, Hungary
| | - Miklos Nyíri
- CellCall Ltd, Röppentyű utca 48, Budapest, 1134, Hungary
| | - Laura Kovács
- CellCall Ltd, Röppentyű utca 48, Budapest, 1134, Hungary
| | - Sebe Attila
- Institute of Pathophysiology, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary
| | | | - Adrienn Géresi
- CellCall Ltd, Röppentyű utca 48, Budapest, 1134, Hungary
| | - Adrienn Kocsis
- CellCall Ltd, Röppentyű utca 48, Budapest, 1134, Hungary
| | - John O'Leary
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Laboratory, Department of Pathology, Coombe Women and Infants University Hospital, Dublin, 8, Ireland
| | - Cara M Martin
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Laboratory, Department of Pathology, Coombe Women and Infants University Hospital, Dublin, 8, Ireland
| | - Csaba Jeney
- Department of Medical Microbiology, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary.
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31
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Iacovides D, Rizki G, Lapathitis G, Strati K. Direct conversion of mouse embryonic fibroblasts into functional keratinocytes through transient expression of pluripotency-related genes. Stem Cell Res Ther 2016; 7:98. [PMID: 27473056 PMCID: PMC4966867 DOI: 10.1186/s13287-016-0357-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/12/2016] [Accepted: 06/29/2016] [Indexed: 01/14/2023] Open
Abstract
The insufficient ability of specialized cells such as neurons, cardiac myocytes, and epidermal cells to regenerate after tissue damage poses a great challenge to treat devastating injuries and ailments. Recent studies demonstrated that a diverse array of cell types can be directly derived from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), or somatic cells by combinations of specific factors. The use of iPSCs and direct somatic cell fate conversion, or transdifferentiation, holds great promise for regenerative medicine as these techniques may circumvent obstacles related to immunological rejection and ethical considerations. However, producing iPSC-derived keratinocytes requires a lengthy two-step process of initially generating iPSCs and subsequently differentiating into skin cells, thereby elevating the risk of cellular damage accumulation and tumor formation. In this study, we describe the reprogramming of mouse embryonic fibroblasts into functional keratinocytes via the transient expression of pluripotency factors coupled with directed differentiation. The isolation of an iPSC intermediate is dispensable when using this method. Cells derived with this approach, termed induced keratinocytes (iKCs), morphologically resemble primary keratinocytes. Furthermore they express keratinocyte-specific markers, downregulate mesenchymal markers as well as the pluripotency factors Oct4, Sox2, and Klf4, and they show important functional characteristics of primary keratinocytes. iKCs can be further differentiated by high calcium administration in vitro and are capable of regenerating a fully stratified epidermis in vivo. Efficient conversion of somatic cells into keratinocytes could have important implications for studying genetic skin diseases and designing regenerative therapies to ameliorate devastating skin conditions.
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Affiliation(s)
- Demetris Iacovides
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Gizem Rizki
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.,Current address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Georgios Lapathitis
- Transgenic Mouse Facility, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Katerina Strati
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
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32
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Wang Y, Arribas-Layton M, Chen Y, Lykke-Andersen J, Sen GL. DDX6 Orchestrates Mammalian Progenitor Function through the mRNA Degradation and Translation Pathways. Mol Cell 2015; 60:118-30. [PMID: 26412305 DOI: 10.1016/j.molcel.2015.08.014] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 06/11/2015] [Accepted: 08/18/2015] [Indexed: 12/26/2022]
Abstract
In adult tissues, stem and progenitor cells must balance proliferation and differentiation to maintain homeostasis. How this is done is unclear. Here, we show that the DEAD box RNA helicase, DDX6 is necessary for maintaining adult progenitor cell function. DDX6 loss results in premature differentiation and decreased proliferation of epidermal progenitor cells. To maintain self-renewal, DDX6 associates with YBX1 to bind the stem loops found in the 3' UTRs of regulators of proliferation/self-renewal (CDK1, EZH2) and recruit them to EIF4E to facilitate their translation. To prevent premature differentiation of progenitor cells, DDX6 regulates the 5' UTR of differentiation inducing transcription factor, KLF4 and degrades its transcripts through association with mRNA degradation proteins. Our results demonstrate that progenitor function is maintained by DDX6 complexes through two distinct pathways that include the degradation of differentiation-inducing transcripts and by promoting the translation of self-renewal and proliferation mRNAs.
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Affiliation(s)
- Ying Wang
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093-0869, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0869, USA; UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Marc Arribas-Layton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Yifang Chen
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093-0869, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0869, USA; UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - George L Sen
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093-0869, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0869, USA; UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA.
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33
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Abstract
Epithelial to mesenchymal transition transcription factors (EMT-TFs) such as SNAI2 have been found to be expressed endogenously in epidermal stem and progenitor cells and downregulated upon differentiation. The presence of SNAI2 in progenitor cells is necessary to repress the expression of differentiation genes by binding directly to their promoters. SNAI2 is downregulated upon differentiation which allows expression of differentiation genes. Furthermore overexpression of SNAI2 can block the differentiation process suggesting that the levels of SNAI2 are crucial to epidermal cell fate decisions. To address on a genome wide level the genes that are impacted by changing the levels of SNAI2, we performed microarray analysis on SNAI2 knockdown and overexpressing epidermal progenitor cells. Here we provide detailed methods and analysis on these microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE55269.
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34
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Transdifferentiation of Human Hair Follicle Mesenchymal Stem Cells into Red Blood Cells by OCT4. Stem Cells Int 2015; 2015:389628. [PMID: 25755671 PMCID: PMC4337757 DOI: 10.1155/2015/389628] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
Shortage of red blood cells (RBCs, erythrocytes) can have potentially life-threatening consequences for rare or unusual blood type patients with massive blood loss resulting from various conditions. Erythrocytes have been derived from human pluripotent stem cells (PSCs), but the risk of potential tumorigenicity cannot be ignored, and a majority of these cells produced from PSCs express embryonic ε- and fetal γ-globins with little or no adult β-globin and remain nucleated. Here we report a method to generate erythrocytes from human hair follicle mesenchymal stem cells (hHFMSCs) by enforcing OCT4 gene expression and cytokine stimulation. Cells generated from hHFMSCs expressed mainly the adult β-globin chain with minimum level of the fetal γ-globin chain. Furthermore, these cells also underwent multiple maturation events and formed enucleated erythrocytes with a biconcave disc shape. Gene expression analyses showed that OCT4 regulated the expression of genes associated with both pluripotency and erythroid development during hHFMSC transdifferentiation toward erythroid cells. These findings show that mature erythrocytes can be generated from adult somatic cells, which may serve as an alternative source of RBCs for potential autologous transfusion.
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35
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Sethi I, Sinha S, Buck MJ. Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes. BMC Genomics 2014; 15:1042. [PMID: 25433490 PMCID: PMC4302094 DOI: 10.1186/1471-2164-15-1042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/18/2014] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The Transcription Factor (TF) p63 is a master regulator of epidermal development and differentiation as evident from the remarkable skin phenotype of p63 mouse knockouts. Furthermore, ectopic expression of p63 alone is sufficient to convert simple epithelium into stratified epithelial tissues in vivo and p63 is required for efficient transdifferentiation of fibroblasts into keratinocytes. However, little is known about the molecular mechanisms of p63 function, in particular how it selects its target sites in the genome. p63, which acts both as an activator and repressor of transcription, recognizes a canonical binding motif that occurs over 1 million times in the human genome. But, in human keratinocytes less than 12,000 of these sites are bound in vivo suggesting that underlying chromatin architecture and cooperating TFs mediate p63-genome interactions. RESULTS We find that the chromatin architecture at p63-bound targets possess distinctive features and can be used to categorize p63 targets into proximal promoters (1%), enhancers (59%) and repressed or inactive (40%) regulatory elements. Our analysis shows that the chromatin modifications H3K4me1, H3K27me3, along with overall chromatin accessibility status can accurately predict bonafide p63-bound sites without a priori DNA sequence information. Interestingly, however there exists a qualitative correlation between the p63 binding motif and accessibility and H3K4me1 levels. Furthermore, we use a comprehensive in silico approach that leverages ENCODE data to identify several known TFs such as AP1, AP2 and novel TFs (RFX5 for e.g.) that can potentially cooperate with p63 to modulate its myriad biological functions in keratinocytes. CONCLUSIONS Our analysis shows that p63 bound genomic locations in keratinocytes are accessible, marked by active histone modifications, and co-targeted by other developmentally important transcriptional regulators. Collectively, our results suggest that p63 might actively remodel and/or influence chromatin dynamics at its target sites and in the process dictate its own DNA binding and possibly that of adjacent TFs.
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Affiliation(s)
| | - Satrajit Sinha
- Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, USA.
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