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Dou C, Wu L, Zhang J, He H, Xu T, Yu Z, Su P, Zhang X, Wang J, Miao YL, Zhou J. The transcriptional activator Klf5 recruits p300-mediated H3K27ac for maintaining trophoblast stem cell pluripotency. J Mol Cell Biol 2024; 15:mjad045. [PMID: 37533201 PMCID: PMC10768793 DOI: 10.1093/jmcb/mjad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 08/04/2023] Open
Abstract
The effective proliferation and differentiation of trophoblast stem cells (TSCs) is indispensable for the development of the placenta, which is the key to maintaining normal fetal growth during pregnancy. Kruppel-like factor 5 (Klf5) is implicated in the activation of pluripotency gene expression in embryonic stem cells (ESCs), yet its function in TSCs is poorly understood. Here, we showed that Klf5 knockdown resulted in the downregulation of core TSC-specific genes, consequently causing rapid differentiation of TSCs. Consistently, Klf5-depleted embryos lost the ability to establish TSCs in vitro. At the molecular level, Klf5 preferentially occupied the proximal promoter regions and maintained an open chromatin architecture of key TSC-specific genes. Deprivation of Klf5 impaired the enrichment of p300, a major histone acetyl transferase of H3 lysine 27 acetylation (H3K27ac), and further reduced the occupancy of H3K27ac at promoter regions, leading to decreased transcriptional activity of TSC pluripotency genes. Thus, our findings highlight a novel mechanism of Klf5 in regulating the self-renewal and differentiation of TSCs and provide a reference for understanding placental development and improving pregnancy rates.
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Affiliation(s)
- Chengli Dou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Hainan He
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Tian Xu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Zhisheng Yu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Peng Su
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Junling Wang
- Department of Reproductive Medicine, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic, Edong Healthcare Group, Huangshi 435000, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jilong Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
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2
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Alanis-Lobato G, Bartlett TE, Huang Q, Simon CS, McCarthy A, Elder K, Snell P, Christie L, Niakan KK. MICA: a multi-omics method to predict gene regulatory networks in early human embryos. Life Sci Alliance 2024; 7:e202302415. [PMID: 37879938 PMCID: PMC10599980 DOI: 10.26508/lsa.202302415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
Recent advances in single-cell omics have transformed characterisation of cell types in challenging-to-study biological contexts. In contexts with limited single-cell samples, such as the early human embryo inference of transcription factor-gene regulatory network (GRN) interactions is especially difficult. Here, we assessed application of different linear or non-linear GRN predictions to single-cell simulated and human embryo transcriptome datasets. We also compared how expression normalisation impacts on GRN predictions, finding that transcripts per million reads outperformed alternative methods. GRN inferences were more reproducible using a non-linear method based on mutual information (MI) applied to single-cell transcriptome datasets refined with chromatin accessibility (CA) (called MICA), compared with alternative network prediction methods tested. MICA captures complex non-monotonic dependencies and feedback loops. Using MICA, we generated the first GRN inferences in early human development. MICA predicted co-localisation of the AP-1 transcription factor subunit proto-oncogene JUND and the TFAP2C transcription factor AP-2γ in early human embryos. Overall, our comparative analysis of GRN prediction methods defines a pipeline that can be applied to single-cell multi-omics datasets in especially challenging contexts to infer interactions between transcription factor expression and target gene regulation.
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Affiliation(s)
| | | | - Qiulin Huang
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
- https://ror.org/013meh722 Department of Physiology, Development and Neuroscience, The Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Claire S Simon
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | | | | | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
- https://ror.org/013meh722 Department of Physiology, Development and Neuroscience, The Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Wellcome - Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
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3
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Zhu W, Bu G, Hu R, Zhang J, Qiao L, Zhou K, Wang T, Li Q, Zhang J, Wu L, Xie Y, Hu T, Yang S, Guan J, Chu X, Shi J, Zhang X, Lu F, Liu X, Miao YL. KLF4 facilitates chromatin accessibility remodeling in porcine early embryos. SCIENCE CHINA. LIFE SCIENCES 2024; 67:96-112. [PMID: 37698691 DOI: 10.1007/s11427-022-2349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/20/2023] [Indexed: 09/13/2023]
Abstract
Chromatin accessibility remodeling driven by pioneer factors is critical for the development of early embryos. Current studies have illustrated several pioneer factors as being important for agricultural animals, but what are the pioneer factors and how the pioneer factors remodel the chromatin accessibility in porcine early embryos is not clear. By employing low-input DNase-seq (liDNase-seq), we profiled the landscapes of chromatin accessibility in porcine early embryos and uncovered a unique chromatin accessibility reprogramming pattern during porcine preimplantation development. Our data revealed that KLF4 played critical roles in remodeling chromatin accessibility in porcine early embryos. Knocking down of KLF4 led to the reduction of chromatin accessibility in early embryos, whereas KLF4 overexpression promoted the chromatin openness in porcine blastocysts. Furthermore, KLF4 deficiency resulted in mitochondrial dysfunction and developmental failure of porcine embryos. In addition, we found that overexpression of KLF4 in blastocysts promoted lipid droplet accumulation, whereas knockdown of KLF4 disrupted this process. Taken together, our study revealed the chromatin accessibility dynamics and identified KLF4 as a key regulator in chromatin accessibility and cellular metabolism during porcine preimplantation embryo development.
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Affiliation(s)
- Wei Zhu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Guowei Bu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Ruifeng Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jixiang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lianyong Qiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kai Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Tingting Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Qiao Li
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Yali Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taotao Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Shichun Yang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jiaqi Guan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Xiaoyu Chu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Juanjuan Shi
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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4
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Selvarajah K, Tan JJ, Shaharuddin B. Corneal Epithelial Development and the Role of Induced Pluripotent Stem Cells for Regeneration. Curr Stem Cell Res Ther 2024; 19:292-306. [PMID: 36915985 DOI: 10.2174/1574888x18666230313094121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/02/2022] [Accepted: 01/02/2023] [Indexed: 03/16/2023]
Abstract
Severe corneal disorders due to infective aetiologies, trauma, chemical injuries, and chronic cicatricial inflammations, are among vision-threatening pathologies leading to permanent corneal scarring. The whole cornea or lamellar corneal transplantation is often used as a last resort to restore vision. However, limited autologous tissue sources and potential adverse post-allotransplantation sequalae urge the need for more robust and strategic alternatives. Contemporary management using cultivated corneal epithelial transplantation has paved the way for utilizing stem cells as a regenerative potential. Humaninduced pluripotent stem cells (hiPSCs) can generate ectodermal progenitors and potentially be used for ocular surface regeneration. This review summarizes the process of corneal morphogenesis and the signaling pathways underlying the development of corneal epithelium, which is key to translating the maturation and differentiation process of hiPSCs in vitro. The current state of knowledge and methodology for driving efficient corneal epithelial cell differentiation from pluripotent stem cells are highlighted.
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Affiliation(s)
- Komathi Selvarajah
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
| | - Jun Jie Tan
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
| | - Bakiah Shaharuddin
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
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5
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Torre D, Francoeur NJ, Kalma Y, Gross Carmel I, Melo BS, Deikus G, Allette K, Flohr R, Fridrikh M, Vlachos K, Madrid K, Shah H, Wang YC, Sridhar SH, Smith ML, Eliyahu E, Azem F, Amir H, Mayshar Y, Marazzi I, Guccione E, Schadt E, Ben-Yosef D, Sebra R. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun 2023; 14:6902. [PMID: 37903791 PMCID: PMC10616205 DOI: 10.1038/s41467-023-42558-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023] Open
Abstract
Human preimplantation development involves extensive remodeling of RNA expression and splicing. However, its transcriptome has been compiled using short-read sequencing data, which fails to capture most full-length mRNAs. Here, we generate an isoform-resolved transcriptome of early human development by performing long- and short-read RNA sequencing on 73 embryos spanning the zygote to blastocyst stages. We identify 110,212 unannotated isoforms transcribed from known genes, including highly conserved protein-coding loci and key developmental regulators. We further identify 17,964 isoforms from 5,239 unannotated genes, which are largely non-coding, primate-specific, and highly associated with transposable elements. These isoforms are widely supported by the integration of published multi-omics datasets, including single-cell 8CLC and blastoid studies. Alternative splicing and gene co-expression network analyses further reveal that embryonic genome activation is associated with splicing disruption and transient upregulation of gene modules. Together, these findings show that the human embryo transcriptome is far more complex than currently known, and will act as a valuable resource to empower future studies exploring development.
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Affiliation(s)
- Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Yael Kalma
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Ilana Gross Carmel
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Betsaida S Melo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ron Flohr
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel
| | - Maya Fridrikh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shwetha H Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Foad Azem
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Hadar Amir
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Yoav Mayshar
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Ivan Marazzi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT); Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalit Ben-Yosef
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel.
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel.
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel.
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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6
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Lyu Y, Guan Y, Deliu L, Humphrey E, Frontera JK, Yang YJ, Zamler D, Kim KH, Mohanty V, Jin K, Mohanty V, Liu V, Dou J, Veillon LJ, Kumar SV, Lorenzi PL, Chen Y, McAndrews KM, Grivennikov S, Song X, Zhang J, Xi Y, Wang J, Chen K, Nagarajan P, Ge Y. KLF5 governs sphingolipid metabolism and barrier function of the skin. Genes Dev 2022; 36:gad.349662.122. [PMID: 36008138 PMCID: PMC9480852 DOI: 10.1101/gad.349662.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/15/2022] [Indexed: 01/03/2023]
Abstract
Stem cells are fundamental units of tissue remodeling whose functions are dictated by lineage-specific transcription factors. Home to epidermal stem cells and their upward-stratifying progenies, skin relies on its secretory functions to form the outermost protective barrier, of which a transcriptional orchestrator has been elusive. KLF5 is a Krüppel-like transcription factor broadly involved in development and regeneration whose lineage specificity, if any, remains unclear. Here we report KLF5 specifically marks the epidermis, and its deletion leads to skin barrier dysfunction in vivo. Lipid envelopes and secretory lamellar bodies are defective in KLF5-deficient skin, accompanied by preferential loss of complex sphingolipids. KLF5 binds to and transcriptionally regulates genes encoding rate-limiting sphingolipid metabolism enzymes. Remarkably, skin barrier defects elicited by KLF5 ablation can be rescued by dietary interventions. Finally, we found that KLF5 is widely suppressed in human diseases with disrupted epidermal secretion, and its regulation of sphingolipid metabolism is conserved in human skin. Altogether, we established KLF5 as a disease-relevant transcription factor governing sphingolipid metabolism and barrier function in the skin, likely representing a long-sought secretory lineage-defining factor across tissue types.
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Affiliation(s)
- Ying Lyu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yinglu Guan
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lisa Deliu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ericka Humphrey
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Joanna K Frontera
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Youn Joo Yang
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Daniel Zamler
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kun Hee Kim
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kevin Jin
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Rice University, Houston, Texas 77005, USA
| | - Vakul Mohanty
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Rice University, Houston, Texas 77005, USA
| | - Virginia Liu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Rice University, Houston, Texas 77005, USA
| | - Jinzhuang Dou
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lucas J Veillon
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shwetha V Kumar
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yang Chen
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kathleen M McAndrews
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sergei Grivennikov
- Department of Medicine, Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Department of Biomedical Sciences, Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yejing Ge
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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7
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Liberti DC, Liberti Iii WA, Kremp MM, Penkala IJ, Cardenas-Diaz FL, Morley MP, Babu A, Zhou S, Fernandez Iii RJ, Morrisey EE. Klf5 defines alveolar epithelial type 1 cell lineage commitment during lung development and regeneration. Dev Cell 2022; 57:1742-1757.e5. [PMID: 35803279 DOI: 10.1016/j.devcel.2022.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 06/13/2022] [Indexed: 12/11/2022]
Abstract
Alveolar epithelial cell fate decisions drive lung development and regeneration. Using transcriptomic and epigenetic profiling coupled with genetic mouse and organoid models, we identified the transcription factor Klf5 as an essential determinant of alveolar epithelial cell fate across the lifespan. We show that although dispensable for both adult alveolar epithelial type 1 (AT1) and alveolar epithelial type 2 (AT2) cell homeostasis, Klf5 enforces AT1 cell lineage fidelity during development. Using infectious and non-infectious models of acute respiratory distress syndrome, we demonstrate that Klf5 represses AT2 cell proliferation and enhances AT2-AT1 cell differentiation in a spatially restricted manner during lung regeneration. Moreover, ex vivo organoid assays identify that Klf5 reduces AT2 cell sensitivity to inflammatory signaling to drive AT2-AT1 cell differentiation. These data define the roll of a major transcriptional regulator of AT1 cell lineage commitment and of the AT2 cell response to inflammatory crosstalk during lung regeneration.
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Affiliation(s)
- Derek C Liberti
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine Philadelphia, PA 19104, USA
| | - William A Liberti Iii
- Department of Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley, CA 94720, USA
| | - Madison M Kremp
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian J Penkala
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine Philadelphia, PA 19104, USA
| | - Fabian L Cardenas-Diaz
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael P Morley
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apoorva Babu
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Su Zhou
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rafael J Fernandez Iii
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edward E Morrisey
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Seong J, Frias-Aldeguer J, Holzmann V, Kagawa H, Sestini G, Heidari Khoei H, Scholte Op Reimer Y, Kip M, Pradhan SJ, Verwegen L, Vivié J, Li L, Alemany A, Korving J, Darmis F, van Oudenaarden A, Ten Berge D, Geijsen N, Rivron NC. Epiblast inducers capture mouse trophectoderm stem cells in vitro and pattern blastoids for implantation in utero. Cell Stem Cell 2022; 29:1102-1118.e8. [PMID: 35803228 DOI: 10.1016/j.stem.2022.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
The embryo instructs the allocation of cell states to spatially regulate functions. In the blastocyst, patterning of trophoblast (TR) cells ensures successful implantation and placental development. Here, we defined an optimal set of molecules secreted by the epiblast (inducers) that captures in vitro stable, highly self-renewing mouse trophectoderm stem cells (TESCs) resembling the blastocyst stage. When exposed to suboptimal inducers, these stem cells fluctuate to form interconvertible subpopulations with reduced self-renewal and facilitated differentiation, resembling peri-implantation cells, known as TR stem cells (TSCs). TESCs have enhanced capacity to form blastoids that implant more efficiently in utero due to inducers maintaining not only local TR proliferation and self-renewal, but also WNT6/7B secretion that stimulates uterine decidualization. Overall, the epiblast maintains sustained growth and decidualization potential of abutting TR cells, while, as known, distancing imposed by the blastocyst cavity differentiates TR cells for uterus adhesion, thus patterning the essential functions of implantation.
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Affiliation(s)
- Jinwoo Seong
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Javier Frias-Aldeguer
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Maastricht University, Maastricht, the Netherlands
| | - Viktoria Holzmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Harunobu Kagawa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Giovanni Sestini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heidar Heidari Khoei
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Yvonne Scholte Op Reimer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Maarten Kip
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Saurabh J Pradhan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Lucas Verwegen
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Judith Vivié
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Linfeng Li
- Maastricht University, Maastricht, the Netherlands
| | - Anna Alemany
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Frank Darmis
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | | | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Niels Geijsen
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Department of Anatomy and Embryology, LUMC, Leiden University, Leiden, the Netherlands
| | - Nicolas C Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria; Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Maastricht University, Maastricht, the Netherlands.
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9
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Ito J, Seita Y, Kojima S, Parrish NF, Sasaki K, Sato K. A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells. PLoS Genet 2022; 18:e1009846. [PMID: 35551519 PMCID: PMC9128956 DOI: 10.1371/journal.pgen.1009846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/24/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
Mammalian germ cells stem from primordial germ cells (PGCs). Although the gene regulatory network controlling the development of germ cells such as PGCs is critical for ensuring gamete integrity, substantial differences exist in this network among mammalian species, suggesting that this network has been modified during mammalian evolution. Here, we show that a hominoid-specific group of endogenous retroviruses, LTR5_Hs, discloses enhancer-like signatures in human in vitro-induced PGCs, PGC-like cells (PGCLCs). Human PGCLCs exhibit a transcriptome signature similar to that of naïve-state pluripotent cells. LTR5_Hs are epigenetically activated in both PGCLCs and naïve pluripotent cells, and the expression of genes in the vicinity of LTR5_Hs is coordinately upregulated in these cell types, contributing to the establishment of the transcriptome similarity between these cell types. LTR5_Hs are preferentially bound by transcription factors that are highly expressed in both PGCLCs and naïve pluripotent cells (KLF4, TFAP2C, NANOG, and CBFA2T2), suggesting that these transcription factors contribute to the epigenetic activation of LTR5_Hs in these cells. Comparative transcriptome analysis between humans and macaques suggests that the expression of many genes in PGCLCs and naïve pluripotent cells is upregulated by LTR5_Hs insertions in the hominoid lineage. Together, this study suggests that LTR5_Hs insertions may have finetuned the gene regulatory network shared between PGCLCs and naïve pluripotent cells and coordinately altered the gene expression in these cells during hominoid evolution. To ensure the health of the next generation and the continuation of a species, the development of germ cells, including primordial germ cells (PGCs), is strictly controlled by a complex gene regulatory network. Nevertheless, the gene regulatory network controlling the germ cell development has been substantially diversified during mammalian or even primate evolution. Here, our integrated analyses using multiomics and comparative genomics resources suggest that hominoid-specific insertions of endogenous retroviruses are epigenetically activated in both in vitro-induced PGCs and naïve pluripotent cells and may have coordinately altered the expression of the adjacent genes in these cells. This study provides evidence suggesting that the gene regulatory network shared between PGCs and naïve pluripotent cells may have been rewired by ERV insertions during hominoid evolution.
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Affiliation(s)
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasunari Seita
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Bell Research Center for Reproductive Health and Cancer, Nagoya, Aichi, Japan
| | - Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Kotaro Sasaki
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (KS); (KS)
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- * E-mail: (KS); (KS)
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10
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Talukdar KR, Saikia P, Sarma HN. Kruppel-like factor 5 (Klf5) in fetal-maternal tissue during periimplantation and effects of ovarian steroid hormone antagonist on its expression during uterine receptivity of albino mice. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2022. [DOI: 10.1186/s43043-021-00092-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Embryo implantation is a tightly regulated sequence of events regulated by ovarian steroids, estrogen and progesterone, and their downstream targets. Ovarian steroids regulate most of the genes involved in embryo implantation and pregnancy. However, some factors are not regulated by ovarian steroids, estrogen, progesterone, or both. Kruppel-like factor 5 (Klf5) is an example of an ovarian steroid–independent factor having a role in cellular proliferation, differentiation. The detailed expression profile of Klf5 during uterine receptivity and periimplantation has not been studied till now. In the present research work, an attempt was made to investigate the expression pattern of Klf5 in mice fetal-maternal tissue during periimplantation (day 4–day 8). The expressional and functional independence of Klf5 on the ovarian steroids was studied using estrogen and progesterone antagonist. The study was carried out in female Swiss albino mice of LACA strain during the periimplantation period. KLF5 was localized in the fetal-maternal tissues using the immunofluorescence technique in paraffin-embedded tissues. Ovarian steroid antagonists were administered subcutaneously from day 1 to day 3 of gestation, and the uterus was collected on the morning of day 4. Klf5 protein and mRNA levels were studied by western blot and quantitative real-time PCR (qPCR), respectively.
Results
KLF5 was localized in the embryo, uterine luminal epithelium, glandular epithelium, and proliferating stromal cells during periimplantation. In ovarian steroid antagonist–treated groups, KLF5 was localized in the luminal and glandular epithelium and stroma. Western blot and qPCR confirmed translation and transcription of KLF5 during the experimental period. The KLF5 protein level significantly increased on day 6, day 7, and day 8 when compared with day 4 (P < 0.05). The mRNA level of Klf5 increased significantly on day 7 and day 8 when compared with day 4 (P < 0.05). In ovarian steroid antagonist–treated groups, protein and mRNA corresponding to Klf5 were observed. From this finding, it can be assumed that Klf5 may be a steroid-independent factor expressed during uterine receptivity.
Conclusion
Spatiotemporal KLF5 expression in fetal-maternal tissue was observed during the experimental period. The results suggest that Klf5 is an ovarian steroid–independent factor that may play a pivotal role in implantation, decidualization, and embryogenesis.
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11
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Takeda T, Yokoyama Y, Takahashi H, Okuzaki D, Asai K, Itakura H, Miyoshi N, Kobayashi S, Uemura M, Fujita T, Ueno H, Mori M, Doki Y, Fujii H, Eguchi H, Yamamoto H. A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells. Br J Cancer 2022; 126:109-119. [PMID: 34707247 PMCID: PMC8727571 DOI: 10.1038/s41416-021-01579-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND KLF5 plays a crucial role in stem cells of colorectum in cooperation with Lgr5 gene. In this study, we aimed to explicate a regulatory mechanism of the KLF5 gene product from a view of three-dimensional genome structure in colorectal cancer (CRC). METHODS In vitro engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP)-seq method was used to identify the regions that bind to the KLF5 promoter. RESULTS We revealed that the KLF5 promoter region interacted with the KLF5 enhancer region as well as the transcription start site (TSS) region of the Colon Cancer Associated Transcript 1 (CCAT1) gene. Notably, the heterodeletion mutants of KLF5 enhancer impaired the cancer stem-like properties of CRC cells. The KLF5 protein participated in the core-regulatory circuitry together with co-factors (BRD4, MED1, and RAD21), which constructs the three-dimensional genome structures consisting of KLF5 promoter, enhancer and CCAT1 TSS region. In vitro analysis indicated that KLF5 regulated CCAT1 expression and we found that CCAT1 expression was highly correlated with KLF5 expression in CRC clinical samples. CONCLUSIONS Our data propose the mechanistic insight that the KLF5 protein constructs the core-regulatory circuitry with co-factors in the three-dimensional genome structure and coordinately regulates KLF5 and CCAT1 expression in CRC.
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Affiliation(s)
- Takashi Takeda
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuhki Yokoyama
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7, Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hidekazu Takahashi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kaho Asai
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroaki Itakura
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norikatsu Miyoshi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shogo Kobayashi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mamoru Uemura
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hiroo Ueno
- Department of Stem Cell Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Masaki Mori
- School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Yuichiro Doki
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hirofumi Yamamoto
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
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12
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Lea RA, McCarthy A, Boeing S, Fallesen T, Elder K, Snell P, Christie L, Adkins S, Shaikly V, Taranissi M, Niakan KK. KLF17 promotes human naïve pluripotency but is not required for its establishment. Development 2021; 148:272511. [PMID: 34661235 PMCID: PMC8645209 DOI: 10.1242/dev.199378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/11/2021] [Indexed: 12/11/2022]
Abstract
Current knowledge of the transcriptional regulation of human pluripotency is incomplete, with lack of interspecies conservation observed. Single-cell transcriptomics analysis of human embryos previously enabled us to identify transcription factors, including the zinc-finger protein KLF17, that are enriched in the human epiblast and naïve human embryonic stem cells (hESCs). Here, we show that KLF17 is expressed coincident with the known pluripotency-associated factors NANOG and SOX2 across human blastocyst development. We investigate the function of KLF17 using primed and naïve hESCs for gain- and loss-of-function analyses. We find that ectopic expression of KLF17 in primed hESCs is sufficient to induce a naïve-like transcriptome and that KLF17 can drive transgene-mediated resetting to naïve pluripotency. This implies a role for KLF17 in establishing naïve pluripotency. However, CRISPR-Cas9-mediated knockout studies reveal that KLF17 is not required for naïve pluripotency acquisition in vitro. Transcriptome analysis of naïve hESCs identifies subtle effects on metabolism and signalling pathways following KLF17 loss of function, and possible redundancy with other KLF paralogues. Overall, we show that KLF17 is sufficient, but not necessary, for naïve pluripotency under the given in vitro conditions. Summary: Given that KLF17 was shown to be sufficient, but not necessary, to establish naïve pluripotent hESCs, KLF17 might function as a peripheral regulator of human pluripotent stem cells.
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Affiliation(s)
- Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Todd Fallesen
- Crick Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kay Elder
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | - Phil Snell
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | | | - Sarah Adkins
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | - Valerie Shaikly
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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13
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Kinisu M, Choi YJ, Cattoglio C, Liu K, Roux de Bezieux H, Valbuena R, Pum N, Dudoit S, Huang H, Xuan Z, Kim SY, He L. Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes. Cell Rep 2021; 37:109982. [PMID: 34758315 PMCID: PMC8711565 DOI: 10.1016/j.celrep.2021.109982] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 07/30/2021] [Accepted: 10/20/2021] [Indexed: 01/05/2023] Open
Abstract
Early blastomeres of mouse preimplantation embryos exhibit bi-potential cell fate, capable of generating both embryonic and extra-embryonic lineages in blastocysts. Here we identify three major two-cell-stage (2C)-specific endogenous retroviruses (ERVs) as the molecular hallmark of this bi-potential plasticity. Using the long terminal repeats (LTRs) of all three 2C-specific ERVs, we identify Krüppel-like factor 5 (Klf5) as their major upstream regulator. Klf5 is essential for bi-potential cell fate; a single Klf5-overexpressing embryonic stem cell (ESC) generates terminally differentiated embryonic and extra-embryonic lineages in chimeric embryos, and Klf5 directly induces inner cell mass (ICM) and trophectoderm (TE) specification genes. Intriguingly, Klf5 and Klf4 act redundantly during ICM specification, whereas Klf5 deficiency alone impairs TE specification. Klf5 is regulated by multiple 2C-specific transcription factors, particularly Dux, and the Dux/Klf5 axis is evolutionarily conserved. The 2C-specific transcription program converges on Klf5 to establish bi-potential cell fate, enabling a cell state with dual activation of ICM and TE genes. Using multiple 2C-specific ERV cell fate markers, Kinisu et al. identify Klf5 as a key transcription factor that confers a 2C-like developmental potential and activates ICM and TE specification genes. Klf5 and Klf4 act redundantly for ICM and TE specification in mouse preimplantation embryos.
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Affiliation(s)
- Martin Kinisu
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Yong Jin Choi
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Claudia Cattoglio
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ke Liu
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hector Roux de Bezieux
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raeline Valbuena
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Nicole Pum
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA
| | - Sandrine Dudoit
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Haiyan Huang
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zhenyu Xuan
- Department of Molecular and Cell Biology, University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Sang Yong Kim
- Department of Pathology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94705, USA.
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14
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The Modes of Dysregulation of the Proto-Oncogene T-Cell Leukemia/Lymphoma 1A. Cancers (Basel) 2021; 13:cancers13215455. [PMID: 34771618 PMCID: PMC8582492 DOI: 10.3390/cancers13215455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/19/2022] Open
Abstract
Simple Summary T-cell leukemia/lymphoma 1A (TCL1A) is a proto-oncogene that is mainly expressed in embryonic and fetal tissues, as well as in some lymphatic cells. It is frequently overexpressed in a variety of T- and B-cell lymphomas and in some solid tumors. In chronic lymphocytic leukemia and in T-prolymphocytic leukemia, TCL1A has been implicated in the pathogenesis of these conditions, and high-level TCL1A expression correlates with more aggressive disease characteristics and poorer patient survival. Despite the modes of TCL1A (dys)regulation still being incompletely understood, there are recent advances in understanding its (post)transcriptional regulation. This review summarizes the current concepts of TCL1A’s multi-faceted modes of regulation. Understanding how TCL1A is deregulated and how this can lead to tumor initiation and sustenance can help in future approaches to interfere in its oncogenic actions. Abstract Incomplete biological concepts in lymphoid neoplasms still dictate to a large extent the limited availability of efficient targeted treatments, which entertains the mostly unsatisfactory clinical outcomes. Aberrant expression of the embryonal and lymphatic TCL1 family of oncogenes, i.e., the paradigmatic TCL1A, but also TML1 or MTCP1, is causally implicated in T- and B-lymphocyte transformation. TCL1A also carries prognostic information in these particular T-cell and B-cell tumors. More recently, the TCL1A oncogene has been observed also in epithelial tumors as part of oncofetal stemness signatures. Although the concepts on the modes of TCL1A dysregulation in lymphatic neoplasms and solid tumors are still incomplete, there are recent advances in defining the mechanisms of its (de)regulation. This review presents a comprehensive overview of TCL1A expression in tumors and the current understanding of its (dys)regulation via genomic aberrations, epigenetic modifications, or deregulation of TCL1A-targeting micro RNAs. We also summarize triggers that act through such transcriptional and translational regulation, i.e., altered signals by the tumor microenvironment. A refined mechanistic understanding of these modes of dysregulations together with improved concepts of TCL1A-associated malignant transformation can benefit future approaches to specifically interfere in TCL1A-initiated or -driven tumorigenesis.
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Bogliotti YS, Chung N, Paulson EE, Chitwood J, Halstead M, Kern C, Schultz RM, Ross PJ. Transcript profiling of bovine embryos implicates specific transcription factors in the maternal-to-embryo transition. Biol Reprod 2021; 102:671-679. [PMID: 31711115 DOI: 10.1093/biolre/ioz209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/29/2019] [Accepted: 11/01/2019] [Indexed: 12/28/2022] Open
Abstract
Full-grown oocytes are transcriptionally quiescent. Following maturation and fertilization, the early stages of embryonic development occur in the absence (or low levels) of transcription that results in a period of development relying on maternally derived products (e.g., mRNAs and proteins). Two critical steps occur during the transition from maternal to embryo control of development: maternal mRNA clearance and embryonic genome activation with an associated dramatic reprogramming of gene expression required for further development. By combining an RNA polymerase II inhibitor with RNA sequencing, we were able not only to distinguish maternally derived from embryonic transcripts in bovine preimplantation embryos but also to establish that embryonic gene activation is required for clearance of maternal mRNAs as well as to identify putative transcription factors that are likely critical for early bovine development.
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Affiliation(s)
| | - Nhi Chung
- Department of Animal Science, University of California, Davis, CA, USA
| | - Erika E Paulson
- Department of Animal Science, University of California, Davis, CA, USA
| | - James Chitwood
- Department of Animal Science, University of California, Davis, CA, USA
| | - Michelle Halstead
- Department of Animal Science, University of California, Davis, CA, USA
| | - Colin Kern
- Department of Animal Science, University of California, Davis, CA, USA
| | - Richard M Schultz
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA, and.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, CA, USA
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Li L, Wang H, Chen X, Li X, Wang G, Jie Z, Zhao X, Sun X, Huang H, Fan S, Xie Z, Wang J. Oxidative Stress-Induced Hypermethylation of KLF5 Promoter Mediated by DNMT3B Impairs Osteogenesis by Diminishing the Interaction with β-Catenin. Antioxid Redox Signal 2021; 35:1-20. [PMID: 33588625 DOI: 10.1089/ars.2020.8200] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aims: Emerging evidence suggests that the pathogenesis of osteoporosis, characterized by impaired osteogenesis, is shifting from estrogen centric to oxidative stress. Our previous studies have shown that the zinc-finger transcription factor krüppel-like factor 5 (KLF5) plays a key role in the degeneration of nucleus pulposus and cartilage. However, its role in osteoporosis remains unknown. We aimed to investigate the effect and mechanism of KLF5 on osteogenesis under oxidative stress. Results: First, KLF5 was required for osteogenesis and stimulated osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). KLF5 was hypermethylated and downregulated in ovariectomy-induced osteoporosis mice and in BMSCs treated with H2O2. Interestingly, DNA methyltransferases 3B (DNMT3B) upregulation mediated the hypermethylation of KLF5 induced by oxidative stress, thereby impairing osteogenic differentiation. The inhibition of KLF5 hypermethylation using DNMT3B siRNA or 5-AZA-2-deoxycytidine (5-AZA) protected osteogenic differentiation of BMSCs from oxidative stress. Regarding the downstream mechanism, KLF5 induced β-catenin expression. More importantly, KLF5 promoted the nuclear translocation of β-catenin, which was mediated by the armadillo repeat region of β-catenin. Consistently, oxidative stress-induced KLF5 hypermethylation inhibited osteogenic differentiation by reducing the expression and nuclear translocation of β-catenin. Innovation: We describe the novel effect and mechanism of KLF5 on osteogenesis under oxidative stress, which is linked to osteoporosis for the first time. Conclusion: Our results suggested that oxidative stress-induced hypermethylation of KLF5 mediated by DNMT3B impairs osteogenesis by diminishing the interaction with β-catenin, which is likely to contribute to osteoporosis. Targeting the hypermethylation of KLF5 might be a new strategy for the treatment of osteoporosis. Antioxid. Redox Signal. 35, 1-20.
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Affiliation(s)
- Liangping Li
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
- Department of Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Haoming Wang
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Xiaoying Chen
- Department of Emergency, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Xiang Li
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Gangliang Wang
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Zhiwei Jie
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Xiangde Zhao
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Xuewu Sun
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Hai Huang
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Shunwu Fan
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Ziang Xie
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Jian Wang
- Department of Orthopaedics, Medical College of Zhejiang University, Sir Run Run Shaw Hospital, Hangzhou, People's Republic of China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
- Department of Orthopaedics, Tongde Hospital of Zhejiang Province, Hangzhou, People's Republic of China
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López-Ferreras L, Martínez-García N, Maeso-Alonso L, Martín-López M, Díez-Matilla Á, Villoch-Fernandez J, Alonso-Olivares H, Marques MM, Marin MC. Deciphering the Nature of Trp73 Isoforms in Mouse Embryonic Stem Cell Models: Generation of Isoform-Specific Deficient Cell Lines Using the CRISPR/Cas9 Gene Editing System. Cancers (Basel) 2021; 13:cancers13133182. [PMID: 34202306 PMCID: PMC8268375 DOI: 10.3390/cancers13133182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The Trp73 gene is involved in the regulation of multiple biological processes such as response to stress, differentiation and tissue architecture. This gene gives rise to structurally different N and C-terminal isoforms which lead to differences in its biological activity in a cell type dependent manner. However, there is a current lack of physiological models to study these isoforms. The aim of this study was to generate specific p73-isoform-deficient mouse embryonic stem cell lines using the CRISPR/Cas9 system. Their special features, self-renewal and pluripotency, make embryonic stem cells a useful research tool that allows the generation of cells from any of the three germ layers carrying specific inactivation of p73-isoforms. Characterization of the generated cell lines indicates that while the individual elimination of TA- or DN-p73 isoform is compatible with pluripotency, it results in alterations of the transcriptional profiles and the pluripotent state of the embryonic stem cells in an isoform-specific manner. Abstract The p53 family has been widely studied for its role in various physiological and pathological processes. Imbalance of p53 family proteins may contribute to developmental abnormalities and pathologies in humans. This family exerts its functions through a profusion of isoforms that are generated by different promoter usage and alternative splicing in a cell type dependent manner. In particular, the Trp73 gene gives rise to TA and DN-p73 isoforms that confer p73 a dual nature. The biological relevance of p73 does not only rely on its tumor suppression effects, but on its pivotal role in several developmental processes. Therefore, the generation of cellular models that allow the study of the individual isoforms in a physiological context is of great biomedical relevance. We generated specific TA and DN-p73-deficient mouse embryonic stem cell lines using the CRISPR/Cas9 gene editing system and validated them as physiological bona fide p73-isoform knockout models. Global gene expression analysis revealed isoform-specific alterations of distinctive transcriptional networks. Elimination of TA or DN-p73 is compatible with pluripotency but prompts naïve pluripotent stem cell transition into the primed state, compromising adequate lineage differentiation, thus suggesting that differential expression of p73 isoforms acts as a rheostat during early cell fate determination.
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Affiliation(s)
- Lorena López-Ferreras
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
- Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | - Nicole Martínez-García
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
- Departamento de Producción Animal, Universidad de León, 24071 León, Spain
| | - Laura Maeso-Alonso
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
- Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | - Marta Martín-López
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
- Biomar Microbial Technologies, Parque Tecnológico de León, Armunia, 24009 León, Spain
| | - Ángela Díez-Matilla
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
| | - Javier Villoch-Fernandez
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
- Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | - Hugo Alonso-Olivares
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
- Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | - Margarita M. Marques
- Departamento de Producción Animal, Universidad de León, 24071 León, Spain
- Instituto de Desarrollo Ganadero y Sanidad Animal (INDEGSAL), Universidad de León, 24071 León, Spain
- Correspondence: (M.M.M.); (M.C.M.); Tel.: +34-987-291757 (M.M.M.); +34-987-291490 (M.C.M.)
| | - Maria C. Marin
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; (L.L.-F.); (N.M.-G.); (L.M.-A.); (M.M.-L.); (Á.D.-M.); (J.V.-F.); (H.A.-O.)
- Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
- Correspondence: (M.M.M.); (M.C.M.); Tel.: +34-987-291757 (M.M.M.); +34-987-291490 (M.C.M.)
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Tao L, He XY, Wang FY, Pan LX, Wang XY, Gan SQ, Di R, Chu MX. Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep. Anim Genet 2021; 52:545-549. [PMID: 34002409 DOI: 10.1111/age.13078] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
Litter size is one of the most important reproductive traits of sheep, which has pronounced effects on the profit of husbandry enterprises and enthusiasm of breeders. Despite the importance of litter size, the underlying genetic mechanisms have not been entirely elucidated. Therefore, based on a high-density SNP chip, genome-wide comparative analysis was performed between two groups with different fecundity to reveal candidate genes linked to litter size via detection of homozygosity and selection signatures in Luzhong mutton sheep. Consequently, nine promising genes were identified from six runs of homozygosity islands, and functionally linked to reproduction (ACTL7A, ACTL7B, and ELP1), embryonic development (KLF5 and PIBF1), and cell cycle (DACH1, BORA, DIS3, and MZT1). A total of 128 genes were observed under selection, of which HECW1 and HTR1E were related to total lambs born, GABRG3, LRP1B, and MACROD2 to teat number, and AGBL1 to reproductive seasonality. Additionally, the presence of inbreeding depression implies the urgency of reasonable mating system to increase litter size in the present herd. These findings provide a comprehensive insight to the genetic makeup of litter size, and also contribute to implementation of marker-assisted selection in sheep.
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Affiliation(s)
- L Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - X Y He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - F Y Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L X Pan
- Ji'nan Laiwu Yingtai Agriculture and Animal Husbandry Technology Co., Ltd, Ji'nan, Shandong, 271114, China
| | - X Y Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - S Q Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, 832000, China
| | - R Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - M X Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Li J, Liu L, Zhou W, Cai L, Xu Z, Rane MJ. Roles of Krüppel-like factor 5 in kidney disease. J Cell Mol Med 2021; 25:2342-2355. [PMID: 33523554 PMCID: PMC7933973 DOI: 10.1111/jcmm.16332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Transcription factor Krüppel-like factor 5 (KLF5) is a member of the Krüppel-like factors' (KLFs) family. KLF5 regulates a number of cellular functions, such as apoptosis, proliferation and differentiation. Therefore, KLF5 can play a role in many diseases, including, cancer, cardiovascular disease and gastrointestinal disorders. An important role for KLF5 in the kidney was recently reported, such that KLF5 regulated podocyte apoptosis, renal cell proliferation, tubulointerstitial inflammation and renal fibrosis. In this review, we have summarized the available information in the literature with a brief description on how transcriptional, post-transcriptional and post-translational modifications of KLF5 modulate its function in a variety of organs including the kidney with a focus of its importance on the pathogenesis of various kidney diseases. Furthermore, we also have outlined the current and possible mechanisms of KLF5 activation in kidney diseases. These studies suggest a need for more systemic investigations, particularly for generation of animal models with renal cell-specific deletion or overexpression of KLF5 gene to examine direct contributions of KLF5 to various kidney diseases. This will promote further experimentation in the development of therapies to prevent or treat various kidney diseases.
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Affiliation(s)
- Jia Li
- Department of NephrologyThe First Hospital of Jilin UniversityChangchunChina
- Department of PediatricsPediatric Research InstituteUniversity of LouisvilleLouisvilleKYUSA
| | - Liang Liu
- Department of RadiologyChina‐Japan Union Hospital of Jilin UniversityChangchunChina
| | - Wen‐Qian Zhou
- Department of PediatricsPediatric Research InstituteUniversity of LouisvilleLouisvilleKYUSA
- The Center of Cardiovascular DiseasesThe First Hospital of Jilin UniversityChangchunChina
| | - Lu Cai
- Department of PediatricsPediatric Research InstituteUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
| | - Zhong‐Gao Xu
- Department of NephrologyThe First Hospital of Jilin UniversityChangchunChina
| | - Madhavi J. Rane
- Department of MedicineDivision of NephrologyDepartment of Biochemistry and Molecular GeneticsUniversity of LouisvilleLouisvilleKYUSA
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Abstract
Although common cancer therapies, such as chemotherapy and radiation therapy, have recently improved and yielded good results, evaluated as tumor shrinkage, disease recurrence is still a common event for most cancer patients. This is termed refractory cancer. This tumor regrowth following therapy is generally thought to be caused by a small, specific population of tumor cells called cancer stem cells (CSCs). Similar to other stem cells, CSCs have the capacity for self-renewal and multipotent differentiation, and they have been identified in many tumor types based on cell surface protein expression. This specific cell population has stemness characteristics as examined by serial transplantation in animal models. Previous studies have developed a specific signature of cell surface markers and biological functions that can identify CSCs in many solid tumors. In this review, we summarize the characterization of CSCs using new techniques for identifying and quantifying them in situ. These techniques and concepts could be valuable for evaluating the effects of therapies on this cell population. Finally, we conclude by discussing several unique preclinical treatment strategies to targets CSCs, such as reprogramming CSCs or inducing attack by immune cells. Therapeutic and diagnostic methodologies that can target and quantify CSCs will be valuable tools for eradicating refractory cancer.
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The Key Role of MicroRNAs in Self-Renewal and Differentiation of Embryonic Stem Cells. Int J Mol Sci 2020; 21:ijms21176285. [PMID: 32877989 PMCID: PMC7504502 DOI: 10.3390/ijms21176285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/17/2022] Open
Abstract
Naïve pluripotent embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) represent distinctive developmental stages, mimicking the pre- and the post-implantation events during the embryo development, respectively. The complex molecular mechanisms governing the transition from ESCs into EpiSCs are orchestrated by fluctuating levels of pluripotency transcription factors (Nanog, Oct4, etc.) and wide-ranging remodeling of the epigenetic landscape. Recent studies highlighted the pivotal role of microRNAs (miRNAs) in balancing the switch from self-renewal to differentiation of ESCs. Of note, evidence deriving from miRNA-based reprogramming strategies underscores the role of the non-coding RNAs in the induction and maintenance of the stemness properties. In this review, we revised recent studies concerning the functions mediated by miRNAs in ESCs, with the aim of giving a comprehensive view of the highly dynamic miRNA-mediated tuning, essential to guarantee cell cycle progression, pluripotency maintenance and the proper commitment of ESCs.
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Khorasani N, Sadeghi M, Nowzari-Dalini A. A computational model of stem cell molecular mechanism to maintain tissue homeostasis. PLoS One 2020; 15:e0236519. [PMID: 32730297 PMCID: PMC7392222 DOI: 10.1371/journal.pone.0236519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/07/2020] [Indexed: 11/24/2022] Open
Abstract
Stem cells, with their capacity to self-renew and to differentiate to more specialized cell types, play a key role to maintain homeostasis in adult tissues. To investigate how, in the dynamic stochastic environment of a tissue, non-genetic diversity and the precise balance between proliferation and differentiation are achieved, it is necessary to understand the molecular mechanisms of the stem cells in decision making process. By focusing on the impact of stochasticity, we proposed a computational model describing the regulatory circuitry as a tri-stable dynamical system to reveal the mechanism which orchestrate this balance. Our model explains how the distribution of noise in genes, linked to the cell regulatory networks, affects cell decision-making to maintain homeostatic state. The noise effect on tissue homeostasis is achieved by regulating the probability of differentiation and self-renewal through symmetric and/or asymmetric cell divisions. Our model reveals, when mutations due to the replication of DNA in stem cell division, are inevitable, how mutations contribute to either aging gradually or the development of cancer in a short period of time. Furthermore, our model sheds some light on the impact of more complex regulatory networks on the system robustness against perturbations.
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Affiliation(s)
- Najme Khorasani
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
| | - Mehdi Sadeghi
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Abbas Nowzari-Dalini
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
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Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones. Nat Genet 2020; 52:418-427. [PMID: 32203463 PMCID: PMC7901023 DOI: 10.1038/s41588-020-0591-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Abstract
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. But a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short alpha-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
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Klf5 acetylation regulates luminal differentiation of basal progenitors in prostate development and regeneration. Nat Commun 2020; 11:997. [PMID: 32081850 PMCID: PMC7035357 DOI: 10.1038/s41467-020-14737-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/20/2019] [Indexed: 12/28/2022] Open
Abstract
Prostate development depends on balanced cell proliferation and differentiation, and acetylated KLF5 is known to alter epithelial proliferation. It remains elusive whether post-translational modifications of transcription factors can differentially determine adult stem/progenitor cell fate. Here we report that, in human and mouse prostates, Klf5 is expressed in both basal and luminal cells, with basal cells preferentially expressing acetylated Klf5. Functionally, Klf5 is indispensable for maintaining basal progenitors, their luminal differentiation, and the proliferation of their basal and luminal progenies. Acetylated Klf5 is also essential for basal progenitors' maintenance and proper luminal differentiation, as deacetylation of Klf5 causes excess basal-to-luminal differentiation; attenuates androgen-mediated organoid organization; and retards postnatal prostate development. In basal progenitor-derived luminal cells, Klf5 deacetylation increases their proliferation and attenuates their survival and regeneration following castration and subsequent androgen restoration. Mechanistically, Klf5 deacetylation activates Notch signaling. Klf5 and its acetylation thus contribute to postnatal prostate development and regeneration by controlling basal progenitor cell fate.
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Morimoto Y, Mizushima T, Wu X, Okuzaki D, Yokoyama Y, Inoue A, Hata T, Hirose H, Qian Y, Wang J, Miyoshi N, Takahashi H, Haraguchi N, Matsuda C, Doki Y, Mori M, Yamamoto H. miR-4711-5p regulates cancer stemness and cell cycle progression via KLF5, MDM2 and TFDP1 in colon cancer cells. Br J Cancer 2020; 122:1037-1049. [PMID: 32066912 PMCID: PMC7109136 DOI: 10.1038/s41416-020-0758-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/31/2019] [Accepted: 01/30/2020] [Indexed: 11/11/2022] Open
Abstract
Background It is important to establish cancer stem cell (CSC)-targeted therapies to eradicate cancer. As it is a CSC marker, we focused on Kruppel-like factor 5 (KLF5) in this study. Methods We searched for candidate microRNAs (miRNAs) that inhibited KLF5 expression by in silico analyses and screened them in colon cancer cell lines. Results We identified one promising miRNA, miR-4711-5p, that downregulated KLF5 expression by direct binding. This miRNA suppressed cell proliferation, migration and invasion ability, as well as stemness, including decreased stem cell marker expression, reactive oxygen species activity and sphere formation ability. MiR-4711-5p inhibited the growth of DLD-1 xenografts in nude mice with no adverse effects. We found that miR-4711-5p provoked G1 arrest, which could be attributed to direct binding of miR-4711-5p to TFDP1 (a heterodimeric partner of the E2F family). Our findings also suggested that direct binding of miR-4711-5p to MDM2 could upregulate wild-type p53, leading to strong induction of apoptosis. Finally, we found that miR-4711-5p had a potent tumour-suppressive effect compared with a putative anti-oncomiR, miR-34a, in tumour cell cultures derived from five patients with colorectal cancer. Conclusions Our data suggest that miR-4711-5p could be a promising target for CSC therapy.
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Affiliation(s)
- Yoshihiro Morimoto
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Tsunekazu Mizushima
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Xin Wu
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita city, Osaka, 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Centre, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita city, Osaka, 565-0871, Japan
| | - Yuhki Yokoyama
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita city, Osaka, 565-0871, Japan
| | - Akira Inoue
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Tsuyoshi Hata
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Haruka Hirose
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita city, Osaka, 565-0871, Japan
| | - Yamin Qian
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita city, Osaka, 565-0871, Japan
| | - Jiaqi Wang
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita city, Osaka, 565-0871, Japan
| | - Norikatsu Miyoshi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Hidekazu Takahashi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Naotsugu Haraguchi
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Chu Matsuda
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Yuichiro Doki
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan
| | - Masaki Mori
- Department of Surgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka city, Fukuoka, 812-8582, Japan
| | - Hirofumi Yamamoto
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita city, Osaka, 565-0871, Japan. .,Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita city, Osaka, 565-0871, Japan.
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26
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Gonnot F, Langer D, Bourillot PY, Doerflinger N, Savatier P. Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells. Cell Cycle 2019; 18:2697-2712. [PMID: 31462142 PMCID: PMC6773236 DOI: 10.1080/15384101.2019.1656475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Continuous, non-cell cycle-dependent expression of cyclin E is a characteristic feature of mouse embryonic stem cells (mESCs). We studied the 5′ regulatory region of Cyclin E, also known as Ccne1, and identified binding sites for transcription factors of the naïve pluripotency network, including Esrrb, Klf4, and Tfcp2l1 within 1 kilobase upstream of the transcription start site. Luciferase assay and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChiP–qPCR) study highlighted one binding site for Esrrb that is essential to transcriptional activity of the promoter region, and three binding sites for Klf4 and Tfcp2l1. Knockdown of Esrrb, Klf4, and Tfcp2l1 reduced Cyclin E expression whereas overexpression of Esrrb and Klf4 increased it, indicating a strong correlation between the expression level of these factors and that of cyclin E. We observed that cyclin E overexpression delays differentiation induced by Esrrb depletion, suggesting that cyclin E is an important target of Esrrb for differentiation blockade. We observed that mESCs express a low level of miR-15a and that transfection of a miR-15a mimic decreases Cyclin E mRNA level. These results lead to the conclusion that the high expression level of Cyclin E in mESCs can be attributed to transcriptional activation by Esrrb as well as to the absence of its negative regulator, miR-15a.
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Affiliation(s)
- Fabrice Gonnot
- Stem Cell and Brain Research Institute, Univ Lyon, Université Lyon 1, Inserm , Bron , France
| | - Diana Langer
- Stem Cell and Brain Research Institute, Univ Lyon, Université Lyon 1, Inserm , Bron , France
| | - Pierre-Yves Bourillot
- Stem Cell and Brain Research Institute, Univ Lyon, Université Lyon 1, Inserm , Bron , France
| | - Nathalie Doerflinger
- Stem Cell and Brain Research Institute, Univ Lyon, Université Lyon 1, Inserm , Bron , France
| | - Pierre Savatier
- Stem Cell and Brain Research Institute, Univ Lyon, Université Lyon 1, Inserm , Bron , France
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27
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Schüle KM, Leichsenring M, Andreani T, Vastolo V, Mallick M, Musheev MU, Karaulanov E, Niehrs C. GADD45 promotes locus-specific DNA demethylation and 2C cycling in embryonic stem cells. Genes Dev 2019; 33:782-798. [PMID: 31171699 PMCID: PMC6601511 DOI: 10.1101/gad.325696.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/02/2019] [Indexed: 12/16/2022]
Abstract
In this study, Schüle et al. report an unexpected role of GADD45 proteins in regulation of the cycling of ESCs in the 2C state. Using methylome analysis of Gadd45 triple-mutant ESCs, they found a role for GADD45 in demethylation of specific TET targets and partial deregulation of ZGA genes at the two-cell stage. Mouse embryonic stem cell (ESC) cultures contain a rare cell population of “2C-like” cells resembling two-cell embryos, the key stage of zygotic genome activation (ZGA). Little is known about positive regulators of the 2C-like state and two-cell stage embryos. Here we show that GADD45 (growth arrest and DNA damage 45) proteins, regulators of TET (TET methylcytosine dioxygenase)-mediated DNA demethylation, promote both states. Methylome analysis of Gadd45a,b,g triple-knockout (TKO) ESCs reveal locus-specific DNA hypermethylation of ∼7000 sites, which are enriched for enhancers and loci undergoing TET–TDG (thymine DNA glycosylase)-mediated demethylation. Gene expression is misregulated in TKOs, notably upon differentiation, and displays signatures of DNMT (DNA methyltransferase) and TET targets. TKOs manifest impaired transition into the 2C-like state and exhibit DNA hypermethylation and down-regulation of 2C-like state-specific genes. Gadd45a,b double-mutant mouse embryos display embryonic sublethality, deregulated ZGA gene expression, and developmental arrest. Our study reveals an unexpected role of GADD45 proteins in embryonic two-cell stage regulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Christof Niehrs
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.,German Cancer Research Center (DKFZ), Division of Molecular Embryology, 69120 Heidelberg, Germany
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28
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Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency. Cell Stem Cell 2019; 24:785-801.e7. [PMID: 31031137 PMCID: PMC6509416 DOI: 10.1016/j.stem.2019.03.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 11/01/2018] [Accepted: 03/21/2019] [Indexed: 02/02/2023]
Abstract
The gene regulatory network (GRN) of naive mouse embryonic stem cells (ESCs) must be reconfigured to enable lineage commitment. TCF3 sanctions rewiring by suppressing components of the ESC transcription factor circuitry. However, TCF3 depletion only delays and does not prevent transition to formative pluripotency. Here, we delineate additional contributions of the ETS-family transcription factor ETV5 and the repressor RBPJ. In response to ERK signaling, ETV5 switches activity from supporting self-renewal and undergoes genome relocation linked to commissioning of enhancers activated in formative epiblast. Independent upregulation of RBPJ prevents re-expression of potent naive factors, TBX3 and NANOG, to secure exit from the naive state. Triple deletion of Etv5, Rbpj, and Tcf3 disables ESCs, such that they remain largely undifferentiated and locked in self-renewal, even in the presence of differentiation stimuli. Thus, genetic elimination of three complementary drivers of network transition stalls developmental progression, emulating environmental insulation by small-molecule inhibitors.
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29
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Sivakumar A, de Las Heras JI, Schirmer EC. Spatial Genome Organization: From Development to Disease. Front Cell Dev Biol 2019; 7:18. [PMID: 30949476 PMCID: PMC6437099 DOI: 10.3389/fcell.2019.00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/01/2019] [Indexed: 12/29/2022] Open
Abstract
Every living organism, from bacteria to humans, contains DNA encoding anything from a few hundred genes in intracellular parasites such as Mycoplasma, up to several tens of thousands in many higher organisms. The first observations indicating that the nucleus had some kind of organization were made over a hundred years ago. Understanding of its significance is both limited and aided by the development of techniques, in particular electron microscopy, fluorescence in situ hybridization, DamID and most recently HiC. As our knowledge about genome organization grows, it becomes apparent that the mechanisms are conserved in evolution, even if the individual players may vary. These mechanisms involve DNA binding proteins such as histones, and a number of architectural proteins, some of which are very much conserved, with some others having diversified and multiplied, acquiring specific regulatory functions. In this review we will look at the principles of genome organization in a hierarchical manner, from DNA packaging to higher order genome associations such as TADs, and the significance of radial positioning of genomic loci. We will then elaborate on the dynamics of genome organization during development, and how genome architecture plays an important role in cell fate determination. Finally, we will discuss how misregulation can be a factor in human disease.
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Affiliation(s)
- Aishwarya Sivakumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jose I de Las Heras
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Eric C Schirmer
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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30
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Genome-Scale CRISPRa Screen Identifies Novel Factors for Cellular Reprogramming. Stem Cell Reports 2019; 12:757-771. [PMID: 30905739 PMCID: PMC6450436 DOI: 10.1016/j.stemcr.2019.02.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 01/03/2023] Open
Abstract
Primed epiblast stem cells (EpiSCs) can be reverted to a pluripotent embryonic stem cell (ESC)-like state by expression of single reprogramming factor. We used CRISPR activation to perform a genome-scale, reprogramming screen in EpiSCs and identified 142 candidate genes. Our screen validated a total of 50 genes, previously not known to contribute to reprogramming, of which we chose Sall1 for further investigation. We show that Sall1 augments reprogramming of mouse EpiSCs and embryonic fibroblasts and that these induced pluripotent stem cells are indeed fully pluripotent including formation of chimeric mice. We also demonstrate that Sall1 synergizes with Nanog in reprogramming and that overexpression in ESCs delays their conversion back to EpiSCs. Lastly, using RNA sequencing, we identify and validate Klf5 and Fam189a2 as new downstream targets of Sall1 and Nanog. In summary, our work demonstrates the power of using CRISPR technology in understanding molecular mechanisms that mediate complex cellular processes such as reprogramming. Genome-scale CRISPRa screen in mouse EpiSCs identifies novel reprogramming factors 50 novel genes, including Sall1 and Fam189a2, identified to mediate reprogramming Sall1 synergizes with Nanog to increase reprogramming efficiency in EpiSCs and MEFs RNA-seq provides insight into downstream pathways of Sall1 and Nanog-mediated reprogramming
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31
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Park CS, Lewis A, Chen T, Lacorazza D. Concise Review: Regulation of Self-Renewal in Normal and Malignant Hematopoietic Stem Cells by Krüppel-Like Factor 4. Stem Cells Transl Med 2019; 8:568-574. [PMID: 30790473 PMCID: PMC6525558 DOI: 10.1002/sctm.18-0249] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/07/2019] [Indexed: 12/11/2022] Open
Abstract
Pluripotent and tissue‐specific stem cells, such as blood‐forming stem cells, are maintained through a balance of quiescence, self‐renewal, and differentiation. Self‐renewal is a specialized cell division that generates daughter cells with the same features as the parental stem cell. Although many factors are involved in the regulation of self‐renewal, perhaps the most well‐known factors are members of the Krüppel‐like factor (KLF) family, especially KLF4, because of the landmark discovery that this protein is required to reprogram somatic cells into induced pluripotent stem cells. Because KLF4 regulates gene expression through transcriptional activation or repression via either DNA binding or protein‐to‐protein interactions, the outcome of KLF4‐mediated regulation largely depends on the cellular context, cell cycle regulation, chromatin structure, and the presence of oncogenic drivers. This study first summarizes the current understanding of the regulation of self‐renewal by KLF proteins in embryonic stem cells through a KLF circuitry and then delves into the potential function of KLF4 in normal hematopoietic stem cells and its emerging role in leukemia‐initiating cells from pediatric patients with T‐cell acute lymphoblastic leukemia via repression of the mitogen‐activated protein kinase 7 pathway. stem cells translational medicine2019;8:568–574
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Affiliation(s)
- Chun S Park
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Andrew Lewis
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Taylor Chen
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Daniel Lacorazza
- Department Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
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32
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Azami T, Bassalert C, Allègre N, Estrella LV, Pouchin P, Ema M, Chazaud C. Regulation of ERK signalling pathway in the developing mouse blastocyst. Development 2019; 146:dev.177139. [DOI: 10.1242/dev.177139] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/11/2019] [Indexed: 12/24/2022]
Abstract
Activation of the ERK signalling pathway is essential for the differentiation of the inner cell mass (ICM) during mouse preimplantation development. We show here that ERK phosphorylation is present in ICM precursor cells, in differentiated Primitive Endoderm (PrE) cells as well as in the mature, formative state Epiblast (Epi). We further show that DUSP4 and ETV5, factors often involved in negative feedback loops of the FGF pathway are differently regulated. While DUSP4 presence clearly depends on ERK phosphorylation in PrE cells, ETV5 localises mainly to Epi cells. Unexpectedly, ETV5 accumulation does not depend on direct activation by ERK but requires NANOG activity. Indeed ETV5, like Fgf4 expression, is not present in Nanog mutant embryos. Our results lead us to propose that in pluripotent early Epi cells, NANOG induces the expression of both Fgf4 and Etv5 to enable the differentiation of neighbouring cells into PrE while protecting the Epi identity from autocrine signalling.
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Affiliation(s)
- Takuya Azami
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Cécilia Bassalert
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Nicolas Allègre
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Lorena Valverde Estrella
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Pierre Pouchin
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study 606-8501, Japan
| | - Claire Chazaud
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
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33
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Azami T, Matsumoto K, Jeon H, Waku T, Muratani M, Niwa H, Takahashi S, Ema M. Klf5 suppresses ERK signaling in mouse pluripotent stem cells. PLoS One 2018; 13:e0207321. [PMID: 30452437 PMCID: PMC6242311 DOI: 10.1371/journal.pone.0207321] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/29/2018] [Indexed: 01/05/2023] Open
Abstract
Mouse embryonic stem cells (ESCs) are pluripotent stem cells, which have the ability to differentiate into all three germ layers: mesoderm, endoderm, and ectoderm. Proper levels of phosphorylated extracellular signal-regulated kinase (pERK) are critical for maintaining pluripotency, as elevated pERK evoked by fibroblast growth factor (FGF) receptor activation results in differentiation of ESCs, while, conversely, reduction of pERK by a MEK inhibitor maintains a pluripotent ground state. However, mechanisms underlying proper control of pERK levels in mouse ESCs are not fully understood. Here, we find that Klf5, a Krüppel-like transcription factor family member, is a component of pERK regulation in mouse ESCs. We show that ERK signaling is overactivated in Klf5-KO ESCs and the overactivated ERK in Klf5-KO ESCs is suppressed by the introduction of Klf5, but not Klf2 or Klf4, indicating a unique role for Klf5 in ERK suppression. Moreover, Klf5 regulates Spred1, a negative regulator of the FGF-ERK pathway. Klf5 also facilitates reprogramming of EpiSCs into a naïve state in combination with a glycogen synthase kinase 3 inhibitor and LIF, and in place of a MEK inhibitor. Taken together, these results show for the first time that Klf5 has a unique role suppressing ERK activity in mouse ESCs.
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Affiliation(s)
- Takuya Azami
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, Japan
| | - Ken Matsumoto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, Japan
| | - Hyojung Jeon
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tsuyoshi Waku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Transborder Medical Research Center (TMRC), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Laboratory Animal Resource Center (LARC), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
- * E-mail:
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34
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Liu R, Shi P, Zhou Z, Zhang H, Li W, Zhang H, Chen C. Krüpple-like factor 5 is essential for mammary gland development and tumorigenesis. J Pathol 2018; 246:497-507. [PMID: 30101462 DOI: 10.1002/path.5153] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/26/2018] [Accepted: 08/06/2018] [Indexed: 12/21/2022]
Abstract
Krüpple-like factor 5 (KLF5) is required for the development of the embryo and multiple organs, such as the lung and intestine. KLF5 plays a pro-proliferative and oncogenic role in several carcinomas, including breast cancer. However, its role in normal mammary gland development and oncogenesis has not been elucidated in vivo. In this study, we used mammary gland-specific Klf5 conditional knockout mice derived by mating Klf5-LoxP and MMTV-Cre mice. The genetic ablation of Klf5 suppresses mammary gland ductal elongation and lobuloalveolar formation. Klf5 deficiency inhibits mammary epithelial cell proliferation, survival, and stem cell maintenance. Klf5 promotes mammary stemness, at least partially, by directly promoting the transcription of Slug. Finally, Klf5 depletion suppressed PyMT-induced mammary gland tumor cell stemness, tumor initiation, and growth in vivo. Slug also mediated these functions of Klf5 in vivo. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, PR China
| | - Peiguo Shi
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Hailin Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Wei Li
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, PR China
| | - Hong Zhang
- Department of Nuclear Medicine, Second Hospital of Zhejiang University School of Medicine, Hangzhou, PR China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
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T Cell Leukemia/Lymphoma 1A is essential for mouse epidermal keratinocytes proliferation promoted by insulin-like growth factor 1. PLoS One 2018; 13:e0204775. [PMID: 30286151 PMCID: PMC6171881 DOI: 10.1371/journal.pone.0204775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/13/2018] [Indexed: 12/25/2022] Open
Abstract
T Cell Leukemia/Lymphoma 1A is expressed during B-cell differentiation and, when over-expressed, acts as an oncogene in mouse (Tcl1a) and human (TCL1A) B-cell chronic lymphocytic leukemia (B-CLL) and T-cell prolymphocytic leukemia (T-PLL). Furthermore, in the murine system Tcl1a is expressed in the ovary, testis and in pre-implantation embryos, where it plays an important role in blastomere proliferation and in embryonic stem cell (ESC) proliferation and self-renewal. We have also observed that Tcl1-/- adult mice exhibit alopecia and deep ulcerations. This finding has led us to investigate the role of TCL1 in mouse skin and hair follicles. We have found that TCL1 is expressed in the proliferative structure (i.e. the secondary hair germ) and in the stem cell niche (i.e. the bulge) of the hair follicle during regeneration phase and it is constitutively expressed in the basal layer of epidermis where it is required for the correct proliferative–differentiation program of the keratinocytes (KCs). Taking advantage of the murine models we have generated, including the Tcl1-/- and the K14-TCL1 transgenic mouse, we have analysed the function of TCL1 in mouse KCs and the molecular pathways involved. We provide evidence that in the epidermal compartment TCL1 has a role in the regulation of KC proliferation, differentiation, and apoptosis. In particular, the colony-forming efficiency (CFE) and the insulin-like growth factor 1 (IGF1)-induced proliferation are dramatically impaired, while apoptosis is increased, in KCs from Tcl1-/- mice when compared to WT. Moreover, the expression of differentiation markers such as cytokeratin 6 (KRT6), filaggrin (FLG) and involucrin (IVL) are profoundly altered in mutant mice (Tcl1-/-). Importantly, by over-expressing TCL1A in basal KCs of the K14-TCL1 transgenic mouse model, we observed a significant rescue of cell proliferation, differentiation and apoptosis of the mutant phenotype. Finally, we found TCL1 to act, at least in part, via increasing phospho-ERK1/2 and decreasing phospho-P38 MAPK. Hence, our data demonstrate that regulated levels of Tcl1a are necessary for the correct proliferation and differentiation of the interfollicular KCs.
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van Mierlo G, Wester RA, Marks H. Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state. Stem Cell Res 2018; 33:135-145. [PMID: 30352361 DOI: 10.1016/j.scr.2018.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/13/2018] [Accepted: 09/17/2018] [Indexed: 11/26/2022] Open
Abstract
The ground state of pluripotency is defined as a minimal unrestricted epigenetic state as present in the Inner Cell Mass. Mouse embryonic stem cells (ESCs) grown in a defined serum-free medium with two kinase inhibitors ("2i ESCs") have been postulated to reflect ground-state pluripotency, whereas ESCs grown in the presence of serum ("serum ESCs") share more similarities with post-implantation epiblast cells. Pluripotency results from an intricate interplay between cytoplasmic, nuclear and chromatin-associated proteins. Here, we perform quantitative subcellular proteomics to gain insight in the molecular mechanisms sustaining the pluripotent states reflected by 2i and serum ESCs. We describe a full SILAC workflow and quality controls for proteomic comparison of 2i and serum ESCs, allowing subcellular proteomics of the cytoplasm, nucleoplasm and chromatin. The obtained quantitative information revealed increased levels of naïve pluripotency factors on the chromatin of 2i ESCs. Surprisingly, the cytoplasmic proteome suggests that 2i and serum ESCs utilize distinct metabolic programs, which include upregulation of free radical buffering by the glutathione pathway in 2i ESCs. Through induction of intracellular radicals, we show that the altered metabolic environment renders 2i ESCs less sensitive to oxidative stress. Altogether, this work provides novel insights into the proteomic landscape underlying ground state pluripotency.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein 26/28, 6525GA Nijmegen, the Netherlands
| | - Roelof A Wester
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein 26/28, 6525GA Nijmegen, the Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein 26/28, 6525GA Nijmegen, the Netherlands.
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Temporal expression of pluripotency-associated transcription factors in sheep and cattle preimplantation embryos. ZYGOTE 2018; 26:270-278. [PMID: 30033902 DOI: 10.1017/s0967199418000175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SummaryPluripotency-associated transcription factors (PATFs) modulate gene expression during early mammalian embryogenesis. Despite a strong understanding of PATFs during mouse embryogenesis, limited progress has been made in ruminants. This work aimed to describe the temporal expression of eight PATFs during both sheep and cattle preimplantation development. Transcript availability of PATFs was evaluated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in eggs, cleavage-stage embryos, morulae, and blastocysts. Transcripts of five genes were detected in all developmental stages of both species (KLF5, OCT4, RONIN, ZFP281, and ZFX). Furthermore, CMYC was detected in all cattle samples but was found from cleavage-stage onwards in sheep. In contrast, NR0B1 was detected in all sheep samples but was not detected in cattle morulae. GLIS1 displayed the most significant variation in temporal expression between species, as this PATF was only detected in cattle eggs and sheep cleavage-stage embryos and blastocysts. In silico analysis suggested that cattle and sheep PATFs share similar size, isometric point and molecular weight. A phenetic analysis showed two patterns of PATF clustering between cattle and sheep, among several mammalian species. In conclusion, the temporal expression of pluripotency-associated transcription factors differs between sheep and cattle, suggesting species-specific regulation during preimplantation development.
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Paul B, Li Y, Tollefsbol TO. The Effects of Combinatorial Genistein and Sulforaphane in Breast Tumor Inhibition: Role in Epigenetic Regulation. Int J Mol Sci 2018; 19:ijms19061754. [PMID: 29899271 PMCID: PMC6032337 DOI: 10.3390/ijms19061754] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
Dietary compounds that possess the properties of altering epigenetic processes are gaining popularity as targets for cancer prevention studies. These compounds when administered at optimal concentrations and especially in combination can have enhanced effects in cancer prevention or therapy. It is important to study the interaction of two or more compounds in order to assess their role in enhancing prevention. Genistein (GEN), found in soy, has been extensively studied for its role as an epigenetic modifier especially as a DNA methyltransferase (DNMT) inhibitor and sulforaphane (SFN), found in cruciferous vegetables, is known as a histone deacetylase (HDAC) inhibitor. However, very little is known about the effects of these two compounds in conjunction in breast cancer prevention or therapy. In our current study, we determined that, at certain doses, the compounds have synergistic effects in decreasing cellular viability of breast cancer cell lines. Our results indicate that the combination of GEN and SFN is much more effective than their single doses in increasing the rate of apoptosis and lowering the colony forming potential of these cells. We determined that these compounds inhibit cell cycle progression to G2 phase in MDA-MB-231 and G1 phase in MCF-7 breast cancer cell lines. Additionally, we determined that the combination is effective as an HDAC and histone methyltransferase (HMT) inhibitor. Furthermore, we demonstrated that this combination downregulates the levels of HDAC2 and HDAC3 both at the mRNA and protein levels. We also found that these compounds have the potential to downregulate KLF4 levels, which plays an important role in stem cell formation. The combination of GEN and SFN is also effective in downregulating hTERT levels, which is known to be activated when KLF4 binds to its promoter region. Our hypothesis is further strengthened by in vivo studies, where the combination is administered to transgenic mice in the form of genistein and SFN-enriched broccoli sprouts. We have demonstrated that the combination is more effective in preventing or treating mammary cancer via extending tumor latency and reducing tumor volumes/sizes than either of these dietary components administered alone. These results are consistent with our in vitro study suggesting potential preventive and therapeutic effects of this novel dietary combinatorial approach against breast cancer.
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Affiliation(s)
- Bidisha Paul
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Yuanyuan Li
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Yamane M, Ohtsuka S, Matsuura K, Nakamura A, Niwa H. Overlapping functions of Krüppel-like factor family members: targeting multiple transcription factors to maintain the naïve pluripotency of mouse embryonic stem cells. Development 2018; 145:dev.162404. [PMID: 29739838 DOI: 10.1242/dev.162404] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/30/2018] [Indexed: 01/02/2023]
Abstract
Krüppel-like factors (Klfs) have a pivotal role in maintaining self-renewal of mouse embryonic stem cells (mESCs). The functions of three Klf family members (Klf2, Klf4 and Klf5) have been identified, and are suggested to largely overlap. For further dissection of their functions, we applied an inducible knockout system for these Klf family members and assessed the effects of combinatorial loss of function. As a result, we confirmed that any one of Klf2, Klf4 and Klf5 was sufficient to support self-renewal, whereas the removal of all three compromised it. The activity of any single transcription factor, except for a Klf family member, was not sufficient to restore self-renewal of triple-knockout mESCs. However, some particular combinations of transcription factors were capable of the restoration. The triple-knockout mESCs were successfully captured at primed state. These data indicate that the pivotal function of a Klf family member is transduced into the activation of multiple transcription factors in a naïve-state-specific manner.
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Affiliation(s)
- Mariko Yamane
- Laboratory for Pluripotent Stem Cell Studies, RIKEN Center for Developmental Biology (CDB), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Satoshi Ohtsuka
- Laboratory for Pluripotent Stem Cell Studies, RIKEN Center for Developmental Biology (CDB), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Life Science, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada kahoku, Ishikawa 920-0293, Japan
| | - Kumi Matsuura
- Laboratory for Pluripotent Stem Cell Studies, RIKEN Center for Developmental Biology (CDB), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Hitoshi Niwa
- Laboratory for Pluripotent Stem Cell Studies, RIKEN Center for Developmental Biology (CDB), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan .,Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan.,JST, CREST, Sanbancho, Chiyoda-ku, Tokyo 1020075, Japan
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Abstract
Tissue-specific transcription factors primarily act to define the phenotype of the cell. The power of a single transcription factor to alter cell fate is often minimal, as seen in gain-of-function analyses, but when multiple transcription factors cooperate synergistically it potentiates their ability to induce changes in cell fate. By contrast, transcription factor function is often dispensable in the maintenance of cell phenotype, as is evident in loss-of-function assays. Why does this phenomenon, commonly known as redundancy, occur? Here, I discuss the role that transcription factor networks play in collaboratively regulating stem cell fate and differentiation by providing multiple explanations for their functional redundancy.
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Affiliation(s)
- Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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41
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Okada H, Yamada M, Kamimoto K, Kok CYY, Kaneko K, Ema M, Miyajima A, Itoh T. The transcription factor Klf5 is essential for intrahepatic biliary epithelial tissue remodeling after cholestatic liver injury. J Biol Chem 2018. [PMID: 29523685 DOI: 10.1074/jbc.ra118.002372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Under various conditions of liver injury, the intrahepatic biliary epithelium undergoes dynamic tissue expansion and remodeling, a process known as ductular reaction. Mouse models defective in inducing such a tissue-remodeling process are more susceptible to liver injury, suggesting a crucial role of this process in liver regeneration. However, the molecular mechanisms regulating the biliary epithelial cell (BEC) dynamics in the ductular reaction remain largely unclear. Here, we demonstrate that the transcription factor Krüppel-like factor 5 (Klf5) is highly enriched in mouse liver BECs and plays a key role in regulating the ductular reaction, specifically under cholestatic injury conditions. Although mice lacking Klf5 in the entire liver epithelium, including both hepatocytes and BECs (Klf5-LKO (liver epithelial-specific knockout) mice), did not exhibit any apparent phenotype in the hepatobiliary system under normal conditions, they exhibited significant defects in biliary epithelial tissue remodeling upon 3,5-diethoxycarbonyl-1,4-dihydrocollidine-induced cholangitis, concomitantly with exacerbated cholestasis and reduced survival rate. In contrast, mice lacking Klf5 solely in hepatocytes did not exhibit any such phenotypes, confirming Klf5's specific role in BECs. RNA-sequencing analyses of BECs isolated from the Klf5-LKO mouse livers revealed that the Klf5 deficiency primarily affected expression of cell cycle-related genes. Moreover, immunostaining analysis with the proliferation marker Ki67 disclosed that the Klf5-LKO mice had significantly reduced BEC proliferation levels upon injury. These results indicate that Klf5 plays a critical role in the ductular reaction and biliary epithelial tissue expansion and remodeling by inducing BEC proliferation and thereby contributing to liver regeneration.
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Affiliation(s)
- Hajime Okada
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Minami Yamada
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Kenji Kamimoto
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Cindy Yuet-Yin Kok
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Kota Kaneko
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Masatsugu Ema
- the Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Atsushi Miyajima
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Tohru Itoh
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
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42
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Suzuki S, Minami N. CHD1 Controls Cell Lineage Specification Through Zygotic Genome Activation. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2018; 229:15-30. [PMID: 29177762 DOI: 10.1007/978-3-319-63187-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In mammals, the processes spanning from fertilization to the generation of a new organism are very complex and are controlled by multiple genes. Life begins with the encounter of eggs and spermatozoa, in which gene expression is inactive prior to fertilization. After several cell divisions, cells arise that are specialized in implantation, a developmental process unique to mammals. Cells involved in the establishment and maintenance of implantation differentiate from totipotent embryos, and the remaining cells generate the embryo proper. Although this process of differentiation, termed cell lineage specification, is supported by various gene expression networks, many components have yet to be identified. Moreover, despite extensive research it remains unclear which genes are controlled by each of the factors involved. Although it has become clear that epigenetic factors regulate gene expression, elucidation of the underlying mechanisms remains challenging. In this chapter, we propose that the chromatin remodeling factor CHD1, together with epigenetic factors, is involved in a subset of gene expression networks involved in processes spanning from zygotic genome activation to cell lineage specification.
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Affiliation(s)
- Shinnosuke Suzuki
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8052, Japan.
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43
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Regulatory crosstalk between KLF5, miR-29a and Fbw7/CDC4 cooperatively promotes atherosclerotic development. Biochim Biophys Acta Mol Basis Dis 2017; 1864:374-386. [PMID: 29074464 DOI: 10.1016/j.bbadis.2017.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/01/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022]
Abstract
Atherogenesis is a chronic inflammatory process that involves complex interactions between endothelial dysfunction, lipid deposition and vascular smooth-muscle cell (VSMC) proliferation. However, the molecular mechanism is still unclear. We found that a pro-atherosclerotic factor (oxLDL) induced the expression of Krüppel-like factor 5 (KLF5), which in turn increased miR-29a expression levels. The increased miR-29a was retained within HASMCs and down-regulated Fbw7/CDC4 expression by targeting the 3´UTR of Fbw7/CDC4, subsequently increasing KLF5 stability by reducing the Fbw7/CDC4-dependent ubiquitination of KLF5, forming a positive feedback loop to enhance VSMC proliferation and promote atherogenesis. These results indicate a potentially important role for the oxLDL-activated feedback mechanism in VSMC proliferation and atherogenesis. Suppression of miR-29a may be an effective way to attenuate atherosclerosis. In conclusion, our data are the first to reveal that the regulatory crosstalk between KLF5, miR-29a, and Fbw7/CDC4 cooperatively promotes atherosclerotic development.
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44
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Tang L, Wang M, Liu D, Gong M, Ying QL, Ye S. Sp5 induces the expression of Nanog to maintain mouse embryonic stem cell self-renewal. PLoS One 2017; 12:e0185714. [PMID: 28961274 PMCID: PMC5621696 DOI: 10.1371/journal.pone.0185714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/18/2017] [Indexed: 11/22/2022] Open
Abstract
Activation of signal transducer and activator of transcription 3 (STAT3) by leukemia inhibitory factor (LIF) maintains mouse embryonic stem cell (mESC) self-renewal. Our previous study showed that trans-acting transcription factor 5 (Sp5), an LIF/STAT3 downstream target, supports mESC self-renewal. However, the mechanism by which Sp5 exerts these effects remains elusive. Here, we found that Nanog is a direct target of Sp5 and mediates the self-renewal-promoting effect of Sp5 in mESCs. Overexpression of Sp5 induced Nanog expression, while knockdown or knockout of Sp5 decreased the Nanog level. Moreover, chromatin immunoprecipitation (ChIP) assays showed that Sp5 directly bound to the Nanog promoter. Functional studies revealed that knockdown of Nanog eliminated the mESC self-renewal-promoting ability of Sp5. Finally, we demonstrated that the self-renewal-promoting function of Sp5 was largely dependent on its zinc finger domains. Taken together, our study provides unrecognized functions of Sp5 in mESCs and will expand our current understanding of the regulation of mESC pluripotency.
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Affiliation(s)
- Ling Tang
- Center for Stem Cell and Translational Medicine, School of Life Science, Anhui University, Hefei, PR China
| | - Manman Wang
- Center for Stem Cell and Translational Medicine, School of Life Science, Anhui University, Hefei, PR China
| | - Dahai Liu
- Center for Stem Cell and Translational Medicine, School of Life Science, Anhui University, Hefei, PR China
| | - Mengting Gong
- Center for Stem Cell and Translational Medicine, School of Life Science, Anhui University, Hefei, PR China
| | - Qi-Long Ying
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Shoudong Ye
- Center for Stem Cell and Translational Medicine, School of Life Science, Anhui University, Hefei, PR China
- * E-mail:
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45
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Bialkowska AB, Yang VW, Mallipattu SK. Krüppel-like factors in mammalian stem cells and development. Development 2017; 144:737-754. [PMID: 28246209 DOI: 10.1242/dev.145441] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Krüppel-like factors (KLFs) are a family of zinc-finger transcription factors that are found in many species. Recent studies have shown that KLFs play a fundamental role in regulating diverse biological processes such as cell proliferation, differentiation, development and regeneration. Of note, several KLFs are also crucial for maintaining pluripotency and, hence, have been linked to reprogramming and regenerative medicine approaches. Here, we review the crucial functions of KLFs in mammalian embryogenesis, stem cell biology and regeneration, as revealed by studies of animal models. We also highlight how KLFs have been implicated in human diseases and outline potential avenues for future research.
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Affiliation(s)
- Agnieszka B Bialkowska
- Division of Gastroenterology, Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA
| | - Vincent W Yang
- Division of Gastroenterology, Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA.,Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA
| | - Sandeep K Mallipattu
- Division of Nephrology, Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA
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46
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Jiang Y, Han K, Cai M, Wang Y, Zhang Z. Characterization and Spatiotemporal Expression of Klf4 in Large Yellow Croaker Larimichthys crocea. DNA Cell Biol 2017; 36:655-671. [DOI: 10.1089/dna.2017.3663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yonghua Jiang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
| | - Kunhuang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
| | - Mingyi Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Ltd., Ningde, China
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47
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Chen Z, Zhang Q, Wang H, Li W, Wang F, Wan C, Deng S, Chen H, Yin Y, Li X, Xie Z, Chen S. Klf5 Mediates Odontoblastic Differentiation through Regulating Dentin-Specific Extracellular Matrix Gene Expression during Mouse Tooth Development. Sci Rep 2017; 7:46746. [PMID: 28440310 PMCID: PMC5404268 DOI: 10.1038/srep46746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/23/2017] [Indexed: 12/21/2022] Open
Abstract
Klf5, a member of the Krüppel-like transcription factor family, has essential roles during embryonic development, cell proliferation, differentiation, migration and apoptosis. This study was to define molecular mechanism of Klf5 during the odontoblastic differentiation. The expression of Klf5, odontoblast-differentiation markers, Dspp and Dmp1 was co-localized in odontoblastic cells at different stages of mouse tooth development and mouse dental papilla mesenchymal cells. Klf5 was able to promote odontoblastic differentiation and enhance mineral formation of mouse dental papilla mesenchymal cells. Furthermore, overexpression of Klf5 could up-regulate Dspp and Dmp1 gene expressions in mouse dental papilla mesenchymal cells. In silico analysis identified that several putative Klf5 binding sites in the promoter and first intron of Dmp1 and Dspp genes that are homologous across species lines. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis indicated that Klf5 bound to these motifs in vitro and in intact cells. The responsible regions of Dmp1 gene were located in the promoter region while effect of Klf5 on Dspp activity was in the first intron of Dspp gene. Our results identify Klf5 as an activator of Dmp1 and Dspp gene transcriptions by different mechanisms and demonstrate that Klf5 plays a pivotal role in odontoblast differentiation.
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Affiliation(s)
- Zhuo Chen
- Key Laboratory for Oral Biomedical Research of Zhejiang Province, Affiliated Hospital of Stomatology, Medical College, Zhejiang University, Hangzhou, China.,Department of Developmental Dentistry, Dental School, The University of Texas Health Science Center at San Antonio, San Antonio, United States of America
| | - Qi Zhang
- Department of Endodontics, School &Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Han Wang
- Shangyang Dental Clinic, Hangzhou, China
| | - Wentong Li
- Department of Developmental Dentistry, Dental School, The University of Texas Health Science Center at San Antonio, San Antonio, United States of America
| | - Feng Wang
- Department of Developmental Dentistry, Dental School, The University of Texas Health Science Center at San Antonio, San Antonio, United States of America
| | - Chunyan Wan
- Department of Developmental Dentistry, Dental School, The University of Texas Health Science Center at San Antonio, San Antonio, United States of America.,Department of Stomatology, Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, College of Somatology, Qingdao University, Qingdao, China
| | - Shuli Deng
- Key Laboratory for Oral Biomedical Research of Zhejiang Province, Affiliated Hospital of Stomatology, Medical College, Zhejiang University, Hangzhou, China
| | - Hui Chen
- Key Laboratory for Oral Biomedical Research of Zhejiang Province, Affiliated Hospital of Stomatology, Medical College, Zhejiang University, Hangzhou, China
| | - Yixin Yin
- Department of Developmental Dentistry, Dental School, The University of Texas Health Science Center at San Antonio, San Antonio, United States of America
| | - Xiaoyan Li
- Department of Developmental Dentistry, Dental School, The University of Texas Health Science Center at San Antonio, San Antonio, United States of America
| | - Zhijian Xie
- Key Laboratory for Oral Biomedical Research of Zhejiang Province, Affiliated Hospital of Stomatology, Medical College, Zhejiang University, Hangzhou, China
| | - Shuo Chen
- Department of Developmental Dentistry, Dental School, The University of Texas Health Science Center at San Antonio, San Antonio, United States of America
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48
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Zinovyeva MV, Kostina MB, Chernov IP, Kondratyeva LG, Sverdlov ED. KLF5, a new player and new target in the permanently changing set of pancreatic cancer molecular drivers. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162016060157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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49
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Azami T, Waku T, Matsumoto K, Jeon H, Muratani M, Kawashima A, Yanagisawa J, Manabe I, Nagai R, Kunath T, Nakamura T, Kurimoto K, Saitou M, Takahashi S, Ema M. Klf5 maintains the balance of primitive endoderm to epiblast specification during mouse embryonic development by suppression of Fgf4. Development 2017; 144:3706-3718. [DOI: 10.1242/dev.150755] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/25/2017] [Indexed: 12/17/2022]
Abstract
The inner cell mass of the mouse blastocyst gives rise to the pluripotent epiblast (EPI), which forms the embryo proper, and the primitive endoderm (PrE), which forms extra-embryonic yolk sac tissues. All inner cells co-express lineage markers such as Nanog and Gata6 at embryonic day (E) 3.25, and the EPI and PrE precursor cells eventually segregate to exclusively express Nanog and Gata6, respectively. Fibroblast growth factor (FGF)/extracellular signal-regulated kinase (ERK) signalling is involved in segregation of the EPI and PrE lineages; however, the mechanism involved in Fgf4-regulation is poorly understood. Here, we identified Klf5 as an upstream repressor of Fgf4. While Fgf4 was markedly upregulated in Klf5 knockout (KO) embryos at E3.0, it was downregulated in embryos overexpressing Klf5. Furthermore, Klf5 KO and overexpressing blastocysts showed skewed lineage specification phenotypes, similar to FGF4-treated preimplantation embryos and Fgf4 KO embryos, respectively. Inhibitors of the FGF receptor and ERK pathways reversed the skewed lineage specification of Klf5 KO blastocysts. These data demonstrate that Klf5 suppresses Fgf4-Fgfr-ERK signalling, thus preventing precocious activation of the PrE specification programme.
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Affiliation(s)
- Takuya Azami
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8575, Japan
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Tsuyoshi Waku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ken Matsumoto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Hyojung Jeon
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8575, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Akihiro Kawashima
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8575, Japan
| | - Jun Yanagisawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Ichiro Manabe
- Department of Cardiovascular Medicine, The University of Tokyo Graduate School of Medicine, Bunkyo, Tokyo 113-8655, Japan
| | - Ryozo Nagai
- Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Tomonori Nakamura
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuki Kurimoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Reprogramming Science, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin Yoshida, Sakyo-ku, Kyoto 606-8507, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8575, Japan
- Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- International Institute for Integrative Sleep Medicine, Life Science Center, and Laboratory Animal Resource Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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Xue YK, Tan J, Dou DW, Chen D, Chen LJ, Ren HP, Chen LB, Xiong XG, Zheng H. Effect of Kruppel-like factor 4 on Notch pathway in hepatic stellate cells. ACTA ACUST UNITED AC 2016; 36:811-816. [PMID: 27924515 DOI: 10.1007/s11596-016-1667-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/15/2016] [Indexed: 02/06/2023]
Abstract
The relationship between Kruppel-like factor 4 (KLF4) and the Notch pathway was determined to investigate the effect of KLF4 on the activation of hepatic stellate cells and underlying mechanisms. Fifty SPF BALB/c mice were randomly divided into two groups. A liver fibrosis model was established in 25 mice as the experimental group, and the remaining 25 mice served as controls. On the day 0, 7, 14, and 35, liver tissues were removed for immunofluorescent detection. The Notch pathway inhibitor DAPT was added to the primary original hepatic stellate cells, and KLF4 and Notch-associated factor expression was detected by qRT-PCR. Additionally, the hepatic stellate cell line LX-2 was used to establish control and experimental groups, and was cultured in vitro. LX-2 cells in the experimental groups were treated with DAPT and the Notch activator transforming growth factor-beta 1 separately, whereas those in the control group were given isotonic culture medium. After 48 h, KLF4 expression was examined by Western blotting. After transient transfection of LX-2 cells to increase KLF4, the expression of Notch factor was examined. Immunofluorescence analysis showed that, with the aggravation of liver fibrosis, the absorbance (A) values of KLF4 were decreased (day 0: 980.73±153.19; day 7: 1087.99±230.23; day 14: 390.95±93.56; day 35: 245.99±87.34). The expression of Notch pathway- related factors (Notch-1, Notch-2, and Jagged-1) in the hepatic stellate cell membrane was negatively correlated to KLF4 expression. With the increase of KLF4 expression, Notch-2 (0.73±0.13) and Jagged-1 (0.43±0.12) expression decreased, whereas Notch-1 level was not detectable. When the Notch pathway was inhibited, KLF4 levels generally increased (18.12±1.31). Our results indicate that KLF4 expression is negatively correlated to the Notch pathway in hepatic stellate cells, which may provide a reference for the treatment of hepatic fibrosis.
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Affiliation(s)
- Yin-Kai Xue
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China
| | - Jun Tan
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China
| | - Dong-Wei Dou
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China
| | - Ding Chen
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China
| | - Lu-Jia Chen
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China
| | - Huan-Ping Ren
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China
| | - Li-Bo Chen
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China
| | - Xin-Gao Xiong
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China.
| | - Hai Zheng
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong Univerfsity of Science and Technology, Wuhan, 430022, China.
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