1
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Ito T, Kubiura-Ichimaru M, Miura F, Tajima S, Surani MA, Ito T, Yamaguchi S, Tada M. DNMT1 can induce primary germ layer differentiation through de novo DNA methylation. Genes Cells 2024; 29:549-566. [PMID: 38811355 DOI: 10.1111/gtc.13130] [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: 02/17/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
DNA methyltransferases and Ten-Eleven Translocation (TET) proteins regulate the DNA methylation and demethylation cycles during mouse embryonic development. Although DNMT1 mainly plays a role in the maintenance of DNA methylation after DNA replication, it is also reported to possess de novo methyltransferase capacity. However, its physiological significance remains unclear. Here, we demonstrate that full-length DNMT1 (FL) and a mutant lacking the N-terminus necessary for its maintenance activity (602) confer the differentiation potential of mouse Dnmt1, Dnmt3a, and Dnmt3b (Dnmts-TKO) embryonic stem cells (ESCs). Both FL and 602 inhibit the spontaneous differentiation of Dnmts-TKO ESCs in the undifferentiated state. Dnmts-TKO ESCs showed loss of DNA methylation and de-repression of primitive endoderm-related genes, but these defects were partially restored in Dnmts-TKO + FL and Dnmts-TKO + 602 ESCs. Upon differentiation, Dnmts-TKO + FL ESCs show increased 5mC and 5hmC levels across chromosomes, including pericentromeric regions. In contrast, Dnmts-TKO + 602 ESCs didn't accumulate 5mC, and sister chromatids showed 5hmC asynchronously. Furthermore, in comparison with DNMT1_602, DNMT1_FL effectively promoted commitment to the epiblast-like cells and beyond, driving cell-autonomous mesendodermal and germline differentiation through embryoid body-based methods. With precise target selectivity achieved by its N-terminal region, DNMT1 may play a role in gene regulation leading to germline development.
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Affiliation(s)
- Takamasa Ito
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| | - Musashi Kubiura-Ichimaru
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics Institute for Protein Research, Osaka University, Suita, Japan
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge, UK
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinpei Yamaguchi
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| | - Masako Tada
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
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2
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Lozovska A, Korovesi AG, Dias A, Lopes A, Fowler DA, Martins GG, Nóvoa A, Mallo M. Tgfbr1 controls developmental plasticity between the hindlimb and external genitalia by remodeling their regulatory landscape. Nat Commun 2024; 15:2509. [PMID: 38509075 PMCID: PMC10954616 DOI: 10.1038/s41467-024-46870-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 03/13/2024] [Indexed: 03/22/2024] Open
Abstract
The hindlimb and external genitalia of present-day tetrapods are thought to derive from an ancestral common primordium that evolved to generate a wide diversity of structures adapted for efficient locomotion and mating in the ecological niche occupied by the species. We show that despite long evolutionary distance from the ancestral condition, the early primordium of the mouse external genitalia preserved the capacity to take hindlimb fates. In the absence of Tgfbr1, the pericloacal mesoderm generates an extra pair of hindlimbs at the expense of the external genitalia. It has been shown that the hindlimb and the genital primordia share many of their key regulatory factors. Tgfbr1 controls the response to those factors by modulating the accessibility status of regulatory elements that control the gene regulatory networks leading to the formation of genital or hindlimb structures. Our work uncovers a remarkable tissue plasticity with potential implications in the evolution of the hindlimb/genital area of tetrapods, and identifies an additional mechanism for Tgfbr1 activity that might also contribute to the control of other physiological or pathological processes.
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Affiliation(s)
- Anastasiia Lozovska
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Artemis G Korovesi
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - André Dias
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alexandre Lopes
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Donald A Fowler
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Gabriel G Martins
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Ana Nóvoa
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Moisés Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
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3
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Cheng T, Xing YY, Liu C, Li YF, Huang Y, Liu X, Zhang YJ, Zhao GQ, Dong Y, Fu XX, Tian YM, Shu LP, Megason SG, Xu PF. Nodal coordinates the anterior-posterior patterning of germ layers and induces head formation in zebrafish explants. Cell Rep 2023; 42:112351. [PMID: 37018074 DOI: 10.1016/j.celrep.2023.112351] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 01/16/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Much progress has been made toward generating analogs of early embryos, such as gastruloids and embryoids, in vitro. However, methods for how to fully mimic the cell movements of gastrulation and coordinate germ-layer patterning to induce head formation are still lacking. Here, we show that a regional Nodal gradient applied to zebrafish animal pole explant can generate a structure that recapitulates the key cell movements of gastrulation. Using single-cell transcriptome and in situ hybridization analysis, we assess the dynamics of the cell fates and patterning of this structure. The mesendoderm differentiates into the anterior endoderm, prechordal plate, notochord, and tailbud-like cells along an anterior-posterior axis, and an anterior-posterior-patterned head-like structure (HLS) progressively forms during late gastrulation. Among 105 immediate Nodal targets, 14 genes contain axis-induction ability, and 5 of them induce a complete or partial head structure when overexpressed in the ventral side of zebrafish embryos.
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Affiliation(s)
- Tao Cheng
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan-Yi Xing
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Hangzhou, Zhejiang, China
| | - Cong Liu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun-Fei Li
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Huang
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiang Liu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying-Jie Zhang
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guo-Qin Zhao
- Department of Immunology, Guizhou Medical University, Guiyang 550004, China
| | - Yang Dong
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xin-Xin Fu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yi-Meng Tian
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li-Ping Shu
- Department of Immunology, Guizhou Medical University, Guiyang 550004, China
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
| | - Peng-Fei Xu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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4
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Caumon H, Vernoux T. A matter of time: auxin signaling dynamics and the regulation of auxin responses during plant development. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad132. [PMID: 37042516 DOI: 10.1093/jxb/erad132] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 06/19/2023]
Abstract
As auxin is a major regulator of plant development, studying the signaling mechanisms by which auxin influences cellular activities is of primary importance. In this review, we describe the current knowledge on the different modalities of signaling, from the well-characterized canonical nuclear auxin pathway, to the more recently discovered or re-discovered non-canonical modes of auxin signaling. In particular, we discuss how both the modularity of the nuclear auxin pathway and the dynamic regulation of its core components allow to trigger specific transcriptomic responses. We highlight the fact that the diversity of modes of auxin signaling allows for a wide range of timescales of auxin responses, from second-scale cytoplasmic responses to minute/hour-scale modifications of gene expression. Finally, we question the extent to which the temporality of auxin signaling and responses contributes to development in both the shoot and the root meristems. We conclude by stressing the fact that future investigations should allow to build an integrative view not only of the spatial control, but also of the temporality of auxin-mediated regulation of plant development, from the cell to the whole organism.
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Affiliation(s)
- Hugo Caumon
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
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5
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Davis JL, Kennedy C, Clerkin S, Treacy NJ, Dodd T, Moss C, Murphy A, Brazil DP, Cagney G, Brougham DF, Murad R, Finlay D, Vuori K, Crean J. Single-cell multiomics reveals the complexity of TGFβ signalling to chromatin in iPSC-derived kidney organoids. Commun Biol 2022; 5:1301. [PMID: 36435939 PMCID: PMC9701233 DOI: 10.1038/s42003-022-04264-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
Abstract
TGFβ1 plays a regulatory role in the determination of renal cell fate and the progression of renal fibrosis. Here we show an association between SMAD3 and the histone methyltransferase, EZH2, during cell differentiation; ChIP-seq revealed that SMAD3 and EZH2 co-occupy the genome in iPSCs and in iPSC-derived nephron progenitors. Through integration of single cell gene expression and epigenome profiling, we identified de novo ACTA2+ve/POSTN+ve myofibroblasts in kidney organoids treated with TGFβ1, characterised by increased SMAD3-dependent cis chromatin accessibility and gene expression associated with fibroblast activation. We have identified fibrosis-associated regulons characterised by enrichment of SMAD3, AP1, the ETS family of transcription factors, and NUAK1, CREB3L1, and RARG, corresponding to enriched motifs at accessible loci identified by scATACseq. Treatment with the EZH2 specific inhibitor GSK343, blocked SMAD3-dependent cis co-accessibility and inhibited myofibroblast activation. This mechanism, through which TGFβ signals directly to chromatin, represents a critical determinant of fibrotic, differentiated states.
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Affiliation(s)
- Jessica L. Davis
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Ciaran Kennedy
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Shane Clerkin
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Niall J. Treacy
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Thomas Dodd
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Catherine Moss
- grid.7886.10000 0001 0768 2743UCD Genomics Core Facility, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Alison Murphy
- grid.7886.10000 0001 0768 2743UCD Genomics Core Facility, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Derek P. Brazil
- grid.4777.30000 0004 0374 7521Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, BT9 7BL Northern Ireland, UK
| | - Gerard Cagney
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Dermot F. Brougham
- grid.7886.10000 0001 0768 2743UCD School of Chemistry, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Rabi Murad
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - Darren Finlay
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - Kristiina Vuori
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - John Crean
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4, Ireland.
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6
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The oncogenic JAG1 intracellular domain is a transcriptional cofactor that acts in concert with DDX17/SMAD3/TGIF2. Cell Rep 2022; 41:111626. [DOI: 10.1016/j.celrep.2022.111626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/23/2022] Open
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7
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Coda DM, Patel H, Gori I, Gaarenstroom TE, Song OR, Howell M, Hill CS. A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses. J Cell Sci 2022; 135:jcs259972. [PMID: 35302162 PMCID: PMC9080556 DOI: 10.1242/jcs.259972] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
SMAD2, an effector of the NODAL/Activin signalling pathway, regulates developmental processes by sensing distinct chromatin states and interacting with different transcriptional partners. However, the network of factors that controls SMAD2 chromatin binding and shapes its transcriptional programme over time is poorly characterised. Here, we combine ATAC-seq with computational footprinting to identify temporal changes in chromatin accessibility and transcription factor activity upon NODAL/Activin signalling. We show that SMAD2 binding induces chromatin opening genome wide. We discover footprints for FOXI3, FOXO3 and ZIC3 at the SMAD2-bound enhancers of the early response genes, Pmepa1 and Wnt3, respectively, and demonstrate their functionality. Finally, we determine a mechanism by which NODAL/Activin signalling induces delayed gene expression, by uncovering a self-enabling transcriptional cascade whereby activated SMADs, together with ZIC3, induce the expression of Wnt3. The resultant activated WNT pathway then acts together with the NODAL/Activin pathway to regulate expression of delayed target genes in prolonged NODAL/Activin signalling conditions. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Davide M. Coda
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Tessa E. Gaarenstroom
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ok-Ryul Song
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Caroline S. Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
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8
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Moody SC, Whiley PAF, Western PS, Loveland KL. The Impact of Activin A on Fetal Gonocytes: Chronic Versus Acute Exposure Outcomes. Front Endocrinol (Lausanne) 2022; 13:896747. [PMID: 35721752 PMCID: PMC9205402 DOI: 10.3389/fendo.2022.896747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Activin A, a TGFβ superfamily member, is important for normal testis development through its actions on Sertoli cell development. Our analyses of altered activin A mouse models indicated gonocyte abnormalities, implicating activin A as a key determinant of early germline formation. Whether it acts directly or indirectly on germ cells is not understood. In humans, the fetal testis may be exposed to abnormally elevated activin A levels during preeclampsia, maternal infections, or following ingestion of certain medications. We hypothesized that this may impact fetal testis development and ultimately affect adult fertility. Germ cells from two mouse models of altered activin bioactivity were analysed. RNA-Seq of gonocytes purified from E13.5 and E15.5 Inhba KO mice (activin A subunit knockout) identified 46 and 44 differentially expressed genes (DEGs) respectively, and 45 in the E13.5 Inha KO (inhibin alpha subunit knockout; increased activin A) gonocytes. To discern direct effects of altered activin bioactivity on germline transcripts, isolated E13.5 gonocytes were cultured for 24h with activin A or with the activin/Nodal/TGFβ inhibitor, SB431542. Gonocytes responded directly to altered signalling, with activin A promoting a more differentiated transcript profile (increased differentiation markers Dnmt3l, Nanos2 and Piwil4; decreased early germ cell markers Kit and Tdgf1), while SB431542 had a reciprocal effect (decreased Nanos2 and Piwil4; increased Kit). To delineate direct and indirect effects of activin A exposure on gonocytes, whole testes were cultured 48h with activin A or SB431542 and collected for histological and transcript analyses, or EdU added at the end of culture to measure germ and Sertoli cell proliferation using flow cytometry. Activin increased, and SB431542 decreased, Sertoli cell proliferation. SB431542-exposure resulted in germ cells escaping mitotic arrest. Analysis of FACS-isolated gonocytes following whole testis culture showed SB431542 increased the early germ cell marker Kit, however there was a general reduction in the impact of altered activin A bioavailability in the normal somatic cell environment. This multifaceted approach identifies a capacity for activin A to directly influence fetal germ cell development, highlighting the potential for altered activin A levels in utero to increase the risk of testicular pathologies that arise from impaired germline maturation.
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Affiliation(s)
- Sarah C. Moody
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Penny A. F. Whiley
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Patrick S. Western
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Kate L. Loveland
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- *Correspondence: Kate L. Loveland,
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9
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Guglielmi L, Heliot C, Kumar S, Alexandrov Y, Gori I, Papaleonidopoulou F, Barrington C, East P, Economou AD, French PMW, McGinty J, Hill CS. Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways. Nat Commun 2021; 12:6374. [PMID: 34737283 PMCID: PMC8569018 DOI: 10.1038/s41467-021-26486-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptional effector SMAD4 is a core component of the TGF-β family signaling pathways. However, its role in vertebrate embryo development remains unresolved. To address this, we deleted Smad4 in zebrafish and investigated the consequences of this on signaling by the TGF-β family morphogens, BMPs and Nodal. We demonstrate that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling. However, unexpectedly, Nodal signaling is maintained, but lacks robustness. This Smad4-independent Nodal signaling is sufficient for mesoderm specification, but not for optimal endoderm specification. Furthermore, using Optical Projection Tomography in combination with 3D embryo morphometry, we have generated a BMP morphospace and demonstrate that Smad4 mutants are morphologically indistinguishable from embryos in which BMP signaling has been genetically/pharmacologically perturbed. Smad4 is thus differentially required for signaling by different TGF-β family ligands, which has implications for diseases where Smad4 is mutated or deleted.
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Affiliation(s)
- Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Claire Heliot
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sunil Kumar
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Yuriy Alexandrov
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Philip East
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andrew D Economou
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Paul M W French
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - James McGinty
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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10
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Xie X, Shirasu T, Guo LW, Kent KC. Smad2 inhibition of MET transcription potentiates human vascular smooth muscle cell apoptosis. ATHEROSCLEROSIS PLUS 2021; 44:31-42. [PMID: 35445204 PMCID: PMC9017589 DOI: 10.1016/j.athplu.2021.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Background: Vascular smooth muscle cell (SMC) apoptosis is involved in major cardiovascular diseases. Smad2 is a transcription factor implicated in aortic aneurysm. The molecular mediators of Smad2-driven SMC apoptosis are not well defined. Here we have identified a Smad2-directed mechanism involving MET and FAS, both encoding cell membrane signaling receptors. Methods and results: Guided by microarray analysis in human primary aortic SMCs, loss/gain-of-function (siRNA/overexpression) indicated that Smad2 negatively and positively regulated, respectively, the gene expression of Met which was identified herein as anti-apoptotic and that of Fas, a known pro-apoptotic factor. While co-immunoprecipitation suggested a physical association of Smad2 with p53, chromatin immunoprecipitation followed by quantitative PCR revealed their co-occupancy in the same region of the MET promoter. Activating p53 with nutlin3a further potentiated the suppression of MET promoter-dependent luciferase activity and the exacerbation of SMC apoptosis that were caused by Smad2 overexpression. These results indicated that Smad2 in SMCs repressed the transcription of MET by cooperating with p53, and that Smad2 also activated FAS, a target gene of its transcription factor activity. Conclusions: Our study suggests a pro-apoptotic mechanism in human SMCs, whereby Smad2 negatively and positively regulates MET and FAS, genes encoding anti-apoptotic and pro-apoptotic factors, respectively.
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Affiliation(s)
- Xiujie Xie
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Takuro Shirasu
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - K Craig Kent
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
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11
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Wong JYK, Mukherjee R, Miao J, Bilyk O, Triana V, Miskolzie M, Henninot A, Dwyer JJ, Kharchenko S, Iampolska A, Volochnyuk DM, Lin YS, Postovit LM, Derda R. Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL. Chem Sci 2021; 12:9694-9703. [PMID: 34349940 PMCID: PMC8294009 DOI: 10.1039/d1sc01916c] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
In this manuscript, we developed a two-fold symmetric linchpin (TSL) that converts readily available phage-displayed peptides libraries made of 20 common amino acids to genetically-encoded libraries of bicyclic peptides displayed on phage. TSL combines an aldehyde-reactive group and two thiol-reactive groups; it bridges two side chains of cysteine [C] with an N-terminal aldehyde group derived from the N-terminal serine [S], yielding a novel bicyclic topology that lacks a free N-terminus. Phage display libraries of SX1CX2X3X4X5X6X7C sequences, where X is any amino acid but Cys, were converted to a library of bicyclic TSL-[S]X1[C]X2X3X4X5X6X7[C] peptides in 45 ± 15% yield. Using this library and protein morphogen NODAL as a target, we discovered bicyclic macrocycles that specifically antagonize NODAL-induced signaling in cancer cells. At a 10 μM concentration, two discovered bicyclic peptides completely suppressed NODAL-induced phosphorylation of SMAD2 in P19 embryonic carcinoma cells. The TSL-[S]Y[C]KRAHKN[C] bicycle inhibited NODAL-induced proliferation of NODAL-TYK-nu ovarian carcinoma cells with apparent IC50 of 1 μM. The same bicycle at 10 μM concentration did not affect the growth of the control TYK-nu cells. TSL-bicycles remained stable over the course of the 72 hour-long assays in a serum-rich cell-culture medium. We further observed general stability in mouse serum and in a mixture of proteases (Pronase™) for 21 diverse bicyclic macrocycles of different ring sizes, amino acid sequences, and cross-linker geometries. TSL-constrained peptides to expand the previously reported repertoire of phage-displayed bicyclic architectures formed by cross-linking Cys side chains. We anticipate that it will aid the discovery of proteolytically stable bicyclic inhibitors for a variety of protein targets.
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Affiliation(s)
- Jeffrey Y-K Wong
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Olena Bilyk
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Vivian Triana
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Mark Miskolzie
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | | | - John J Dwyer
- Ferring Research Institute San Diego California 92121 USA
| | | | - Anna Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Lynne-Marie Postovit
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
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12
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Dieters-Castator D, Dantonio PM, Piaseczny M, Zhang G, Liu J, Kuljanin M, Sherman S, Jewer M, Quesnel K, Kang EY, Köbel M, Siegers GM, Leask A, Hess D, Lajoie G, Postovit LM. Embryonic protein NODAL regulates the breast tumor microenvironment by reprogramming cancer-derived secretomes. Neoplasia 2021; 23:375-390. [PMID: 33784590 PMCID: PMC8041663 DOI: 10.1016/j.neo.2021.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The tumor microenvironment (TME) is an important mediator of breast cancer progression. Cancer-associated fibroblasts constitute a major component of the TME and may originate from tissue-associated fibroblasts or infiltrating mesenchymal stromal cells (MSCs). The mechanisms by which cancer cells activate fibroblasts and recruit MSCs to the TME are largely unknown, but likely include deposition of a pro-tumorigenic secretome. The secreted embryonic protein NODAL is clinically associated with breast cancer stage and promotes tumor growth, metastasis, and vascularization. Herein, we show that NODAL expression correlates with the presence of activated fibroblasts in human triple-negative breast cancers and that it directly induces Cancer-associated fibroblasts phenotypes. We further show that NODAL reprograms cancer cell secretomes by simultaneously altering levels of chemokines (e.g., CXCL1), cytokines (e.g., IL-6) and growth factors (e.g., PDGFRA), leading to alterations in MSC chemotaxis. We therefore demonstrate a hitherto unappreciated mechanism underlying the dynamic regulation of the TME.
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Affiliation(s)
| | - Paola M Dantonio
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Matt Piaseczny
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada
| | - Guihua Zhang
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Jiahui Liu
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Miljan Kuljanin
- Robarts Research Institute, London, ON, Canada; Department of Biochemistry, Western University, London, ON, Canada
| | - Stephen Sherman
- Robarts Research Institute, London, ON, Canada; Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Michael Jewer
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada; Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Katherine Quesnel
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Eun Young Kang
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Andrew Leask
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - David Hess
- Robarts Research Institute, London, ON, Canada; Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Gilles Lajoie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Lynne-Marie Postovit
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada; Department of Oncology, University of Alberta, Edmonton, AB, Canada.
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13
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Russo K, Wharton KA. BMP/TGF-β signaling as a modulator of neurodegeneration in ALS. Dev Dyn 2021; 251:10-25. [PMID: 33745185 DOI: 10.1002/dvdy.333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022] Open
Abstract
This commentary focuses on the emerging intersection between BMP/TGF-β signaling roles in nervous system function and the amyotrophic lateral sclerosis (ALS) disease state. Future research is critical to elucidate the molecular underpinnings of this intersection of the cellular processes disrupted in ALS and those influenced by BMP/TGF-β signaling, including synapse structure, neurotransmission, plasticity, and neuroinflammation. Such knowledge promises to inform us of ideal entry points for the targeted modulation of dysfunctional cellular processes in an effort to abrogate ALS pathologies. It is likely that different interventions are required, either at discrete points in disease progression, or across multiple dysfunctional processes which together lead to motor neuron degeneration and death. We discuss the challenging, but intriguing idea that modulation of the pleiotropic nature of BMP/TGF-β signaling could be advantageous, as a way to simultaneously treat defects in more than one cell process across different forms of ALS.
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Affiliation(s)
- Kathryn Russo
- Department of Neuroscience, Brown University, Providence, Rhode Island, USA.,Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, Rhode Island, USA
| | - Kristi A Wharton
- Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, Rhode Island, USA.,Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
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14
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Transient Nodal Signaling in Left Precursors Coordinates Opposed Asymmetries Shaping the Heart Loop. Dev Cell 2020; 55:413-431.e6. [PMID: 33171097 DOI: 10.1016/j.devcel.2020.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/17/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Abstract
The secreted factor Nodal, known as a major left determinant, is associated with severe heart defects. Yet, it has been unclear how it regulates asymmetric morphogenesis such as heart looping, which align cardiac chambers to establish the double blood circulation. Here, we report that Nodal is transiently active in precursors of the mouse heart tube poles, before looping. In conditional mutants, we show that Nodal is not required to initiate asymmetric morphogenesis. We provide evidence of a heart-specific random generator of asymmetry that is independent of Nodal. Using 3D quantifications and simulations, we demonstrate that Nodal functions as a bias of this mechanism: it is required to amplify and coordinate opposed left-right asymmetries at the heart tube poles, thus generating a robust helical shape. We identify downstream effectors of Nodal signaling, regulating asymmetries in cell proliferation, differentiation, and extracellular matrix composition. Our study uncovers how Nodal regulates asymmetric organogenesis.
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15
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Foxh1/Nodal Defines Context-Specific Direct Maternal Wnt/β-Catenin Target Gene Regulation in Early Development. iScience 2020; 23:101314. [PMID: 32650116 PMCID: PMC7347983 DOI: 10.1016/j.isci.2020.101314] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/20/2020] [Accepted: 06/20/2020] [Indexed: 12/19/2022] Open
Abstract
Although Wnt/β-catenin signaling is generally conserved and well understood, the regulatory mechanisms controlling context-specific direct Wnt target gene expression in development and disease are still unclear. The onset of zygotic gene transcription in early embryogenesis represents an ideal, accessible experimental system to investigate context-specific direct Wnt target gene regulation. We combine transcriptomics using RNA-seq with genome-wide β-catenin association using ChIP-seq to identify stage-specific direct Wnt target genes. We propose coherent feedforward regulation involving two distinct classes of direct maternal Wnt target genes, which differ both in expression and persistence of β-catenin association. We discover that genomic β-catenin association overlaps with Foxh1-associated regulatory sequences and demonstrate that direct maternal Wnt target gene expression requires Foxh1 function and Nodal/Tgfβ signaling. Our results support a new paradigm for direct Wnt target gene co-regulation with context-specific mechanisms that will inform future studies of embryonic development and more widely stem cell-mediated homeostasis and human disease. Combining RNA-seq and β-catenin ChIP-seq identifies direct Wnt target genes Two distinct classes of direct maternal Wnt/β-catenin target genes can be discerned We propose coherent feedforward regulation of gene expression of the second class Maternal Wnt target gene expression of both classes requires Nodal/Foxh1 signaling
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16
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Galvan-Ampudia CS, Cerutti G, Legrand J, Brunoud G, Martin-Arevalillo R, Azais R, Bayle V, Moussu S, Wenzl C, Jaillais Y, Lohmann JU, Godin C, Vernoux T. Temporal integration of auxin information for the regulation of patterning. eLife 2020; 9:55832. [PMID: 32379043 PMCID: PMC7205470 DOI: 10.7554/elife.55832] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Positional information is essential for coordinating the development of multicellular organisms. In plants, positional information provided by the hormone auxin regulates rhythmic organ production at the shoot apex, but the spatio-temporal dynamics of auxin gradients is unknown. We used quantitative imaging to demonstrate that auxin carries high-definition graded information not only in space but also in time. We show that, during organogenesis, temporal patterns of auxin arise from rhythmic centrifugal waves of high auxin travelling through the tissue faster than growth. We further demonstrate that temporal integration of auxin concentration is required to trigger the auxin-dependent transcription associated with organogenesis. This provides a mechanism to temporally differentiate sites of organ initiation and exemplifies how spatio-temporal positional information can be used to create rhythmicity. Plants, like animals and many other multicellular organisms, control their body architecture by creating organized patterns of cells. These patterns are generally defined by signal molecules whose levels differ across the tissue and change over time. This tells the cells where they are located in the tissue and therefore helps them know what tasks to perform. A plant hormone called auxin is one such signal molecule and it controls when and where plants produce new leaves and flowers. Over time, this process gives rise to the dashing arrangements of spiraling organs exhibited by many plant species. The leaves and flowers form from a relatively small group of cells at the tip of a growing stem known as the shoot apical meristem. Auxin accumulates at precise locations within the shoot apical meristem before cells activate the genes required to make a new leaf or flower. However, the precise role of auxin in forming these new organs remained unclear because the tools to observe the process in enough detail were lacking. Galvan-Ampudia, Cerutti et al. have now developed new microscopy and computational approaches to observe auxin in a small plant known as Arabidopsis thaliana. This showed that dozens of shoot apical meristems exhibited very similar patterns of auxin. Images taken over a period of several hours showed that the locations where auxin accumulated were not fixed on a group of cells but instead shifted away from the center of the shoot apical meristems faster than the tissue grew. This suggested the cells experience rapidly changing levels of auxin. Further experiments revealed that the cells needed to be exposed to a high level of auxin over time to activate genes required to form an organ. This mechanism sheds a new light on how auxin regulates when and where plants make new leaves and flowers. The tools developed by Galvan-Ampudia, Cerutti et al. could be used to study the role of auxin in other plant tissues, and to investigate how plants regulate the response to other plant hormones.
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Affiliation(s)
- Carlos S Galvan-Ampudia
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Guillaume Cerutti
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Jonathan Legrand
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Géraldine Brunoud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Romain Azais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Steven Moussu
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Christian Wenzl
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Christophe Godin
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
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17
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Itoh Y, Koinuma D, Omata C, Ogami T, Motizuki M, Yaguchi SI, Itoh T, Miyake K, Tsutsumi S, Aburatani H, Saitoh M, Miyazono K, Miyazawa K. A comparative analysis of Smad-responsive motifs identifies multiple regulatory inputs for TGF-β transcriptional activation. J Biol Chem 2019; 294:15466-15479. [PMID: 31481467 DOI: 10.1074/jbc.ra119.009877] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/29/2019] [Indexed: 12/17/2022] Open
Abstract
Smad proteins are transcriptional regulators activated by TGF-β. They are known to bind to two distinct Smad-responsive motifs, namely the Smad-binding element (SBE) (5'-GTCTAGAC-3') and CAGA motifs (5'-AGCCAGACA-3' or 5'-TGTCTGGCT-3'). However, the mechanisms by which these motifs promote Smad activity are not fully elucidated. In this study, we performed DNA CASTing, binding assays, ChIP sequencing, and quantitative RT-PCR to dissect the details of Smad binding and function of the SBE and CAGA motifs. We observed a preference for Smad3 to bind CAGA motifs and Smad4 to bind SBE, and that either one SBE or a triple-CAGA motif forms a cis-acting functional half-unit for Smad-dependent transcription activation; combining two half-units allows efficient activation. Unexpectedly, the extent of Smad binding did not directly correlate with the abilities of Smad-binding sequences to induce gene expression. We found that Smad proteins are more tolerant of single bp mutations in the context of the CAGA motifs, with any mutation in the SBE disrupting function. CAGA and CAGA-like motifs but not SBE are widely distributed among stimulus-dependent Smad2/3-binding sites in normal murine mammary gland epithelial cells, and the number of CAGA and CAGA-like motifs correlates with fold-induction of target gene expression by TGF-β. These data, demonstrating Smad responsiveness can be tuned by both sequence and number of repeats, provide a compelling explanation for why CAGA motifs are predominantly used for Smad-dependent transcription activation in vivo.
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Affiliation(s)
- Yuka Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Daizo Koinuma
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Chiho Omata
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Tomohiro Ogami
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mitsuyoshi Motizuki
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - So-Ichi Yaguchi
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Takuma Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan.,Research Training Program for Undergraduates, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Kunio Miyake
- Department of Social Medicine, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Masao Saitoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan.,Center for Medical Education and Science, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Keiji Miyazawa
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
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18
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Fischer P, Chen H, Pacho F, Rieder D, Kimmel RA, Meyer D. FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation. BMC Biol 2019; 17:61. [PMID: 31362746 PMCID: PMC6664792 DOI: 10.1186/s12915-019-0683-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022] Open
Abstract
Background FoxH1 is a forkhead transcription factor with conserved key functions in vertebrate mesoderm induction and left-right patterning downstream of the TGF-beta/Nodal signaling pathway. Binding of the forkhead domain (FHD) of FoxH1 to a highly conserved proximal sequence motif was shown to regulate target gene expression. Results We identify the conserved microRNA-430 family (miR-430) as a novel target of FoxH1. miR-430 levels are increased in foxH1 mutants, resulting in a reduced expression of transcripts that are targeted by miR-430 for degradation. To determine the underlying mechanism of miR-430 repression, we performed chromatin immunoprecipitation studies and overexpression experiments with mutant as well as constitutive active and repressive forms of FoxH1. Our studies reveal a molecular interaction of FoxH1 with miR-430 loci independent of the FHD. Furthermore, we show that previously described mutant forms of FoxH1 that disrupt DNA binding or that lack the C-terminal Smad Interaction Domain (SID) dominantly interfere with miR-430 repression, but not with the regulation of previously described FoxH1 targets. Conclusions We were able to identify the distinct roles of protein domains of FoxH1 in the regulation process of miR-430. We provide evidence that the indirect repression of miR-430 loci depends on the connection to a distal repressive chromosome environment via a non-canonical mode. The widespread distribution of such non-canonical binding sites of FoxH1, found not only in our study, argues against a function restricted to regulating miR-430 and for a more global role of FoxH1 in chromatin folding. Electronic supplementary material The online version of this article (10.1186/s12915-019-0683-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Fischer
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Hao Chen
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Frederic Pacho
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Biocenter, Innsbruck Medical University, Innrain 80, 6020, Innsbruck, Austria
| | - Robin A Kimmel
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Dirk Meyer
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
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19
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Morabito M, Larcher M, Cavalli FM, Foray C, Forget A, Mirabal-Ortega L, Andrianteranagna M, Druillennec S, Garancher A, Masliah-Planchon J, Leboucher S, Debalkew A, Raso A, Delattre O, Puget S, Doz F, Taylor MD, Ayrault O, Bourdeaut F, Eychène A, Pouponnot C. An autocrine ActivinB mechanism drives TGFβ/Activin signaling in Group 3 medulloblastoma. EMBO Mol Med 2019; 11:e9830. [PMID: 31328883 PMCID: PMC6685082 DOI: 10.15252/emmm.201809830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 01/13/2023] Open
Abstract
Medulloblastoma (MB) is a pediatric tumor of the cerebellum divided into four groups. Group 3 is of bad prognosis and remains poorly characterized. While the current treatment involving surgery, radiotherapy, and chemotherapy often fails, no alternative therapy is yet available. Few recurrent genomic alterations that can be therapeutically targeted have been identified. Amplifications of receptors of the TGFβ/Activin pathway occur at very low frequency in Group 3 MB. However, neither their functional relevance nor activation of the downstream signaling pathway has been studied. We showed that this pathway is activated in Group 3 MB with some samples showing a very strong activation. Beside genetic alterations, we demonstrated that an ActivinB autocrine stimulation is responsible for pathway activation in a subset of Group 3 MB characterized by high PMEPA1 levels. Importantly, Galunisertib, a kinase inhibitor of the cognate receptors currently tested in clinical trials for Glioblastoma patients, showed efficacy on orthotopically grafted MB‐PDX. Our data demonstrate that the TGFβ/Activin pathway is active in a subset of Group 3 MB and can be therapeutically targeted.
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Affiliation(s)
- Morgane Morabito
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Magalie Larcher
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Florence Mg Cavalli
- The Arthur and Sonia Labatt Brain Tumour Research Center, The Hospital for Sick Children, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chloé Foray
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Antoine Forget
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Liliana Mirabal-Ortega
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Mamy Andrianteranagna
- PSL Research University, Paris, France.,Institut Curie, Paris, France.,INSERM U830, Paris, France.,Translational Research in Pediatric Oncology, Institut Curie SiRIC, Paris, France.,SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France.,INSERM, U900, Paris, France.,MINES ParisTech, CBIO-Centre for Computational Biology, Paris, France
| | - Sabine Druillennec
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Alexandra Garancher
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Julien Masliah-Planchon
- PSL Research University, Paris, France.,Institut Curie, Paris, France.,INSERM U830, Paris, France.,SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France
| | - Sophie Leboucher
- Institut Curie, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France
| | - Abel Debalkew
- The Arthur and Sonia Labatt Brain Tumour Research Center, The Hospital for Sick Children, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alessandro Raso
- Department of Patology, ASL 3 Genovese, SC Laboratorio d'Analisi, Genova, Italy
| | - Olivier Delattre
- PSL Research University, Paris, France.,Institut Curie, Paris, France.,INSERM U830, Paris, France.,SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France
| | - Stéphanie Puget
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Département Neurochirurgie Pédiatrique, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - François Doz
- Institut Curie, Paris, France.,SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Center, The Hospital for Sick Children, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
| | - Olivier Ayrault
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Franck Bourdeaut
- PSL Research University, Paris, France.,Institut Curie, Paris, France.,INSERM U830, Paris, France.,Translational Research in Pediatric Oncology, Institut Curie SiRIC, Paris, France.,SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France
| | - Alain Eychène
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
| | - Celio Pouponnot
- Institut Curie, Orsay, France.,INSERM U1021, Centre Universitaire, Orsay, France.,CNRS UMR 3347, Centre Universitaire, Orsay, France.,University Paris Sud - Paris-Saclay, Orsay, France.,PSL Research University, Paris, France
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20
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Miller DSJ, Schmierer B, Hill CS. TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation. J Cell Sci 2019; 132:jcs234039. [PMID: 31217285 PMCID: PMC6679586 DOI: 10.1242/jcs.234039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 12/29/2022] Open
Abstract
Growth factor-induced signal transduction pathways are tightly regulated at multiple points intracellularly, but how cells monitor levels of extracellular ligand and translate this information into appropriate downstream responses remains unclear. Understanding signalling dynamics is thus a key challenge in determining how cells respond to external cues. Here, we demonstrate that different TGF-β family ligands, namely activin A and BMP4, signal with distinct dynamics, which differ profoundly from those of TGF-β itself. The signalling dynamics are driven by differences in the localisation and internalisation of receptors for each ligand, which in turn determine the capability of cells to monitor levels of extracellular ligand. By using mathematical modelling, we demonstrate that the distinct receptor behaviours and signalling dynamics observed may be primarily driven by differences in ligand-receptor affinity. Furthermore, our results provide a clear rationale for the different mechanisms of pathway regulation found in vivo for each of these growth factors.
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Affiliation(s)
- Daniel S J Miller
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Bernhard Schmierer
- Karolinska Institutet, Department of Medical Biochemistry and Biophysics and SciLifeLab Biomedicum 9B, Solnavägen 9, SE-171 65 Solna, Stockholm, Sweden
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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21
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Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells. Sci Rep 2019; 9:5372. [PMID: 30926874 PMCID: PMC6440972 DOI: 10.1038/s41598-019-41870-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/20/2019] [Indexed: 12/22/2022] Open
Abstract
The transduction of extracellular signals through signaling pathways that culminate in a transcriptional response is central to many biological processes. However, quantitative relationships between activities of signaling pathway components and transcriptional output of target genes remain poorly explored. Here we developed a dual bioluminescence imaging strategy allowing simultaneous monitoring of nuclear translocation of the SMAD4 and SMAD2 transcriptional activators upon TGF-β stimulation, and the transcriptional response of the endogenous connective tissue growth factor (ctgf) gene. Using cell lines allowing to vary exogenous SMAD4/2 expression levels, we performed quantitative measurements of the temporal profiles of SMAD4/2 translocation and ctgf transcription kinetics in hundreds of individual cells at high temporal resolution. We found that while nuclear translocation efficiency had little impact on initial ctgf transcriptional activation, high total cellular SMAD4 but not SMAD2 levels increased the probability of cells to exhibit a sustained ctgf transcriptional response. The approach we present here allows time-resolved single cell quantification of transcription factor dynamics and transcriptional responses and thereby sheds light on the quantitative relationship between SMADs and target gene responses.
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22
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Miller DSJ, Bloxham RD, Jiang M, Gori I, Saunders RE, Das D, Chakravarty P, Howell M, Hill CS. The Dynamics of TGF-β Signaling Are Dictated by Receptor Trafficking via the ESCRT Machinery. Cell Rep 2018; 25:1841-1855.e5. [PMID: 30428352 PMCID: PMC7615189 DOI: 10.1016/j.celrep.2018.10.056] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 08/03/2018] [Accepted: 10/15/2018] [Indexed: 01/17/2023] Open
Abstract
Signal transduction pathways stimulated by secreted growth factors are tightly regulated at multiple levels between the cell surface and the nucleus. The trafficking of cell surface receptors is emerging as a key step for regulating appropriate cellular responses, with perturbations in this process contributing to human diseases, including cancer. For receptors recognizing ligands of the transforming growth factor β (TGF-β) family, little is known about how trafficking is regulated or how this shapes signaling dynamics. Here, using whole genome small interfering RNA (siRNA) screens, we have identified the ESCRT (endosomal sorting complex required for transport) machinery as a crucial determinant of signal duration. Downregulation of ESCRT components increases the outputs of TGF-β signaling and sensitizes cells to low doses of ligand in their microenvironment. This sensitization drives an epithelial-to-mesenchymal transition (EMT) in response to low doses of ligand, and we demonstrate a link between downregulation of the ESCRT machinery and cancer survival.
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Affiliation(s)
- Daniel S J Miller
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Robert D Bloxham
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ming Jiang
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rebecca E Saunders
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Debipriya Das
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Probir Chakravarty
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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23
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Vincent-Mistiaen Z, Elbediwy A, Vanyai H, Cotton J, Stamp G, Nye E, Spencer-Dene B, Thomas GJ, Mao J, Thompson B. YAP drives cutaneous squamous cell carcinoma formation and progression. eLife 2018; 7:e33304. [PMID: 30231971 PMCID: PMC6147738 DOI: 10.7554/elife.33304] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 06/29/2018] [Indexed: 01/14/2023] Open
Abstract
Squamous cell carcinoma (SCC) can progress to malignant metastatic cancer, including an aggressive subtype known as spindle cell carcinoma (spSCC). spSCC formation involves epithelial-to-mesenchymal transition (EMT), yet the molecular basis of this event remains unknown. The transcriptional co-activator YAP undergoes recurrent amplification in human SCC and overexpression of YAP drives SCC formation in mice. Here, we show that human spSCC tumours also feature strong nuclear localisation of YAP and overexpression of activated YAP (NLS-YAP-5SA) with Keratin-5 (K5-CreERt) is sufficient to induce rapid formation of both SCC and spSCC in mice. spSCC tumours arise at sites of epithelial scratch wounding, where tumour-initiating epithelial cells undergo EMT to generate spSCC. Expression of the EMT transcription factor ZEB1 arises upon wounding and is a defining characteristic of spSCC in mice and humans. Thus, the wound healing response synergises with YAP to drive metaplastic transformation of SCC to spSCC.
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Affiliation(s)
| | | | | | - Jennifer Cotton
- University of Massachusetts Medical SchoolWorcesterUnited States
| | | | - Emma Nye
- The Francis Crick InstituteLondonUnited Kingdom
| | | | - Gareth J Thomas
- Cancer Sciences Unit, Faculty of MedicineUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Junhao Mao
- University of Massachusetts Medical SchoolWorcesterUnited States
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24
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Roy S, Gandra D, Seger C, Biswas A, Kushnir VA, Gleicher N, Kumar TR, Sen A. Oocyte-Derived Factors (GDF9 and BMP15) and FSH Regulate AMH Expression Via Modulation of H3K27AC in Granulosa Cells. Endocrinology 2018; 159:3433-3445. [PMID: 30060157 PMCID: PMC6112599 DOI: 10.1210/en.2018-00609] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022]
Abstract
Anti-Müllerian hormone (AMH) produced by ovarian granulosa cells (GCs) plays a crucial role in ovarian function. It is used as a diagnostic and/or prognostic marker of fertility as well as for pathophysiological conditions in women. In this study, we investigated the underlying mechanism for regulation of AMH expression in GCs using primary mouse GCs and a human GC tumor-derived KGN cell line. We find that growth differentiation factor 9 (GDF9) and bone morphogenetic factor 15 (BMP15) together (GDF9 + BMP15), but not when tested separately, significantly induce AMH expression in vitro and in vivo (serum AMH). Our results show that GDF9 + BMP15 through the PI3K/Akt and Smad2/3 pathways synergistically recruit the coactivator p300 on the AMH promoter region that promotes acetylation of histone 3 lysine 27 (H3K27ac), facilitating AMH/Amh expression. Intriguingly, we also find that FSH inhibits GDF9 + BMP15-induced increase of AMH/Amh expression. This inhibition occurs through FSH-induced protein kinase A/SF1-mediated expression of gonadotropin inducible ovarian transcription factor 1, a transcriptional repressor, that recruits histone deacetylase 2 to deacetylate H3K27ac, resulting in the suppression of AMH/Amh expression. Furthermore, we report that ovarian Amh mRNA levels are significantly higher in Fshβ-null mice (Fshβ-/-) compared with those in wild-type (WT) mice. In addition, ovarian Amh mRNA levels are restored in Fshβ-null mice expressing a human WT FSHβ transgene (FSHβ-/-hFSHβWT). Our study provides a mechanistic insight into the regulation of AMH expression that has many implications in female reproduction/fertility.
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Affiliation(s)
- Sambit Roy
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
| | - Divya Gandra
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
| | - Christina Seger
- Division of Endocrinology and Metabolism, Department of Medicine, University of Rochester Medical Center, Rochester, New York
| | - Anindita Biswas
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
| | | | - Norbert Gleicher
- Center for Human Reproduction, New York, New York
- Stem Cell Biology and Molecular Embryology Laboratory, The Rockefeller University, New York, New York
- Department of Obstetrics and Gynecology, Vienna University of Medicine, Vienna, Austria
| | - T Rajendra Kumar
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz, Denver, Colorado
| | - Aritro Sen
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
- Correspondence: Aritro Sen, PhD, Reproductive and Developmental Sciences Program, Department of Animal Sciences, 1230A Anthony Hall, Michigan State University, East Lansing, Michigan 48824. E-mail:
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25
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Klein RH, Tung PY, Somanath P, Fehling HJ, Knoepfler PS. Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer. Stem Cell Res 2018; 31:83-94. [PMID: 30031967 PMCID: PMC6133722 DOI: 10.1016/j.scr.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/20/2022] Open
Abstract
Developmental pluripotency associated factor 4 (Dppa4) is a highly specific marker of pluripotent cells, and is also overexpressed in certain cancers, but its function in either of these contexts is poorly understood. In this study, we use ChIP-Seq to identify Dppa4 binding genome-wide in three distinct cell types: mouse embryonic stem cells (mESC), embryonal carcinoma cells, and 3T3 fibroblasts ectopically expressing Dppa4. We find a core set of Dppa4 binding sites shared across cell types, and also a substantial number of sites unique to each cell type. Across cell types Dppa4 shows a preference for binding to regions with active chromatin signatures, and can influence chromatin modifications at target genes. In 3T3 fibroblasts with enforced Dppa4 expression, Dppa4 represses the cell cycle inhibitor Cdkn2c and activates Ets family transcription factor Etv4, leading to alterations in the cell cycle that likely contribute to the oncogenic phenotype. Dppa4 also directly regulates Etv4 in mESC but represses it in this context, and binds with Oct4 to a set of shared targets that are largely independent of Sox2 and Nanog, indicating that Dppa4 functions independently of the core pluripotency network in stem cells. Together these data provide novel insights into Dppa4 function in both pluripotent and oncogenic contexts.
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Affiliation(s)
- Rachel Herndon Klein
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Po-Yuan Tung
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Priyanka Somanath
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | | | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States.
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26
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David CJ, Massagué J. Contextual determinants of TGFβ action in development, immunity and cancer. Nat Rev Mol Cell Biol 2018; 19:419-435. [PMID: 29643418 DOI: 10.1038/s41580-018-0007-0] [Citation(s) in RCA: 520] [Impact Index Per Article: 86.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Few cell signals match the impact of the transforming growth factor-β (TGFβ) family in metazoan biology. TGFβ cytokines regulate cell fate decisions during development, tissue homeostasis and regeneration, and are major players in tumorigenesis, fibrotic disorders, immune malfunctions and various congenital diseases. The effects of the TGFβ family are mediated by a combinatorial set of ligands and receptors and by a common set of receptor-activated mothers against decapentaplegic homologue (SMAD) transcription factors, yet the effects can differ dramatically depending on the cell type and the conditions. Recent progress has illuminated a model of TGFβ action in which SMADs bind genome-wide in partnership with lineage-determining transcription factors and additionally integrate inputs from other pathways and the chromatin to trigger specific cellular responses. These new insights clarify the operating logic of the TGFβ pathway in physiology and disease.
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Affiliation(s)
- Charles J David
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tsinghua University School of Medicine, Department of Basic Sciences, Beijing, China
| | - Joan Massagué
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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27
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Hill CS. Spatial and temporal control of NODAL signaling. Curr Opin Cell Biol 2018; 51:50-57. [PMID: 29153705 DOI: 10.1016/j.ceb.2017.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/21/2022]
Abstract
Embryonic development is orchestrated by the activity of signal transduction pathways, amongst which are those downstream of the transforming growth factor β (TGF-β) family. Here I focus on signalling by one of these ligands, NODAL, which is essential for early embryonic axis patterning. I review recent advances in our understanding of how NODAL signalling is transduced from the plasma membrane to the nucleus to regulate the transcription of target genes, and how domains of NODAL activity are established and refined during embryonic development. The duration of signalling is emerging as a key determinant of the specificity of downstream responses in terms of cell fate decisions and I will discuss what is currently known about the underlying mechanisms.
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Affiliation(s)
- Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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28
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Ramachandran A, Vizán P, Das D, Chakravarty P, Vogt J, Rogers KW, Müller P, Hinck AP, Sapkota GP, Hill CS. TGF-β uses a novel mode of receptor activation to phosphorylate SMAD1/5 and induce epithelial-to-mesenchymal transition. eLife 2018; 7:e31756. [PMID: 29376829 PMCID: PMC5832415 DOI: 10.7554/elife.31756] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/26/2018] [Indexed: 12/15/2022] Open
Abstract
The best characterized signaling pathway downstream of transforming growth factor β (TGF-β) is through SMAD2 and SMAD3. However, TGF-β also induces phosphorylation of SMAD1 and SMAD5, but the mechanism of this phosphorylation and its functional relevance is not known. Here, we show that TGF-β-induced SMAD1/5 phosphorylation requires members of two classes of type I receptor, TGFBR1 and ACVR1, and establish a new paradigm for receptor activation where TGFBR1 phosphorylates and activates ACVR1, which phosphorylates SMAD1/5. We demonstrate the biological significance of this pathway by showing that approximately a quarter of the TGF-β-induced transcriptome depends on SMAD1/5 signaling, with major early transcriptional targets being the ID genes. Finally, we show that TGF-β-induced epithelial-to-mesenchymal transition requires signaling via both the SMAD3 and SMAD1/5 pathways, with SMAD1/5 signaling being essential to induce ID1. Therefore, combinatorial signaling via both SMAD pathways is essential for the full TGF-β-induced transcriptional program and physiological responses.
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Affiliation(s)
| | - Pedro Vizán
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Debipriya Das
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Probir Chakravarty
- Bioinformatics and Biostatistics FacilityThe Francis Crick InstituteLondonUnited Kingdom
| | - Janis Vogt
- Medical Research Council Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUnited Kingdom
| | | | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Andrew P Hinck
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghUnited States
| | - Gopal P Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUnited Kingdom
| | - Caroline S Hill
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
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29
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van Boxtel AL, Economou AD, Heliot C, Hill CS. Long-Range Signaling Activation and Local Inhibition Separate the Mesoderm and Endoderm Lineages. Dev Cell 2018; 44:179-191.e5. [PMID: 29275993 PMCID: PMC5791662 DOI: 10.1016/j.devcel.2017.11.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/20/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022]
Abstract
Specification of the three germ layers by graded Nodal signaling has long been seen as a paradigm for patterning through a single morphogen gradient. However, by exploiting the unique properties of the zebrafish embryo to capture the dynamics of signaling and cell fate allocation, we now demonstrate that Nodal functions in an incoherent feedforward loop, together with Fgf, to determine the pattern of endoderm and mesoderm specification. We show that Nodal induces long-range Fgf signaling while simultaneously inducing the cell-autonomous Fgf signaling inhibitor Dusp4 within the first two cell tiers from the margin. The consequent attenuation of Fgf signaling in these cells allows specification of endoderm progenitors, while the cells further from the margin, which receive Nodal and/or Fgf signaling, are specified as mesoderm. This elegant model demonstrates the necessity of feedforward and feedback interactions between multiple signaling pathways for providing cells with temporal and positional information.
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Affiliation(s)
- Antonius L van Boxtel
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew D Economou
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Claire Heliot
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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30
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Adam RC, Yang H, Ge Y, Lien WH, Wang P, Zhao Y, Polak L, Levorse J, Baksh SC, Zheng D, Fuchs E. Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression. Cell Stem Cell 2018; 22:398-413.e7. [PMID: 29337183 DOI: 10.1016/j.stem.2017.12.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/11/2017] [Accepted: 12/08/2017] [Indexed: 11/29/2022]
Abstract
Tissue regeneration relies on resident stem cells (SCs), whose activity and lineage choices are influenced by the microenvironment. Exploiting the synchronized, cyclical bouts of tissue regeneration in hair follicles (HFs), we investigate how microenvironment dynamics shape the emergence of stem cell lineages. Employing epigenetic and ChIP-seq profiling, we uncover how signal-dependent transcription factors couple spatiotemporal cues to chromatin dynamics, thereby choreographing stem cell lineages. Using enhancer-driven reporters, mutagenesis, and genetics, we show that simultaneous BMP-inhibitory and WNT signals set the stage for lineage choices by establishing chromatin platforms permissive for diversification. Mechanistically, when binding of BMP effector pSMAD1 is relieved, enhancers driving HF-stem cell master regulators are silenced. Concomitantly, multipotent, lineage-fated enhancers silent in HF-stem cells become activated by exchanging WNT effectors TCF3/4 for LEF1. Throughout regeneration, lineage enhancers continue reliance upon LEF1 but then achieve specificity by accommodating additional incoming signaling effectors. Barriers to progenitor plasticity increase when diverse, signal-sensitive transcription factors shape LEF1-regulated enhancer dynamics.
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Affiliation(s)
- Rene C Adam
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hanseul Yang
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Yejing Ge
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Wen-Hui Lien
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yilin Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lisa Polak
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - John Levorse
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Sanjeethan C Baksh
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Elaine Fuchs
- Robin Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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31
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Liu C, Peng G, Jing N. TGF-β signaling pathway in early mouse development and embryonic stem cells. Acta Biochim Biophys Sin (Shanghai) 2018; 50:68-73. [PMID: 29190317 DOI: 10.1093/abbs/gmx120] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/31/2017] [Indexed: 12/30/2022] Open
Abstract
TGF-β superfamily signaling pathways essentially contribute to the broad spectrum of early developmental events including embryonic patterning, cell fate determination and dynamic movements. In this review, we first introduced some key developmental processes that require TGF-β signaling to show the fundamental importance of these pathways. Then we discuss how their activities are regulated, and new findings about how the TGF-β superfamily ligands bind to the chromatin to regulate transcription during embryo development.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Guangdun Peng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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