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Di Chiaro P, Nacci L, Arco F, Brandini S, Polletti S, Palamidessi A, Donati B, Soriani C, Gualdrini F, Frigè G, Mazzarella L, Ciarrocchi A, Zerbi A, Spaggiari P, Scita G, Rodighiero S, Barozzi I, Diaferia GR, Natoli G. Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer. Cancer Cell 2024; 42:662-681.e10. [PMID: 38518775 DOI: 10.1016/j.ccell.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/07/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.
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Affiliation(s)
- Pierluigi Di Chiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Lucia Nacci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Fabiana Arco
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Stefania Brandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Sara Polletti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Andrea Palamidessi
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Chiara Soriani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Francesco Gualdrini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy; Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessandro Zerbi
- IRCCS Humanitas Research Hospital, Rozzano, Milano, Italy; Humanitas University, Pieve Emanuele - Milano, Italy
| | | | - Giorgio Scita
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Milano, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Giuseppe R Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
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2
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Russo M, Gualdrini F, Vallelonga V, Prosperini E, Noberini R, Pedretti S, Borriero C, Di Chiaro P, Polletti S, Imperato G, Marenda M, Ghirardi C, Bedin F, Cuomo A, Rodighiero S, Bonaldi T, Mitro N, Ghisletti S, Natoli G. Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide. Mol Cell 2024; 84:967-980.e10. [PMID: 38242130 PMCID: PMC7615796 DOI: 10.1016/j.molcel.2023.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Histone-modifying enzymes depend on the availability of cofactors, with acetyl-coenzyme A (CoA) being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA-producing enzymes translocate to the nucleus suggests that high concentrations of locally synthesized metabolites may impact acylation of histones and other nuclear substrates, thereby controlling gene expression. Here, we show that 2-ketoacid dehydrogenases are stably associated with the Mediator complex, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in lipopolysaccharide-stimulated macrophages, inhibited the activity of Mediator-associated 2-ketoacid dehydrogenases. Elevation of NO levels and the disruption of Mediator complex integrity both affected de novo histone acetylation within a shared set of genomic regions. Our findings indicate that the local supply of acetyl-CoA generated by 2-ketoacid dehydrogenases bound to Mediator is required to maximize acetylation of histone tails at sites of elevated HAT activity.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Gabriele Imperato
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; Department of Hematology and Hematology-Oncology (DIPO), Università degli Studi di Milano, Milano 20122, Italy
| | - Nico Mitro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
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3
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Gualdrini F, Polletti S, Simonatto M, Prosperini E, Pileri F, Natoli G. H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats. Genes Dev 2022; 36:414-432. [PMID: 35361678 PMCID: PMC9067402 DOI: 10.1101/gad.349282.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/16/2022] [Indexed: 12/23/2022]
Abstract
Here, Gualdrini et al. found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. Their findings suggest a role for H3K9me3 in restraining genomic distribution and activity of CTCF, influencing chromatin organization and gene regulation. Six methyltransferases divide labor in establishing genomic profiles of histone H3 lysine 9 methylation (H3K9me), an epigenomic modification controlling constitutive heterochromatin, gene repression, and silencing of retroelements. Among them, SETDB1 is recruited to active chromatin domains to silence the expression of endogenous retroviruses. In the context of experiments aimed at determining the impact of SETDB1 on stimulus-inducible gene expression in macrophages, we found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. CTCF is an essential regulator of chromatin folding that restrains DNA looping by cohesin, thus creating boundaries among adjacent topological domains. Increased CTCF binding to SINE B2 repeats enhanced insulation at hundreds of sites and increased loop formation within topological domains containing lipopolysaccharide-inducible genes, which correlated with their impaired regulation in response to stimulation. These data indicate a role of H3K9me3 in restraining genomic distribution and activity of CTCF, with an impact on chromatin organization and gene regulation.
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Affiliation(s)
- Francesco Gualdrini
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Sara Polletti
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Marta Simonatto
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Elena Prosperini
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Francesco Pileri
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Gioacchino Natoli
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
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Chirichella M, Bianchi N, Džafo E, Foli E, Gualdrini F, Kenyon A, Natoli G, Monticelli S. RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells. PLoS Biol 2022; 20:e3001538. [PMID: 35143476 PMCID: PMC8865640 DOI: 10.1371/journal.pbio.3001538] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 02/23/2022] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
Within the immune system, microRNAs (miRNAs) exert key regulatory functions. However, what are the mRNA targets regulated by miRNAs and how miRNAs are transcriptionally regulated themselves remain for the most part unknown. We found that in primary human memory T helper lymphocytes, miR-150 was the most abundantly expressed miRNA, and its expression decreased drastically upon activation, suggesting regulatory roles. Constitutive MIR150 gene expression required the RFX family of transcription factors, and its activation-induced down-regulation was linked to their reduced expression. By performing miRNA pull-down and sequencing experiments, we identified PDGFA-associated protein 1 (PDAP1) as one main target of miR-150 in human T lymphocytes. PDAP1 acted as an RNA-binding protein (RBP), and its CRISPR/Cas-9–mediated deletion revealed that it prominently contributed to the regulation of T-cell proliferation. Overall, using an integrated approach involving quantitative analysis, unbiased genomics, and genome editing, we identified RFX factors, miR-150, and the PDAP1 RBP as the components of a regulatory axis that restrains proliferation of primary human T lymphocytes. MicroRNAs exert key regulatory functions in the immune system, but their targets are largely unknown. This study shows that the ability of primary human T lymphocytes to proliferate in response to T cell receptor activation is modulated by a network comprising miR-150, transcription factors of the RFX family, and the RNA-binding protein PDAP1.
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Affiliation(s)
- Michele Chirichella
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Niccolò Bianchi
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Emina Džafo
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Elena Foli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Francesco Gualdrini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
- Humanitas University, Milan, Italy
| | - Amy Kenyon
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Gioacchino Natoli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
- Humanitas University, Milan, Italy
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
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Natoli G, Pileri F, Gualdrini F, Ghisletti S. Integration of transcriptional and metabolic control in macrophage activation. EMBO Rep 2021; 22:e53251. [PMID: 34328708 DOI: 10.15252/embr.202153251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
Macrophages react to microbial and endogenous danger signals by activating a broad panel of effector and homeostatic responses. Such responses entail rapid and stimulus-specific changes in gene expression programs accompanied by extensive rewiring of metabolism, with alterations in chromatin modifications providing one layer of integration of transcriptional and metabolic regulation. A systematic and mechanistic understanding of the mutual influences between signal-induced metabolic changes and gene expression is still lacking. Here, we discuss current evidence, controversies, knowledge gaps, and future areas of investigation on how metabolic and transcriptional changes are dynamically integrated during macrophage activation. The cross-talk between metabolism and inflammatory gene expression is in part accounted for by alterations in the production, usage, and availability of metabolic intermediates that impact the macrophage epigenome. In addition, stimulus-inducible gene expression changes alter the production of inflammatory mediators, such as nitric oxide, that in turn modulate the activity of metabolic enzymes thus determining complex regulatory loops. Critical issues remain to be understood, notably whether and how metabolic rewiring can bring about gene-specific (as opposed to global) expression changes.
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Affiliation(s)
- Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy.,Humanitas University, Milan, Italy
| | - Francesco Pileri
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
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Audano M, Pedretti S, Ligorio S, Gualdrini F, Polletti S, Russo M, Ghisletti S, Bean C, Crestani M, Caruso D, De Fabiani E, Mitro N. Zc3h10 regulates adipogenesis by controlling translation and F-actin/mitochondria interaction. J Cell Biol 2021; 220:e202003173. [PMID: 33566069 PMCID: PMC7879490 DOI: 10.1083/jcb.202003173] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/29/2020] [Accepted: 12/04/2020] [Indexed: 12/21/2022] Open
Abstract
The commitment of mesenchymal stem cells to preadipocytes is stimulated by hormonal induction. Preadipocytes induced to differentiate repress protein synthesis, remodel their cytoskeleton, and increase mitochondrial function to support anabolic pathways. These changes enable differentiation into mature adipocytes. Our understanding of the factors that coordinately regulate the early events of adipocyte differentiation remains incomplete. Here, by using multipronged approaches, we have identified zinc finger CCCH-type containing 10 (Zc3h10) as a critical regulator of the early stages of adipogenesis. Zc3h10 depletion in preadipocytes resulted in increased protein translation and impaired filamentous (F)-actin remodeling, with the latter detrimental effect leading to mitochondrial and metabolic dysfunction. These defects negatively affected differentiation to mature adipocytes. In contrast, Zc3h10 overexpression yielded mature adipocytes with remarkably increased lipid droplet size. Overall, our study establishes Zc3h10 as a fundamental proadipogenic transcription factor that represses protein synthesis and promotes F-actin/mitochondria dynamics to ensure proper energy metabolism and favor lipid accumulation.
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Affiliation(s)
- Matteo Audano
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Silvia Pedretti
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Simona Ligorio
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Humanitas University (Hunimed), Pieve Emanuele, Milan, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Marta Russo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Camilla Bean
- Department of Biology, University of Padova, Padua, Italy
- Veneto Institute of Molecular Medicine, Padua, Italy
| | - Maurizio Crestani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Donatella Caruso
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Nico Mitro
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
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Abstract
The association between specific transcription factors (TFs) and defined tissue-specific macrophage phenotypes is far from being univocal. Many TFs that have been associated with tissue-specific macrophages have relatively broad expression profiles suggesting the critical involvement of combinatorial regulation by multiple TFs in bringing about specific phenotypes. In the current issue of The EMBO Journal, Rauschmeier et al (2019) report the identification of the transcriptional repressors BHLHE40 and BHLHE41 as novel regulators of tissue-specific macrophage properties that work both to promote alveolar macrophage (AM) identity and to suppress alternative tissue-specific phenotypes.
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Affiliation(s)
| | - Gioacchino Natoli
- Humanitas University, Pieve Emanuele, Milano, Italy.,Humanitas Clinical Research Institute, IRCCS, Rozzano, Milano, Italy
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8
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Foster CT, Gualdrini F, Treisman R. Mutual dependence of the MRTF-SRF and YAP-TEAD pathways in cancer-associated fibroblasts is indirect and mediated by cytoskeletal dynamics. Genes Dev 2018; 31:2361-2375. [PMID: 29317486 PMCID: PMC5795783 DOI: 10.1101/gad.304501.117] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023]
Abstract
In this study, Foster et al. demonstrate that activation of the MRTF–SRF signaling pathway occurs in cancer-associated fibroblasts (CAFs) and is required for their proinvasive and contractile activity. The investigators also identify shared and specific direct genomic targets for MRTF–SRF and YAP–TEAD and show that MRTF and YAP are independently regulated by cytoskeletal dynamics and that this is the basis for their mutual dependence. Both the MRTF–SRF and the YAP–TEAD transcriptional regulatory networks respond to extracellular signals and mechanical stimuli. We show that the MRTF–SRF pathway is activated in cancer-associated fibroblasts (CAFs). The MRTFs are required in addition to the YAP pathway for CAF contractile and proinvasive properties. We compared MRTF–SRF and YAP–TEAD target gene sets and identified genes directly regulated by one pathway, the other, or both. Nevertheless, the two pathways exhibit mutual dependence. In CAFs, expression of direct MRTF–SRF genomic targets is also dependent on YAP–TEAD activity, and, conversely, YAP–TEAD target gene expression is also dependent on MRTF–SRF signaling. In normal fibroblasts, expression of activated MRTF derivatives activates YAP, while activated YAP derivatives activate MRTF. Cross-talk between the pathways requires recruitment of MRTF and YAP to DNA via their respective DNA-binding partners (SRF and TEAD) and is therefore indirect, arising as a consequence of activation of their target genes. In both CAFs and normal fibroblasts, we found that YAP–TEAD activity is sensitive to MRTF–SRF-induced contractility, while MRTF–SRF signaling responds to YAP–TEAD-dependent TGFβ signaling. Thus, the MRF–SRF and YAP–TEAD pathways interact indirectly through their ability to control cytoskeletal dynamics.
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Affiliation(s)
- Charles T Foster
- Signalling and Transcription Group, Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Francesco Gualdrini
- Signalling and Transcription Group, Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Richard Treisman
- Signalling and Transcription Group, Francis Crick Institute, London NW1 1AT, United Kingdom
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9
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Esnault C, Gualdrini F, Horswell S, Kelly G, Stewart A, East P, Matthews N, Treisman R. ERK-Induced Activation of TCF Family of SRF Cofactors Initiates a Chromatin Modification Cascade Associated with Transcription. Mol Cell 2017; 65:1081-1095.e5. [PMID: 28286024 PMCID: PMC5364370 DOI: 10.1016/j.molcel.2017.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 12/19/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022]
Abstract
We investigated the relationship among ERK signaling, histone modifications, and transcription factor activity, focusing on the ERK-regulated ternary complex factor family of SRF partner proteins. In MEFs, activation of ERK by TPA stimulation induced a common pattern of H3K9acS10ph, H4K16ac, H3K27ac, H3K9acK14ac, and H3K4me3 at hundreds of transcription start site (TSS) regions and remote regulatory sites. The magnitude of the increase in histone modification correlated well with changes in transcription. H3K9acS10ph preceded the other modifications. Most induced changes were TCF dependent, but TCF-independent TSSs exhibited the same hierarchy, indicating that it reflects gene activation per se. Studies with TCF Elk-1 mutants showed that TCF-dependent ERK-induced histone modifications required Elk-1 to be phosphorylated and competent to activate transcription. Analysis of direct TCF-SRF target genes and chromatin modifiers confirmed this and showed that H3S10ph required only Elk-1 phosphorylation. Induction of histone modifications following ERK stimulation is thus directed by transcription factor activation and transcription.
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Affiliation(s)
- Cyril Esnault
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francesco Gualdrini
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aengus Stewart
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Phil East
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Treisman
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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10
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Gualdrini F, Esnault C, Horswell S, Stewart A, Matthews N, Treisman R. SRF Co-factors Control the Balance between Cell Proliferation and Contractility. Mol Cell 2016; 64:1048-1061. [PMID: 27867007 PMCID: PMC5179500 DOI: 10.1016/j.molcel.2016.10.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/26/2016] [Accepted: 10/11/2016] [Indexed: 12/20/2022]
Abstract
The ERK-regulated ternary complex factors (TCFs) act with the transcription factor serum response factor (SRF) to activate mitogen-induced transcription. However, the extent of their involvement in the immediate-early transcriptional response, and their wider functional significance, has remained unclear. We show that, in MEFs, TCF inactivation significantly inhibits over 60% of TPA-inducible gene transcription and impairs cell proliferation. Using integrated SRF ChIP-seq and Hi-C data, we identified over 700 TCF-dependent SRF direct target genes involved in signaling, transcription, and proliferation. These also include a significant number of cytoskeletal gene targets for the Rho-regulated myocardin-related transcription factor (MRTF) SRF cofactor family. The TCFs act as general antagonists of MRTF-dependent SRF target gene expression, competing directly with the MRTFs for access to SRF. As a result, TCF-deficient MEFs exhibit hypercontractile and pro-invasive behavior. Thus, competition between TCFs and MRTFs for SRF determines the balance between antagonistic proliferative and contractile programs of gene expression.
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Affiliation(s)
- Francesco Gualdrini
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Cyril Esnault
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Aengus Stewart
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing STP, Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Richard Treisman
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK.
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Esnault C, Stewart A, Gualdrini F, East P, Horswell S, Matthews N, Treisman R. Rho-actin signaling to the MRTF coactivators dominates the immediate transcriptional response to serum in fibroblasts. Genes Dev 2014; 28:943-58. [PMID: 24732378 PMCID: PMC4018493 DOI: 10.1101/gad.239327.114] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/20/2014] [Indexed: 01/14/2023]
Abstract
The transcription factor SRF (serum response factor) recruits two families of coactivators, the MRTFs (myocardin-related transcription factors) and the TCFs (ternary complex factors), to couple gene transcription to growth factor signaling. Here we investigated the role of the SRF network in the immediate transcriptional response of fibroblasts to serum stimulation. SRF recruited its cofactors in a gene-specific manner, and virtually all MRTF binding was directed by SRF. Much of SRF DNA binding was serum-inducible, reflecting a requirement for MRTF-SRF complex formation in nucleosome displacement. We identified 960 serum-responsive SRF target genes, which were mostly MRTF-controlled, as assessed by MRTF chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq) and/or sensitivity to MRTF-linked signals. MRTF activation facilitates RNA polymerase II (Pol II) recruitment or promoter escape according to gene context. MRTF targets encode regulators of the cytoskeleton, transcription, and cell growth, underpinning the role of SRF in cytoskeletal dynamics and mechanosensing. Finally, we show that specific activation of either MRTFs or TCFs can reset the circadian clock.
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Affiliation(s)
| | | | | | - Phil East
- Bioinformatics and Biostatistics Group
| | | | - Nik Matthews
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
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12
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Gualdrini F, Corvetta D, Cantilena S, Chayka O, Tanno B, Raschellà G, Sala A. Addiction of MYCN amplified tumours to B-MYB underscores a reciprocal regulatory loop. Oncotarget 2011; 1:278-88. [PMID: 21304178 DOI: 10.18632/oncotarget.100808] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
MYCN is a member of the MYC family of oncoproteins frequently amplified or overexpressed in aggressive, paediatric tumours of the nervous system. In this study we have identified the gene B-MYB, encoding the transcription factor also known as MYBL2, as a downstream target of MYCN. Using multiple in silico databases we show that expression of B-MYB significantly correlates with that of MYCN in neuroblastoma patients. MYCN binds to and activates the B-MYB gene in vivo and in vitro. Blunting B-MYB expression by RNA interference causes reduced proliferation of MYCN amplified, but not MYCN-non amplified, neuroblastoma cell lines, indicating that tumour cells are addicted to B-MYB in a MYCN dependent manner. Notably, B-MYB binds in vivo to the MYCN amplicon and is required for its expression. We conclude that MYCN and B-MYB are engaged in a reciprocal regulatory loop whose pharmacological targeting could be beneficial to patients with the aggressive forms of cancer in which MYCN is amplified.
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Affiliation(s)
- Francesco Gualdrini
- Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London, UK
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13
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Gualdrini F, Corvetta D, Cantilena S, Chayka O, Tanno B, Raschellà G, Sala A. Addiction of MYCN amplified tumours to B-MYB underscores a reciprocal regulatory loop. Oncotarget 2010. [PMID: 21304178 PMCID: PMC3248110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
MYCN is a member of the MYC family of oncoproteins frequently amplified or overexpressed in aggressive, paediatric tumours of the nervous system. In this study we have identified the gene B-MYB, encoding the transcription factor also known as MYBL2, as a downstream target of MYCN. Using multiple in silico databases we show that expression of B-MYB significantly correlates with that of MYCN in neuroblastoma patients. MYCN binds to and activates the B-MYB gene in vivo and in vitro. Blunting B-MYB expression by RNA interference causes reduced proliferation of MYCN amplified, but not MYCN-non amplified, neuroblastoma cell lines, indicating that tumour cells are addicted to B-MYB in a MYCN dependent manner. Notably, B-MYB binds in vivo to the MYCN amplicon and is required for its expression. We conclude that MYCN and B-MYB are engaged in a reciprocal regulatory loop whose pharmacological targeting could be beneficial to patients with the aggressive forms of cancer in which MYCN is amplified.
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Affiliation(s)
- Francesco Gualdrini
- 1Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Daisy Corvetta
- 1Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Sandra Cantilena
- 1Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Olesya Chayka
- 1Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Barbara Tanno
- 2ENEA Research Center, Laboratory of Radiation Biology and Biomedicine Via Anguillarese, 301, 00123 S. Maria di Galeria, Rome, Italy
| | - Giuseppe Raschellà
- 2ENEA Research Center, Laboratory of Radiation Biology and Biomedicine Via Anguillarese, 301, 00123 S. Maria di Galeria, Rome, Italy
| | - Arturo Sala
- 1Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
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Gualdrini F, Corvetta D, Cantilena S, Chayka O, Tanno B, Raschellà G, Sala A. Addiction of MYCN Amplified Tumours to B-MYB Underscores a Reciprocal Regulatory Loop. Oncotarget 2010. [DOI: 10.18632/oncotarget.138] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Francesco Gualdrini
- Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Daisy Corvetta
- Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Sandra Cantilena
- Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Olesya Chayka
- Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Barbara Tanno
- ENEA Research Center, Laboratory of Radiation Biology and Biomedicine Via Anguillarese, 301, 00123 S. Maria di Galeria, Rome, Italy
| | - Giuseppe Raschellà
- ENEA Research Center, Laboratory of Radiation Biology and Biomedicine Via Anguillarese, 301, 00123 S. Maria di Galeria, Rome, Italy
| | - Arturo Sala
- Molecular Haeamatology and Cancer Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
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