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Ponzone L, Audrito V, Landi C, Moiso E, Levra Levron C, Ferrua S, Savino A, Vitale N, Gasparrini M, Avalle L, Vantaggiato L, Shaba E, Tassone B, Saoncella S, Orso F, Viavattene D, Marina E, Fiorilla I, Burrone G, Abili Y, Altruda F, Bini L, Deaglio S, Defilippi P, Menga A, Poli V, Porporato PE, Provero P, Raffaelli N, Riganti C, Taverna D, Cavallo F, Calautti E. RICTOR/mTORC2 downregulation in BRAF V600E melanoma cells promotes resistance to BRAF/MEK inhibition. Mol Cancer 2024; 23:105. [PMID: 38755661 PMCID: PMC11097536 DOI: 10.1186/s12943-024-02010-1] [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: 09/30/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND The main drawback of BRAF/MEK inhibitors (BRAF/MEKi)-based targeted therapy in the management of BRAF-mutated cutaneous metastatic melanoma (MM) is the development of therapeutic resistance. We aimed to assess in this context the role of mTORC2, a signaling complex defined by the presence of the essential RICTOR subunit, regarded as an oncogenic driver in several tumor types, including MM. METHODS After analyzing The Cancer Genome Atlas MM patients' database to explore both overall survival and molecular signatures as a function of intra-tumor RICTOR levels, we investigated the effects of RICTOR downregulation in BRAFV600E MM cell lines on their response to BRAF/MEKi. We performed proteomic screening to identify proteins modulated by changes in RICTOR expression, and Seahorse analysis to evaluate the effects of RICTOR depletion on mitochondrial respiration. The combination of BRAFi with drugs targeting proteins and processes emerged in the proteomic screening was carried out on RICTOR-deficient cells in vitro and in a xenograft setting in vivo. RESULTS Low RICTOR levels in BRAF-mutated MM correlate with a worse clinical outcome. Gene Set Enrichment Analysis of low-RICTOR tumors display gene signatures suggestive of activation of the mitochondrial Electron Transport Chain (ETC) energy production. RICTOR-deficient BRAFV600E cells are intrinsically tolerant to BRAF/MEKi and anticipate the onset of resistance to BRAFi upon prolonged drug exposure. Moreover, in drug-naïve cells we observed a decline in RICTOR expression shortly after BRAFi exposure. In RICTOR-depleted cells, both mitochondrial respiration and expression of nicotinamide phosphoribosyltransferase (NAMPT) are enhanced, and their pharmacological inhibition restores sensitivity to BRAFi. CONCLUSIONS Our work unveils an unforeseen tumor-suppressing role for mTORC2 in the early adaptation phase of BRAFV600E melanoma cells to targeted therapy and identifies the NAMPT-ETC axis as a potential therapeutic vulnerability of low RICTOR tumors. Importantly, our findings indicate that the evaluation of intra-tumor RICTOR levels has a prognostic value in metastatic melanoma and may help to guide therapeutic strategies in a personalized manner.
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Affiliation(s)
- Luca Ponzone
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Valentina Audrito
- Department of Science and Technological Innovation, University of Piemonte Orientale, Alessandria, 15121, Italy
| | - Claudia Landi
- Functional Proteomic Section, Department of Life Sciences, University of Siena, Siena, 53100, Italy
| | - Enrico Moiso
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Chiara Levra Levron
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10126, Italy
| | - Sara Ferrua
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Aurora Savino
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Nicoletta Vitale
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Massimiliano Gasparrini
- Department of Agriculture, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Lidia Avalle
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Department of Science and Technological Innovation, University of Piemonte Orientale, Alessandria, 15121, Italy
| | - Lorenza Vantaggiato
- Functional Proteomic Section, Department of Life Sciences, University of Siena, Siena, 53100, Italy
| | - Enxhi Shaba
- Functional Proteomic Section, Department of Life Sciences, University of Siena, Siena, 53100, Italy
| | - Beatrice Tassone
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Department of Personal Care, dsm-firmenich, Kaiseraugst, 4303, Switzerland
| | - Stefania Saoncella
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Francesca Orso
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Daniele Viavattene
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Eleonora Marina
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Irene Fiorilla
- Department of Science and Technological Innovation, University of Piemonte Orientale, Alessandria, 15121, Italy
| | - Giulia Burrone
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, 10124, Italy
| | - Youssef Abili
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- GenomeUp, Rome, 00144, Italy
| | - Fiorella Altruda
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Luca Bini
- Functional Proteomic Section, Department of Life Sciences, University of Siena, Siena, 53100, Italy
| | - Silvia Deaglio
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Medical Sciences, University of Turin, Turin, 10124, Italy
| | - Paola Defilippi
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Alessio Menga
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Valeria Poli
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Paolo Ettore Porporato
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Paolo Provero
- Neuroscience Department "Rita Levi Montalcini", University of Turin, Turin, 10126, Italy
| | - Nadia Raffaelli
- Department of Agriculture, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Chiara Riganti
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Oncology, University of Turin, Turin, 10124, Italy
| | - Daniela Taverna
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Federica Cavallo
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
| | - Enzo Calautti
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Turin, 10126, Italy.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy.
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2
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Levra Levron C, Elettrico L, Duval C, Piacenti G, Proserpio V, Donati G. Bridging tissue repair and epithelial carcinogenesis: epigenetic memory and field cancerization. Cell Death Differ 2024:10.1038/s41418-023-01254-6. [PMID: 38228801 DOI: 10.1038/s41418-023-01254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
The epigenome coordinates spatial-temporal specific gene expression during development and in adulthood, for the maintenance of homeostasis and upon tissue repair. The upheaval of the epigenetic landscape is a key event in the onset of many pathologies including tumours, where epigenetic changes cooperate with genetic aberrations to establish the neoplastic phenotype and to drive cell plasticity during its evolution. DNA methylation, histone modifiers and readers or other chromatin components are indeed often altered in cancers, such as carcinomas that develop in epithelia. Lining the surfaces and the cavities of our body and acting as a barrier from the environment, epithelia are frequently subjected to acute or chronic tissue damages, such as mechanical injuries or inflammatory episodes. These events can activate plasticity mechanisms, with a deep impact on cells' epigenome. Despite being very effective, tissue repair mechanisms are closely associated with tumour onset. Here we review the similarities between tissue repair and carcinogenesis, with a special focus on the epigenetic mechanisms activated by cells during repair and opted by carcinoma cells in multiple epithelia. Moreover, we discuss the recent findings on inflammatory and wound memory in epithelia and describe the epigenetic modifications that characterise them. Finally, as wound memory in epithelial cells promotes carcinogenesis, we highlight how it represents an early step for the establishment of field cancerization.
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Affiliation(s)
- Chiara Levra Levron
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Luca Elettrico
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Carlotta Duval
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Gabriele Piacenti
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy.
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3
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Levra Levron C, Donati G. Multiplicity of stem cell memories of inflammation and tissue repair in epithelia. Trends Cell Biol 2024; 34:3-6. [PMID: 37940416 DOI: 10.1016/j.tcb.2023.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Adaptation enables cells to change their behavior in response to transient stimuli. While adaptive programs of immune cells have been widely described, it has recently emerged that epithelial cells also acquire memories in vivo. Here, we discuss and classify the adaptations identified in epithelia and describe the associated long-term consequences.
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Affiliation(s)
- Chiara Levra Levron
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy; Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy; Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy.
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4
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Jacob T, Annusver K, Czarnewski P, Dalessandri T, Kalk C, Levra Levron C, Campamà Sanz N, Kastriti ME, Mikkola ML, Rendl M, Lichtenberger BM, Donati G, Björklund ÅK, Kasper M. Molecular and spatial landmarks of early mouse skin development. Dev Cell 2023; 58:2140-2162.e5. [PMID: 37591247 PMCID: PMC11088744 DOI: 10.1016/j.devcel.2023.07.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 09/01/2022] [Revised: 05/05/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023]
Abstract
A wealth of specialized cell populations within the skin facilitates its hair-producing, protective, sensory, and thermoregulatory functions. How the vast cell-type diversity and tissue architecture develops is largely unexplored. Here, with single-cell transcriptomics, spatial cell-type assignment, and cell-lineage tracing, we deconstruct early embryonic mouse skin during the key transitions from seemingly uniform developmental precursor states to a multilayered, multilineage epithelium, and complex dermal identity. We identify the spatiotemporal emergence of hair-follicle-inducing, muscle-supportive, and fascia-forming fibroblasts. We also demonstrate the formation of the panniculus carnosus muscle (PCM), sprouting blood vessels without pericyte coverage, and the earliest residence of mast and dendritic immune cells in skin. Finally, we identify an unexpected epithelial heterogeneity within the early single-layered epidermis and a signaling-rich periderm layer. Overall, this cellular and molecular blueprint of early skin development-which can be explored at https://kasperlab.org/tools-establishes histological landmarks and highlights unprecedented dynamic interactions among skin cells.
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Affiliation(s)
- Tina Jacob
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Karl Annusver
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Paulo Czarnewski
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, 17165 Stockholm, Sweden
| | - Tim Dalessandri
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Christina Kalk
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Chiara Levra Levron
- Department of Life Sciences and Systems Biology, Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Nil Campamà Sanz
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Maria Eleni Kastriti
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Marja L Mikkola
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Michael Rendl
- Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Beate M Lichtenberger
- Skin and Endothelium Research Division, Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Åsa K Björklund
- Department of Life Science, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, 41296 Göteborg, Sweden
| | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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5
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Levra Levron C, Watanabe M, Proserpio V, Piacenti G, Lauria A, Kaltenbach S, Tamburrini A, Nohara T, Anselmi F, Duval C, Elettrico L, Donna D, Conti L, Baev D, Natsuga K, Hagai T, Oliviero S, Donati G. Tissue memory relies on stem cell priming in distal undamaged areas. Nat Cell Biol 2023; 25:740-753. [PMID: 37081165 DOI: 10.1038/s41556-023-01120-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/28/2023] [Indexed: 04/22/2023]
Abstract
Epithelial cells that participated in wound repair elicit a more efficient response to future injuries, which is believed to be locally restricted. Here we show that cell adaptation resulting from a localized tissue damage has a wide spatial impact at a scale not previously appreciated. We demonstrate that a specific stem cell population, distant from the original injury, originates long-lasting wound memory progenitors residing in their own niche. Notably, these distal memory cells have not taken part in the first healing but become intrinsically pre-activated through priming. This cell state, maintained at the chromatin and transcriptional level, leads to an enhanced wound repair that is partially recapitulated through epigenetic perturbation. Importantly wound memory has long-term harmful consequences, exacerbating tumourigenesis. Overall, we show that sub-organ-scale adaptation to injury relies on spatially organized memory-dedicated progenitors, characterized by an actionable cell state that establishes an epigenetic field cancerization and predisposes to tumour onset.
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Affiliation(s)
- Chiara Levra Levron
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
| | - Mika Watanabe
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Gabriele Piacenti
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Stefan Kaltenbach
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Annalaura Tamburrini
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Takuma Nohara
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Francesca Anselmi
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
| | - Carlotta Duval
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
| | - Luca Elettrico
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
| | - Daniela Donna
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
| | - Laura Conti
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy
| | - Denis Baev
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Ken Natsuga
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.
- Molecular Biotechnology Center 'Guido Tarone', University of Turin, Torino, Italy.
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6
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Lauria A, Meng G, Proserpio V, Rapelli S, Maldotti M, Polignano IL, Anselmi F, Incarnato D, Krepelova A, Donna D, Levra Levron C, Donati G, Molineris I, Neri F, Oliviero S. DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells. Nat Commun 2023; 14:367. [PMID: 36690616 PMCID: PMC9871038 DOI: 10.1038/s41467-023-35938-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
The correct establishment of DNA methylation patterns during mouse early development is essential for cell fate specification. However, the molecular targets as well as the mechanisms that determine the specificity of the de novo methylation machinery during differentiation are not completely elucidated. Here we show that the DNMT3B-dependent DNA methylation of key developmental regulatory regions at epiblast-like cells (EpiLCs) provides an epigenetic priming that ensures flawless commitment at later stages. Using in vitro stem cell differentiation and loss of function experiments combined with high-throughput genome-wide bisulfite-, bulk-, and single cell RNA-sequencing we dissected the specific role of DNMT3B in cell fate. We identify DNMT3B-dependent regulatory elements on the genome which, in Dnmt3b knockout (3BKO), impair the differentiation into meso-endodermal (ME) progenitors and redirect EpiLCs towards the neuro-ectodermal lineages. Moreover, ectopic expression of DNMT3B in 3BKO re-establishes the DNA methylation of the master regulator Sox2 super-enhancer, downmodulates its expression, and restores the expression of ME markers. Taken together, our data reveal that DNMT3B-dependent methylation at the epiblast stage is essential for the priming of the meso-endodermal lineages and provide functional characterization of the de novo DNMTs during EpiLCs lineage determination.
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Affiliation(s)
- Andrea Lauria
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Guohua Meng
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Stefania Rapelli
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Mara Maldotti
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Isabelle Laurence Polignano
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Francesca Anselmi
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Anna Krepelova
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Daniela Donna
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Chiara Levra Levron
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Ivan Molineris
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy
| | - Francesco Neri
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology & Molecular Biotechnology Center - MBC, Università di Torino, Via Nizza 52, 10126, Torino, Italy.
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060, Candiolo, Torino, Italy.
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7
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Pergolizzi B, Panuzzo C, Ali MS, Lo Iacono M, Levron CL, Ponzone L, Prelli M, Cilloni D, Calautti E, Bozzaro S, Bracco E. Mammals and Dictyostelium rictor mutations swapping reveals two essential Gly residues for mTORC2 activity and integrity. J Cell Sci 2019; 132:jcs.236505. [DOI: 10.1242/jcs.236505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022] Open
Abstract
mTORC2 regulates a variety of vital cellular processes, and its aberrant functioning is often associated with various diseases. Rictor is a peculiar and distinguishing mTORC2 component playing a pivotal role in controlling its assembly and activity. Among living organisms Rictor is conserved from unicellular eukaryotes to metazoan. We replaced two distinct, but conserved, glycines in both the Dictyostelium piaA gene and its human ortholog, rictor. The two conserved residues are spaced by approximately 50 aminoacids and both are embedded within a conserved region falling in between the Ras-GEFN2 and Rictor_V domains. The effects of point mutations on the mTORC2 activity and integrity were assessed by biochemical and functional assays.In both cases, the reciprocal exchange between mammals and Dictyostelium rictor and piaA gene point mutations impaired mTORC2 activity and integrity.Our data indicate that the two Gly residues are essential for the maintenance of mTORC2 activity and integrity in organisms that appear to be distantly related, suggesting a primeval role in the assembly and proper TOR complex 2 functioning.
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Affiliation(s)
- Barbara Pergolizzi
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, 10043 Orbassano (TO), Italy
| | - Cristina Panuzzo
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, 10043 Orbassano (TO), Italy
| | - M. Shahzad Ali
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, 10043 Orbassano (TO), Italy
| | - Marco Lo Iacono
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, 10043 Orbassano (TO), Italy
| | - Chiara Levra Levron
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Via Nizza 52, Torino, Italy
| | - Luca Ponzone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Via Nizza 52, Torino, Italy
| | - Marta Prelli
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Via Nizza 52, Torino, Italy
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, 10043 Orbassano (TO), Italy
| | - Enzo Calautti
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Via Nizza 52, Torino, Italy
| | - Salvatore Bozzaro
- Department of Clinical and Biological Sciences, University of Torino, AOU S. Luigi, 10043 Orbassano (TO), Italy
| | - Enrico Bracco
- Department of Oncology, University of Torino, AOU S. Luigi, 10043 Orbassano (TO), Italy
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