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Lisi S, Trovato M, Vitaloni O, Fantini M, Chirichella M, Tognini P, Cornuti S, Costa M, Groth M, Cattaneo A. Acetylation-Specific Interference by Anti-Histone H3K9ac Intrabody Results in Precise Modulation of Gene Expression. Int J Mol Sci 2022; 23:ijms23168892. [PMID: 36012156 PMCID: PMC9408029 DOI: 10.3390/ijms23168892] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/08/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Among Histone post-translational modifications (PTMs), lysine acetylation plays a pivotal role in the epigenetic regulation of gene expression, mediated by chromatin modifying enzymes. Due to their activity in physiology and pathology, several chemical compounds have been developed to inhibit the function of these proteins. However, the pleiotropy of these classes of proteins represents a weakness of epigenetic drugs. Ideally, a new generation of epigenetic drugs should target with molecular precision individual acetylated lysines on the target protein. We exploit a PTM-directed interference, based on an intrabody (scFv-58F) that selectively binds acetylated lysine 9 of histone H3 (H3K9ac), to test the hypothesis that targeting H3K9ac yields more specific effects than inhibiting the corresponding HAT enzyme that installs that PTM. In yeast scFv-58F modulates, gene expression in a more specific way, compared to two well-established HAT inhibitors. This PTM-specific interference modulated expression of genes involved in ribosome biogenesis and function. In mammalian cells, the scFv-58F induces exclusive changes in the H3K9ac-dependent expression of specific genes. These results suggest the H3K9ac-specific intrabody as the founder of a new class of molecules to directly target histone PTMs, inverting the paradigm from inhibiting the writer enzyme to acting on the PTM.
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Affiliation(s)
- Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Matteo Trovato
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | | | - Paola Tognini
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Sara Cornuti
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Mario Costa
- Institute of Neurosciences, Consiglio Nazionale Delle Ricerche, 56124 Pisa, Italy
| | - Marco Groth
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- Correspondence: ; Tel.: +39-050-509320
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2
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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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3
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De Simone M, Chirichella M, Emming S, Mazzara S, Ranzani V, Gruarin P, Moschetti G, Pulvirenti N, Maglie S, Vasco C, Crosti MC, Rossetti G, Pagani M, Abrignani S, Monticelli S, Geginat J. Ex vivo microRNA and gene expression profiling of human Tr1-like cells suggests a role for miR-92a and -125a in the regulation of EOMES and IL-10R. Eur J Immunol 2021; 51:3243-3246. [PMID: 34528258 PMCID: PMC9293355 DOI: 10.1002/eji.202149315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/22/2021] [Revised: 07/26/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022]
Abstract
Ex vivo gene expression and miRNA profiling of Eomes+ Tr1-like cells suggested that they represent a differentiation stage that is intermediate between Th1-cells and cytotoxic CD4+ T-cells. Several microRNAs were downregulated in Eomes+ Tr1-like cells that might inhibit Tr1-cell differentiation. In particular, miR-92a targeted Eomes, while miR-125a inhibited IFN-g and IL-10R expression.
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Affiliation(s)
- Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Michele Chirichella
- Institute for Research in Biomedicine (IRB)Università della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Stefan Emming
- Institute for Research in Biomedicine (IRB)Università della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Saveria Mazzara
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Giorgia Moschetti
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Nadia Pulvirenti
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Stefano Maglie
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Chiara Vasco
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | | | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- FIRC Institute of Molecular Oncology (IFOM)MilanItaly
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- FIRC Institute of Molecular Oncology (IFOM)MilanItaly
- Department of Medical Biotechnology and Translational MedicineUniversità degli StudiMilanoItaly
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- Department of Clinical Sciences and Community HealthUniversità degli StudiMilanoItaly
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB)Università della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Jens Geginat
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- Department of Clinical Sciences and Community HealthUniversità degli StudiMilanoItaly
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Emming S, Bianchi N, Polletti S, Balestrieri C, Leoni C, Montagner S, Chirichella M, Delaleu N, Natoli G, Monticelli S. A molecular network regulating the proinflammatory phenotype of human memory T lymphocytes. Nat Immunol 2020; 21:388-399. [PMID: 32205878 PMCID: PMC7100912 DOI: 10.1038/s41590-020-0622-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 01/31/2020] [Indexed: 12/11/2022]
Abstract
Understanding the mechanisms that modulate helper T lymphocyte functions is crucial to decipher normal and pathogenic immune responses in humans. To identify molecular determinants influencing the pathogenicity of T cells, we separated ex vivo-isolated primary human memory T lymphocytes on the basis of their ability to produce high levels of inflammatory cytokines. We found that the inflammatory, cytokine-producing phenotype of memory T lymphocytes was defined by a specific core gene signature and was mechanistically regulated by the constitutive activation of the NF-κB pathway and by the expression of the transcriptional repressor BHLHE40. BHLHE40 attenuated the expression of anti-inflammatory factors, including miR-146a, a negative regulator of NF-κB activation and ZC3H12D, an RNase of the Regnase-1 family able to degrade inflammatory transcripts. Our data reveal a molecular network regulating the proinflammatory phenotype of human memory T lymphocytes, with the potential to contribute to disease.
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Affiliation(s)
- Stefan Emming
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Niccolò Bianchi
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology IRCCS (IEO), Milan, Italy
| | - Chiara Balestrieri
- Department of Experimental Oncology, European Institute of Oncology IRCCS (IEO), Milan, Italy
| | - Cristina Leoni
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Sara Montagner
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Michele Chirichella
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Nicolas Delaleu
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, USI, Bellinzona, Switzerland.,2C SysBioMed, Contra, Switzerland.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology IRCCS (IEO), Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland.
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5
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Vincenzetti L, Leoni C, Chirichella M, Kwee I, Monticelli S. The contribution of active and passive mechanisms of 5mC and 5hmC removal in human T lymphocytes is differentiation- and activation-dependent. Eur J Immunol 2019; 49:611-625. [PMID: 30698829 DOI: 10.1002/eji.201847967] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/15/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022]
Abstract
In mammals, the 5'-methylcytosine (5mC) modification in the genomic DNA contributes to the dynamic control of gene expression. 5mC erasure is required for the activation of developmental programs and occurs either by passive dilution through DNA replication, or by enzymatic oxidation of the methyl mark to 5-hydroxymethylcytosine (5hmC), which can persist as such or undergo further oxidation and enzymatic removal. The relative contribution of each mechanism to epigenetic control in dynamic biological systems still remains a compelling question. To explore this critical issue, we used primary human T lymphocytes, in which two cellular states can be clearly identified, namely quiescent naïve T cells, which are slowly or rarely proliferating, and rapidly proliferating activated T cells. We found that active mechanisms of methylation removal were selectively at work in naïve T cells, while memory T lymphocytes entirely relied on passive, replication-dependent dilution, suggesting that proliferative capacity influences the choice of the preferential demethylation mechanism. Active processes of demethylation appear to be critical in quiescent naïve T lymphocytes for the maintenance of regulatory regions poised for rapid responses to physiological stimuli.
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Affiliation(s)
- Lucia Vincenzetti
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Cristina Leoni
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Michele Chirichella
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Ivo Kwee
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
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6
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Cattaneo A, Chirichella M. Targeting the Post-translational Proteome with Intrabodies. Trends Biotechnol 2018; 37:578-591. [PMID: 30577991 DOI: 10.1016/j.tibtech.2018.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 12/22/2022]
Abstract
The complexity of the proteome exceeds that of the genome. Post-translational modifications (PTMs) and conformational changes of proteins trigger new molecular interactions whose systematic elucidation is hampered by the lack of specific tools. PTMs are particularly relevant for epigenetic regulation of gene expression; a field of translational interest. However, state-of-the-art inhibitors used in epigenetic studies and therapies target modifier enzymes such as acetylases and deacetylases, rather than a single PTM protein per se. The systematic development of anti-PTM intrabodies, which allow targeting of intracellular proteins in the context of living cells, will help reaching a new level of precision and specificity in the description of epigenetics, paving the way to new therapeutic opportunities.
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Affiliation(s)
- Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, 7 - 56126 Pisa, Italy.
| | - Michele Chirichella
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, 7 - 56126 Pisa, Italy; Current address: Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
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7
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Emming S, Chirichella M, Monticelli S. MicroRNAs as modulators of T cell functions in cancer. Cancer Lett 2018; 430:172-178. [PMID: 29800683 DOI: 10.1016/j.canlet.2018.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/10/2018] [Accepted: 05/12/2018] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are short RNA molecules that regulate gene expression post-transcriptionally. They have emerged as important modulators of T lymphocyte biology, influencing cell activation, differentiation and proliferation in response to environmental signals. Here, we will discuss how miRNAs expressed by T cells can influence two key aspects of tumorigenesis, namely the direct, cell-intrinsic oncogenic transformation of T lymphocytes, as well as the indirect effects on tumor growth mediated by altered immune surveillance. We will specifically focus on three miRNAs that have been shown to regulate different aspects of T cell biology in both physiological and pathological conditions, namely miR-155, miR-146a and miR-181a. We aim at providing examples of the fundamental importance of miRNA-regulated networks in determining the fate of T lymphocytes during oncogenic transformation and in the control of tumor growth.
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Affiliation(s)
- Stefan Emming
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Michele Chirichella
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland.
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8
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Fantini M, Pandolfini L, Lisi S, Chirichella M, Arisi I, Terrigno M, Goracci M, Cremisi F, Cattaneo A. Assessment of antibody library diversity through next generation sequencing and technical error compensation. PLoS One 2017; 12:e0177574. [PMID: 28505201 PMCID: PMC5432181 DOI: 10.1371/journal.pone.0177574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 11/10/2016] [Accepted: 04/28/2017] [Indexed: 12/30/2022] Open
Abstract
Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error.
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Affiliation(s)
- Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, Pisa, Italy
| | | | - Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, Pisa, Italy
| | | | - Ivan Arisi
- European Brain Research Institute, Roma, Italy
| | - Marco Terrigno
- Bio@SNS Laboratory, Scuola Normale Superiore, Pisa, Italy
| | | | | | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Pisa, Italy
- European Brain Research Institute, Roma, Italy
- * E-mail:
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