29 results on '"Conti, Anastasia"'
Search Results
2. Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts.
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Cantarella, Simona, Carnevali, Davide, Morselli, Marco, Conti, Anastasia, Pellegrini, Matteo, Montanini, Barbara, and Dieci, Giorgio
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Hela Cells ,Fibroblasts ,Humans ,Cell Cycle Proteins ,RNA ,Cell Cycle ,Gene Expression Regulation ,Base Sequence ,Alu Elements ,Genome ,Human ,Genetic Loci ,Alu retrotransposons ,cell cycle ,non-coding RNA ,HeLa Cells ,Biotechnology ,Human Genome ,Cancer ,Genetics ,2.1 Biological and endogenous factors ,1.1 Normal biological development and functioning ,Generic health relevance ,Chemical Physics ,Other Chemical Sciences ,Other Biological Sciences - Abstract
Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.
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- 2019
3. Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines
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Carnevali, Davide, Conti, Anastasia, Pellegrini, Matteo, and Dieci, Giorgio
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,1.1 Normal biological development and functioning ,2.1 Biological and endogenous factors ,Aetiology ,Underpinning research ,Generic health relevance ,Computational Biology ,Gene Expression Profiling ,HeLa Cells ,Humans ,Interspersed Repetitive Sequences ,Plasmids ,Retroelements ,Sequence Analysis ,RNA ,Transcription ,Genetic ,SINE ,mammalian-wide interspersed repeats ,RNA polymerase III ,RNA-Seq ,ENCODE ,Hela Cells ,Plant Biology & Botany - Abstract
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority of Pol III-transcribed MIR elements are cell-specific, we discovered a small set of ubiquitously transcribed MIRs mapping within Pol II-transcribed genes in antisense orientation that could influence the expression of the overlapping gene. We also identified novel Pol III-transcribed ncRNAs, deriving from transcription of annotated MIR fragments flanked by unique MIR-unrelated sequences, and confirmed the role of Pol III-specific internal promoter elements in MIR transcription. Besides demonstrating widespread transcription at these retrotranspositionally inactive elements in human cells, the ability to profile MIR expression at single-locus resolution will facilitate their study in different cell types and states including pathological alterations.
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- 2017
4. Oncogene-induced senescence in hematopoietic progenitors features myeloid restricted hematopoiesis, chronic inflammation and histiocytosis
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Biavasco, Riccardo, Lettera, Emanuele, Giannetti, Kety, Gilioli, Diego, Beretta, Stefano, Conti, Anastasia, Scala, Serena, Cesana, Daniela, Gallina, Pierangela, Norelli, Margherita, Basso-Ricci, Luca, Bondanza, Attilio, Cavalli, Giulio, Ponzoni, Maurilio, Dagna, Lorenzo, Doglioni, Claudio, Aiuti, Alessandro, Merelli, Ivan, Di Micco, Raffaella, and Montini, Eugenio
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- 2021
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5. Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data
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Conti, Anastasia, Carnevali, Davide, Bollati, Valentina, Fustinoni, Silvia, Pellegrini, Matteo, and Dieci, Giorgio
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,1.1 Normal biological development and functioning ,Underpinning research ,Alu Elements ,Gene Expression Profiling ,Gene Silencing ,Genetic Loci ,Genomics ,Humans ,RNA Polymerase III ,Sequence Analysis ,RNA ,Transcription Factors ,Transcription ,Genetic ,Transcriptome ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
Of the ∼ 1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼ 1300 Alu loci corresponding to detectable transcripts, with ∼ 120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5'-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.
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- 2015
6. Molecular and phenotypic blueprint of the hematopoietic compartment reveals proliferation stress as a driver of age-associated human stem cell dysfunctions
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Lettera, Emanuele, primary, Scala, Serena, additional, Basso-Ricci, Luca, additional, Tavella, Teresa, additional, della Volpe, Lucrezia, additional, Lofurno, Elena, additional, Kauffmann, Kerstin, additional, Garcia-Prat, Laura, additional, Quaranta, Pamela, additional, Hernandez, Raisa, additional, Murison, Alexander, additional, Giannetti, Kety, additional, Aguilar-Navarro, Alicia, additional, Beretta, Stefano, additional, Conti, Anastasia, additional, Farina, Giacomo, additional, Flores-Figueroa, Eugenia, additional, Conte, Pietro, additional, Ometti, Marco, additional, Xie, Stephanie Z, additional, Aiuti, Alessandro, additional, and Di Micco, Raffaella, additional
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- 2023
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7. S255: CELLULAR SENESCENCE AND INFLAMMATORY PROGRAMS ARE UNINTENDED CONSEQUENCES OF CRISPR-CAS9 GENE EDITING IN HEMATOPOIETIC STEM AND PROGENITOR CELLS
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Conti, Anastasia, primary, Tavella, Teresa, additional, De Marco, Rosaria, additional, Midena, Federico, additional, Ferrari, Samuele, additional, Beretta, Stefano, additional, Brombin, Chiara, additional, Merelli, Ivan, additional, Naldini, Luigi, additional, and DI Micco, Raffaella, additional
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- 2023
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8. P429: THERAPY-INDUCED SENESCENCE TRIGGERS UPREGULATION OF ANTIGEN PRESENTATION VIA PRC2 INHIBITION AND PROMOTES ANTI-TUMOUR IMMUNITY IN ACUTE MYELOID LEUKAEMIA
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Gilioli, Diego, primary, Fusco, Simona, additional, Tavella, Teresa, additional, Giannetti, Kety, additional, Conti, Anastasia, additional, Antonella, Santoro, additional, Carsana, Edoardo, additional, Beretta, Stefano, additional, Schönlein, Martin, additional, Gambacorta, Valentina, additional, Aletti, Federico, additional, Giovanni Carrabba, Matteo, additional, Bonini, Chiara, additional, Ciceri, Fabio, additional, Merelli, Ivan, additional, Vago, Luca, additional, Schmitt, Clemens A., additional, and DI Micco, Raffaella, additional
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- 2023
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9. P1327: INHIBITING TELOMERIC DNA DAMAGE RESPONSE AS A NEW THERAPEUTIC STRATEGY TO REJUVENATE THE AGEING HEMATOPOIETIC SYSTEM
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Oppezzo, Alessia, primary, Sepe, Sara, additional, Rossiello, Francesca, additional, Conti, Anastasia, additional, Marinelli, Eugenia, additional, Boggio, Sara, additional, Lillo, Alessia DI, additional, Rosso, Ilaria, additional, Tavella, Sara, additional, Matti, Valentina, additional, Cicio, Giada, additional, Cancila, Valeria, additional, Mancheno-Ferris, Alexandra, additional, Bertolazzi, Giorgio, additional, Iannelli, Fabio, additional, Micco, Raffaella DI, additional, Tripodo, Claudio, additional, and D’adda DI Fagagna, Fabrizio, additional
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- 2023
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10. p38 MAPK fuels proliferation stress and DNA damage impairing the functionality of genetically engineered hematopoietic stem and progenitor cells
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Micco, Raffaella Di, primary, Volpe, Lucrezia della, additional, Vacca, Roberta, additional, Midena, Federico, additional, Tavella, Teresa, additional, Naldini, Matteo Maria, additional, Barcella, Matteo, additional, Giannetti, Kety, additional, Ferrari, Samuele, additional, Beretta, Stefano, additional, Farina, Giacomo, additional, Alessandrini, Laura, additional, Santoro, Antonella, additional, Carsana, Edoardo, additional, Varesi, Angelica, additional, Gilioli, Diego, additional, Conti, Anastasia, additional, Merelli, Ivan, additional, Gentner, Bernhard, additional, and Naldini, Luigi, additional
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- 2023
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11. Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs
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Crippa, Stefania, primary, Conti, Anastasia, additional, Vavassori, Valentina, additional, Ferrari, Samuele, additional, Beretta, Stefano, additional, Rivis, Silvia, additional, Bosotti, Roberto, additional, Scala, Serena, additional, Pirroni, Stefania, additional, Jofra-Hernandez, Raisa, additional, Santi, Ludovica, additional, Basso-Ricci, Luca, additional, Merelli, Ivan, additional, Genovese, Pietro, additional, Aiuti, Alessandro, additional, Naldini, Luigi, additional, Di Micco, Raffaella, additional, and Bernardo, Maria Ester, additional
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- 2023
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12. Therapy-induced senescence upregulates antigen presentation machinery and triggers anti-tumor immunity in Acute Myeloid Leukemia
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Gilioli, Diego, primary, Fusco, Simona, additional, Tavella, Teresa, additional, Giannetti, Kety, additional, Conti, Anastasia, additional, Santoro, Antonella, additional, Carsana, Edoardo, additional, Beretta, Stefano, additional, Schönlein, Martin, additional, Gambacorta, Valentina, additional, Aletti, Federico Mario, additional, Carrabba, Matteo Giovanni, additional, Bonini, Chiara, additional, Ciceri, Fabio, additional, Merelli, Ivan, additional, Vago, Luca, additional, Schmitt, Clemens, additional, and Di Micco, Raffaella, additional
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- 2022
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13. Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs
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Crippa, Stefania, primary, Conti, Anastasia, additional, Vavassori, Valentina, additional, Ferrari, Samuele, additional, Beretta, Stefano, additional, Rivis, Silvia, additional, Bosotti, Roberto, additional, Scala, Serena, additional, Pirroni, Stefania, additional, Jofra-Hernandez, Raisa, additional, Santi, Ludovica, additional, Basso-Ricci, Luca, additional, Merelli, Ivan, additional, Genovese, Pietro, additional, Aiuti, Alessandro, additional, Naldini, Luigi, additional, Di Micco, Raffaella, additional, and Bernardo, Maria Ester, additional
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- 2022
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14. Choice of template delivery mitigates the genotoxic risk and adverse impact of editing in human hematopoietic stem cells
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Ferrari, Samuele, primary, Jacob, Aurelien, additional, Cesana, Daniela, additional, Laugel, Marianne, additional, Beretta, Stefano, additional, Varesi, Angelica, additional, Unali, Giulia, additional, Conti, Anastasia, additional, Canarutto, Daniele, additional, Albano, Luisa, additional, Calabria, Andrea, additional, Vavassori, Valentina, additional, Cipriani, Carlo, additional, Castiello, Maria Carmina, additional, Esposito, Simona, additional, Brombin, Chiara, additional, Cugnata, Federica, additional, Adjali, Oumeya, additional, Ayuso, Eduard, additional, Merelli, Ivan, additional, Villa, Anna, additional, Di Micco, Raffaella, additional, Kajaste-Rudnitski, Anna, additional, Montini, Eugenio, additional, Penaud-Budloo, Magalie, additional, and Naldini, Luigi, additional
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- 2022
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15. p53 activation: a checkpoint for precision genome editing?
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Conti, Anastasia and Di Micco, Raffaella
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- 2018
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16. Follicular helper T cell signature of replicative exhaustion, apoptosis, and senescence in common variable immunodeficiency
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Milardi, Giulia, primary, Di Lorenzo, Biagio, additional, Gerosa, Jolanda, additional, Barzaghi, Federica, additional, Di Matteo, Gigliola, additional, Omrani, Maryam, additional, Jofra, Tatiana, additional, Merelli, Ivan, additional, Barcella, Matteo, additional, Filippini, Matteo, additional, Conti, Anastasia, additional, Ferrua, Francesca, additional, Pozzo Giuffrida, Francesco, additional, Dionisio, Francesca, additional, Rovere‐Querini, Patrizia, additional, Marktel, Sarah, additional, Assanelli, Andrea, additional, Piemontese, Simona, additional, Brigida, Immacolata, additional, Zoccolillo, Matteo, additional, Cirillo, Emilia, additional, Giardino, Giuliana, additional, Danieli, Maria Giovanna, additional, Specchia, Fernando, additional, Pacillo, Lucia, additional, Di Cesare, Silvia, additional, Giancotta, Carmela, additional, Romano, Francesca, additional, Matarese, Alessandro, additional, Chetta, Alfredo Antonio, additional, Trimarchi, Matteo, additional, Laurenzi, Andrea, additional, De Pellegrin, Maurizio, additional, Darin, Silvia, additional, Montin, Davide, additional, Marinoni, Maddalena, additional, Dellepiane, Rosa Maria, additional, Sordi, Valeria, additional, Lougaris, Vassilios, additional, Vacca, Angelo, additional, Melzi, Raffaella, additional, Nano, Rita, additional, Azzari, Chiara, additional, Bongiovanni, Lucia, additional, Pignata, Claudio, additional, Cancrini, Caterina, additional, Plebani, Alessandro, additional, Piemonti, Lorenzo, additional, Petrovas, Constantinos, additional, Di Micco, Raffaella, additional, Ponzoni, Maurilio, additional, Aiuti, Alessandro, additional, Cicalese, Maria Pia, additional, and Fousteri, Georgia, additional
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- 2022
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17. 1014 – CELLULAR SENESCENCE: AN UNINTENDED TWIST FOR GENE AND CELL THERAPY APPLICATIONS
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Micco, Raffaella Di, primary, Conti, Anastasia, additional, Volpe, Lucrezia della, additional, Midena, Federico, additional, Ferrari, Samuele, additional, Tavella, Teresa, additional, Merelli, Ivan, additional, and Naldini, Luigi, additional
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- 2022
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18. Premature Senescence and Increased Oxidative Stress in the Thymus of Down Syndrome Patients
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Marcovecchio, Genni Enza, primary, Ferrua, Francesca, additional, Fontana, Elena, additional, Beretta, Stefano, additional, Genua, Marco, additional, Bortolomai, Ileana, additional, Conti, Anastasia, additional, Montin, Davide, additional, Cascarano, Maria Teresa, additional, Bergante, Sonia, additional, D’Oria, Veronica, additional, Giamberti, Alessandro, additional, Amodio, Donato, additional, Cancrini, Caterina, additional, Carotti, Adriano, additional, Di Micco, Raffaella, additional, Merelli, Ivan, additional, Bosticardo, Marita, additional, and Villa, Anna, additional
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- 2021
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19. Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response
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Schiroli, Giulia, primary, Conti, Anastasia, additional, Ferrari, Samuele, additional, della Volpe, Lucrezia, additional, Jacob, Aurelien, additional, Albano, Luisa, additional, Beretta, Stefano, additional, Calabria, Andrea, additional, Vavassori, Valentina, additional, Gasparini, Patrizia, additional, Salataj, Eralda, additional, Ndiaye-Lobry, Delphine, additional, Brombin, Chiara, additional, Chaumeil, Julie, additional, Montini, Eugenio, additional, Merelli, Ivan, additional, Genovese, Pietro, additional, Naldini, Luigi, additional, and Di Micco, Raffaella, additional
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- 2019
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20. An early‐senescence state in aged mesenchymal stromal cells contributes to hematopoietic stem and progenitor cell clonogenic impairment through the activation of a pro‐inflammatory program
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Gnani, Daniela, primary, Crippa, Stefania, additional, della Volpe, Lucrezia, additional, Rossella, Valeria, additional, Conti, Anastasia, additional, Lettera, Emanuele, additional, Rivis, Silvia, additional, Ometti, Marco, additional, Fraschini, Gianfranco, additional, Bernardo, Maria Ester, additional, and Di Micco, Raffaella, additional
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- 2019
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21. Epigenetic and Transcriptional Modifications in Repetitive Elements in Petrol Station Workers Exposed to Benzene and MTBE
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Rota, Federica, primary, Conti, Anastasia, additional, Campo, Laura, additional, Favero, Chiara, additional, Cantone, Laura, additional, Motta, Valeria, additional, Polledri, Elisa, additional, Mercadante, Rosa, additional, Dieci, Giorgio, additional, Bollati, Valentina, additional, and Fustinoni, Silvia, additional
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- 2018
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22. Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines
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Carnevali, Davide, primary, Conti, Anastasia, additional, Pellegrini, Matteo, additional, and Dieci, Giorgio, additional
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- 2016
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23. Studio dell'espressione dei retrotrasposoni umani Alu e LINE-1 e della sua possibile modulazione in risposta a fattori ambientali
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Conti, Anastasia
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LINE-1 ,Environmental chemicals ,MED/44 ,Alu ,Gene expression ,Non compilare - Abstract
Gli elementi trasponibili costituiscono circa il 45% del genoma umano e solo la classe dei retrotrasposoni non-LTR risulta attiva oggigiorno dal punto di vista della retrotrasposizione. Fanno parte di questa classe, gli elementi LINE-1 ed Alu, i quali si inseriscono in un locus genomico diverso da quello di origine, duplicandosi attraverso la generazione di un intermedio ad RNA, aumentando così notevolmente il loro numero di copie genomiche (circa 1 milione per gli elementi Alu e 500 mila per gli elementi L1). Inizialmente considerati DNA “spazzatura”, ovvero una porzione di DNA priva di qualsiasi funzione, attualmente essi sono stati progressivamente rivalutati, innanzitutto in quanto in grado di contribuire alla stabilità e all’evoluzione dei genomi in molteplici modi, in secondo luogo anche in quanto in grado di influenzare numerosi processi cellulari in modi ancora da esplorare. Il fatto che tali elementi si integrino in nuovi siti genomici, fa sì che essi possano generare instabilità sia mediante mutagenesi inserzionale sia attraverso eventi di ricombinazione omologa non allelica. Inoltre gli RNA stessi, prodotti dalla trascrizione dei retrotrasposoni, possono anche interferire con i normali processi cellulari. Analizzare gli elementi ripetuti, in quanto parte del genoma non ancora ben esplorata ma con ruoli emergenti sempre più associati allo sviluppo delle malattie, è quindi di rilievo per capire in dettaglio come sia regolata la loro espressione e le conseguenze di quest’ultima nel contesto cellulare. Inoltre, dal momento che vi sono alcune evidenze di una derepressione trascrizionale degli elementi Alu correlata alla loro ipometilazione e che tale ipometilazione è presente nelle cellule tumorali, si può supporre che uno dei meccanismi alla base della attivazione sia proprio una variazione nel loro stato di metilazione (normalmente gli elementi Alu e L1 sono ipermetilati e silenti) e che la loro espressione sia da considerarsi come un importante, ma ancora inesplorato, marcatore dello stato tumorale (sono riportate alcune evidenze anche della ipometilazione di elementi L1 in cellule tumorali). Ciò risulta di particolare rilievo se si considera che l’esposizione prolungata a differenti fattori ambientali, noti per essere legati alla comparsa di patologie, comporta anche una alterata metilazione (in genere ipometilazione) di elementi Alu e L1: questo avvalora l’ipotesi di una loro attivazione mediante abrogazione del silenziamento genico, e di un loro conseguente possibile coinvolgimento nella patogenesi. La derepressione di retrotrasposoni Alu e L1 in risposta a fattori ambientali rappresenta, pertanto, un fenomeno degno della massima attenzione. Nell’ambito della presente tesi di dottorato si è elaborata una strategia informatica per l’identificazione di elementi Alu trascritti autonomamente dalla RNA polimerasi III a partire da dati grezzi di RNA-seq. Si sono analizzati i dati relativi ai trascrittomi di 7 linee cellulari (tumorali e non tumorali) ottenuti all’interno del progetto ENCODE e si è individuato un sottogruppo di Alu RNA tipo cellulare-specifico che ha permesso di ipotizzare che gli elementi espressi possono avere una particolare sensibilità alla metilazione del DNA e al contesto cromatinico, i quali sono soggetti a variazioni da un tipo cellulare all’altro. Pertanto, l’analisi dei profili di espressione di elementi Alu, resa possibile dal sequenziamento dei trascrittomi cellulari, potrebbe rappresentare un nuovo modo, estremamente fine e sensibile, di monitorare le alterazione dell’epigenoma che accompagnano gli stati fisiologici e patologici, nonchè le esposizioni ambientali. Infatti, nonostante la notevole influenza degli elementi Alu sull’evoluzione del genoma e gli sporadici esempi del loro coinvolgimento in alcune forme tumorali, l’attività trascrizionale dei loci Alu nelle cellule normali e nelle cellule tumorali non è mai stata indagata a fondo. Detto ciò, l’identificazione di profili di Alu RNA potrebbe essere utile per considerarli come bio-marcatori del cancro, pertanto le nostre evidenze hanno aperto la strada ad indagini future sul possibile coinvolgimento degli Alu RNA nei tumori, come riportato per altri RNA non codificanti (come miRNA e lncRNA). La sovraespressione di due Alu RNA in cellule HeLa ha inoltre permesso di mettere in luce un possibile meccanismo di azione degli Alu RNA espressi nelle cellule, in quanto si è osservata la down-regolazione di mRNA contenenti almeno 3 elementi Alu in antisenso nella loro 3’UTR e di lncRNA con almeno 2 elementi Alu senso nella forma matura (post-splicing). Tali evidenze suggeriscono fortemente un meccanismo senso-antisenso (gli Alu RNA sovraespressi sono in orientamento senso) alla base del decremento di espressione dei trascritti codificanti per proteine. Inoltre, fra i geni per proteine deregolati dalla sovraespressione degli elementi Alu si sono trovati gruppi di geni coinvolti nel ciclo cellulare e nella maturazione dell’RNA, e ciò risulta importante in quanto uno dei primi esempi in tale ambito. Infine, si è rivolta l’attenzione all’influenza che i fattori ambientali, ai quali l’uomo è quotidianamente esposto, possono esercitare sull’espressione degli elementi ripetuti Alu e LINE-1, incuriositi dal fatto che l’esposizione ad alcuni agenti è stata associata ad una ipometilazione di tali elementi normalmente silenti, che quindi potrebbe essere interpretata come potenziale causa di una loro derepressione. Trattamenti di cellule THP-1 e staminali ematopoietiche da cordone ombelicale con concentrazioni crescenti di idrochinone, metabolita del benzene scelto come paradigma dell’esposizione ambientale, hanno permesso di osservare un apprezzabile aumento di espressione di Alu e L1 RNA che potrebbe essere correlato con una loro ipometilazione genomica. Tali variazioni di espressione e metilazione si sono rivelati tipo cellulare-indipendenti, facendo supporre che il derivato del benzene eserciti effetti paragonabili in differenti contesti cellulari e che quindi, in ultima analisi, la derepressione degli elementi Alu e L1 possa essere un suo effetto peculiare. Lo studio condotto con l’idrochinone apre la strada all’analisi degli effetti che altri fattori ambientali, generalmente ipometilanti, possono avere sull’espressione di elementi Alu e L1, e aggiungono un tassello verso la conoscenza di un possibile meccanismo alla base dell’insorgenza delle patologie indotte dai tali fattori. Transposable elements (TEs) constitute nearly 45% of the human genome and nowadays non-LTR retrotransposons are the only TEs able to retrotranspose. LINE-1 (L1) and Alu elements (Alus), the most abundant non-LTR retrotransposons with 500 thousand and 1 million copies, respectively, have been extremely successful in populating the human genome through a “copy-and-paste” mode of mobilization requiring transcription by host RNA polymerase II or III followed by retrotranscription. Firstly considered as junk DNA, they have been reevaluated because of their ability to influence genome stability through insertional mutagenesis and unequal non allelic crossing-over and to interfere with cellular pathways in ways that are largely unexplored. In this context, the study of Alus and L1 as the hugest part of the human genome, is principally relevant because of the emerging evidence of their possible roles in causing human diseases. The analysis of the regulation of their expression and the possible consequences of their derepression are interesting mainly because of the sporadic evidence of a connection between Alus transcriptional derepression and the hypomethylation of their sequences. Relevant with this respect are emerging data about TEs’ hypomethylation in tumours, suggesting a potential connection between Alus derepression and their genomic hypomethylation. Along this line, examples of L1 hypomethylation in a few malignancies have been reported. Moreover there are many examples of Alus and L1 hypomethylation upon environmental exposures associated with high risk of pathologies: this increases their possible activation through abrogation of their silencing (they are normally hypermethylated and silent) and their potential involvement in exposure-associate pathologies. Retrotransposons derepression after environmental exposure is thus a phenomenon deserving the most of our attention. The present thesis manuscript reports our work in searching for a bioinformatic pipeline able to distinguish Alu RNAs autonomously transcribed by the RNA polymerase III (Pol III) through ENCODE RNA-seq raw data, corresponding to seven different human cell lines, and we were able to find a tiny subset of cell type-specific Alu RNAs which allow us to conclude that Alus could present different sensitivity to DNA methylation and chromatin status, and that they can be representative of epigenomic states, that are different from one cell line to another. In this sense, the analysis of Alu expression profiles, made possible by sequencing of the transcriptome, might represent a novel, extremely subtle and sensitive way to monitor epigenome alterations accompanying physiological and pathological states and also environmental exposures. Despite their massive influence on genome evolution and sporadic examples of their involvement in tumour, the transcriptional activity of Alu loci in normal and cancer cells has never been satisfactorily investigated so the identification of Alu RNA profiles could be useful in considering them like cancer biomarkers, as previously mentioned. In so doing we were able to open the way for future investigations about Alu RNAs involvement in cancer, as it reported for other ncRNAs (such as miRNA and lncRNA). Furthermore Alu RNA overexpression in HeLa cells allow us to highlight the possible mechanism of action of these transcripts, because of our evidence of downregulation of mRNAs containing almost 3 antisense Alus in their 3’UTRs and of lncRNAs containing almost 2 sense Alus in their post-splicing form. These results strongly suggest a sense-antisense mechanism (we overexpressed sense oriented Alu RNAs) for mRNA downregulation. The pathways’ analysis also emphasized that Alus overexpression affect groups of genes involved in fundamental cellular processes, such as cell-cycle, transcription and splicing of RNAs, and this is relevant because one of the first examples in this context. Finally we examined environmental influence on Alu and LINE-1 expression, considering the reported hypomethylation effects that several environmental chemicals have on these retroelements. According to the fact that DNA hypomethyation is generally associated to transcriptional derepression, our goal was to analyse if the alteration of the methylation status of Alus and L1 loci could be one of the possible cause of their derepression. With this aim, we treated THP-1 and HSC cells with hydroquinone, the most abundant benzene metabolite selected as the paradigm of environmental chemicals, and we found a significant increase of Alus and LINE-1 expression with a possible correlation to the loss of methylation in their sequences. These observations were cell type-independent suggesting that hydroquinone might exert the same effects in different cell lines and that, finally, retrotransposon derepression might be one of its peculiar outcome. The same analysis reported for hydroquinone exposure, could be useful to analyse the influence that other environmental chemicals can have on Alus and LINE-1 expression, and they could increase our knowledge on the possible mechanism underlying the risk of pathologies connected with human’s environmental exposure.
- Published
- 2015
24. Hydroquinone induces DNA hypomethylation-independent overexpression of retroelements in human leukemia and hematopoietic stem cells
- Author
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Conti, Anastasia, primary, Rota, Federica, additional, Ragni, Enrico, additional, Favero, Chiara, additional, Motta, Valeria, additional, Lazzari, Lorenza, additional, Bollati, Valentina, additional, Fustinoni, Silvia, additional, and Dieci, Giorgio, additional
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- 2016
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- View/download PDF
25. Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data
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Conti, Anastasia, primary, Carnevali, Davide, additional, Bollati, Valentina, additional, Fustinoni, Silvia, additional, Pellegrini, Matteo, additional, and Dieci, Giorgio, additional
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- 2014
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- View/download PDF
26. Identification of RNA polymerase III-transcribed genes in eukaryotic genomes
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Dieci, Giorgio, primary, Conti, Anastasia, additional, Pagano, Aldo, additional, and Carnevali, Davide, additional
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- 2013
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27. The Murine PSE/TATA-Dependent Transcriptome: Evidence of Functional Homologies with Its Human Counterpart
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Bruzzone, Maria, primary, Gavazzo, Paola, additional, Massone, Sara, additional, Balbi, Carolina, additional, Villa, Federico, additional, Conti, Anastasia, additional, Dieci, Giorgio, additional, Cancedda, Ranieri, additional, and Pagano, Aldo, additional
- Published
- 2012
- Full Text
- View/download PDF
28. Follicular helper T cell signature of replicative exhaustion, apoptosis, and senescence in common variable immunodeficiency
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Giulia Milardi, Biagio Di Lorenzo, Jolanda Gerosa, Federica Barzaghi, Gigliola Di Matteo, Maryam Omrani, Tatiana Jofra, Ivan Merelli, Matteo Barcella, Matteo Filippini, Anastasia Conti, Francesca Ferrua, Francesco Pozzo Giuffrida, Francesca Dionisio, Patrizia Rovere‐Querini, Sarah Marktel, Andrea Assanelli, Simona Piemontese, Immacolata Brigida, Matteo Zoccolillo, Emilia Cirillo, Giuliana Giardino, Maria Giovanna Danieli, Fernando Specchia, Lucia Pacillo, Silvia Di Cesare, Carmela Giancotta, Francesca Romano, Alessandro Matarese, Alfredo Antonio Chetta, Matteo Trimarchi, Andrea Laurenzi, Maurizio De Pellegrin, Silvia Darin, Davide Montin, Maddalena Marinoni, Rosa Maria Dellepiane, Valeria Sordi, Vassilios Lougaris, Angelo Vacca, Raffaella Melzi, Rita Nano, Chiara Azzari, Lucia Bongiovanni, Claudio Pignata, Caterina Cancrini, Alessandro Plebani, Lorenzo Piemonti, Constantinos Petrovas, Raffaella Di Micco, Maurilio Ponzoni, Alessandro Aiuti, Maria Pia Cicalese, Georgia Fousteri, Milardi, Giulia, Di Lorenzo, Biagio, Gerosa, Jolanda, Barzaghi, Federica, Di Matteo, Gigliola, Omrani, Maryam, Jofra, Tatiana, Merelli, Ivan, Barcella, Matteo, Filippini, Matteo, Conti, Anastasia, Ferrua, Francesca, Pozzo Giuffrida, Francesco, Dionisio, Francesca, Rovere-Querini, Patrizia, Marktel, Sarah, Assanelli, Andrea, Piemontese, Simona, Brigida, Immacolata, Zoccolillo, Matteo, Cirillo, Emilia, Giardino, Giuliana, Danieli, Maria Giovanna, Specchia, Fernando, Pacillo, Lucia, Di Cesare, Silvia, Giancotta, Carmela, Romano, Francesca, Matarese, Alessandro, Chetta, Alfredo Antonio, Trimarchi, Matteo, Laurenzi, Andrea, De Pellegrin, Maurizio, Darin, Silvia, Montin, Davide, Marinoni, Maddalena, Dellepiane, Rosa Maria, Sordi, Valeria, Lougaris, Vassilio, Vacca, Angelo, Melzi, Raffaella, Nano, Rita, Azzari, Chiara, Bongiovanni, Lucia, Pignata, Claudio, Cancrini, Caterina, Plebani, Alessandro, Piemonti, Lorenzo, Petrovas, Constantino, Di Micco, Raffaella, Ponzoni, Maurilio, Aiuti, Alessandro, Cicalese, Maria Pia, Fousteri, Georgia, and Giuffrida, Francesco Pozzo
- Subjects
T cell exhaustion ,B cells ,B cell ,T Follicular Helper Cells ,Immunology ,Programmed Cell Death 1 Receptor ,Apoptosi ,Apoptosis ,T-Lymphocytes, Helper-Inducer ,Common variable immunodeficiency ,Common Variable Immunodeficiency ,Settore MED/02 ,T-cell exhaustion ,Immune aging ,Humans ,T follicular helper cells ,Immunology and Allergy ,T Follicular Helper Cell ,immune aging ,Human - Abstract
Common variable immunodeficiency (CVID) is the most frequent primary antibody deficiency whereby follicular helper T (Tfh) cells fail to establish productive responses with B cells in germinal centers. Here, we analyzed the frequency, phenotype, transcriptome and function of circulating Tfh (cTfh) cells in CVID patients displaying autoimmunity as an additional phenotype. A group of patients showed a high frequency of cTfh1 cells and a prominent expression of PD-1 and ICOS, as well as a cTfh mRNA signature consistent with highly activated, but exhausted, senescent and apoptotic cells. Plasmatic CXCL13 levels were elevated in this group and positively correlated with cTfh1 cell frequency and PD-1 levels. Monoallelic variants in RTEL1, a telomere length- and DNA repair-related gene, were identified in four patients belonging to this group. Their blood lymphocytes showed shortened telomeres, while their cTfh were more prone to apoptosis. These data point toward a novel pathogenetic mechanism in CVID, whereby alterations in DNA repair and telomere elongation might predispose to antibody deficiency. A Th1, highly activated but exhausted and apoptotic cTfh phenotype was associated with this form of CVID. This article is protected by copyright. All rights reserved.
- Published
- 2022
29. Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response
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Raffaella Di Micco, Giulia Schiroli, Valentina Vavassori, Anastasia Conti, Pietro Genovese, Delphine Ndiaye-Lobry, Patrizia Gasparini, Julie Chaumeil, Chiara Brombin, Lucrezia della Volpe, Ivan Merelli, Aurelien Jacob, Eugenio Montini, Andrea Calabria, Samuele Ferrari, Luigi Naldini, Stefano Beretta, Luisa Albano, Eralda Salataj, Schiroli, Giulia, Conti, Anastasia, Ferrari, Samuele, Della Volpe, Lucrezia, Jacob, Aurelien, Albano, Luisa, Beretta, Stefano, Calabria, Andrea, Vavassori, Valentina, Gasparini, Patrizia, Salataj, Eralda, Ndiaye-Lobry, Delphine, Brombin, Chiara, Chaumeil, Julie, Montini, Eugenio, Merelli, Ivan, Genovese, Pietro, Naldini, Luigi, Di Micco, Raffaella, Schiroli, G, Conti, A, Ferrari, S, della Volpe, L, Jacob, A, Albano, L, Beretta, S, Calabria, A, Vavassori, V, Gasparini, P, Salataj, E, Ndiaye-Lobry, D, Brombin, C, Chaumeil, J, Montini, E, Merelli, I, Genovese, P, Naldini, L, and Di Micco, R
- Subjects
DNA damage ,DNA repair ,adeno-associated vector ,Mice, SCID ,Biology ,DNA damage response ,Cell Line ,DNA double strand break ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Genome editing ,Mice, Inbred NOD ,K562 Cell ,Genetics ,medicine ,genome editing ,Animals ,Humans ,CRISPR ,Progenitor cell ,programmable nuclease ,030304 developmental biology ,Gene Editing ,Mice, Knockout ,0303 health sciences ,Animal ,Cas9 ,Hematopoietic stem cell ,Hematopoietic Stem Cell ,Cell Biology ,Hematopoietic Stem Cells ,Cell biology ,hematopoietic stem and progenitor cell ,Haematopoiesis ,medicine.anatomical_structure ,Molecular Medicine ,DNA double strand breaks ,hematopoietic stem and progenitor cells ,p53 pathway ,programmable nucleases ,Tumor Suppressor Protein p53 ,K562 Cells ,030217 neurology & neurosurgery ,Human ,DNA Damage - Abstract
Precise gene editing in hematopoietic stem and progenitor cells (HSPCs) holds promise for treating genetic diseases. However, responses triggered by programmable nucleases in HSPCs are poorly characterized and may negatively impact HSPC engraftment and long-term repopulation capacity. Here, we induced either one or several DNA double-stranded breaks (DSBs) with optimized zinc-finger and CRISPR/Cas9 nucleases and monitored DNA damage response (DDR) foci induction, cell-cycle progression, and transcriptional responses in HSPC subpopulations, with up to single-cell resolution. p53-mediated DDR pathway activation was the predominant response to even single-nuclease-induced DSBs across all HSPC subtypes analyzed. Excess DSB load and/or adeno-associated virus (AAV)-mediated delivery of DNA repair templates induced cumulative p53 pathway activation, constraining proliferation, yield, and engraftment of edited HSPCs. However, functional impairment was reversible when DDR burden was low and could be overcome by transient p53 inhibition. These findings provide molecular and functional evidence for feasible and seamless gene editing in HSPCs. Precise gene editing has the potential to treat immune and hematological diseases. Genovese, Naldini, Di Micco, and colleagues now show that gene-editing procedures are well tolerated by hematopoietic stem cells and provide molecular evidence of the feasibility of seamless gene editing, strengthening translation of such approaches to humans.
- Published
- 2019
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