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192 results on '"Mutarelli, Margherita"'

1. TFEB controls syncytiotrophoblast formation and hormone production in placenta

Author

Cesana, Marcella, Tufano, Gennaro, Panariello, Francesco, Zampelli, Nicolina, Soldati, Chiara, Mutarelli, Margherita, Montefusco, Sandro, Grieco, Giuseppina, Sepe, Lucia Vittoria, Rossi, Barbara, Nusco, Edoardo, Rossignoli, Giada, Panebianco, Giorgia, Merciai, Fabrizio, Salviati, Emanuela, Sommella, Eduardo Maria, Campiglia, Pietro, Martello, Graziano, Cacchiarelli, Davide, Medina, Diego Luis, and Ballabio, Andrea

Published
2024
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3. TFEB regulates murine liver cell fate during development and regeneration.

Author

Pastore, Nunzia, Huynh, Tuong, Herz, Niculin J, Calcagni', Alessia, Klisch, Tiemo J, Brunetti, Lorenzo, Kim, Kangho Ho, De Giorgi, Marco, Hurley, Ayrea, Carissimo, Annamaria, Mutarelli, Margherita, Aleksieva, Niya, D'Orsi, Luca, Lagor, William R, Moore, David D, Settembre, Carmine, Finegold, Milton J, Forbes, Stuart J, and Ballabio, Andrea

Subjects
Bile Ducts, Liver, Spheroids, Cellular, Hepatocytes, Stem Cells, Animals, Mice, Inbred C57BL, Mice, Transgenic, Cholangiocarcinoma, Bile Duct Neoplasms, Regeneration, Cell Differentiation, Cell Proliferation, Down-Regulation, Up-Regulation, Protein Binding, Cell Lineage, Phenotype, Models, Biological, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Promoter Regions, Genetic, SOX9 Transcription Factor, Mice, Inbred C57BL, Transgenic, Models, Biological, Promoter Regions, Genetic, Spheroids, Cellular
Abstract

It is well established that pluripotent stem cells in fetal and postnatal liver (LPCs) can differentiate into both hepatocytes and cholangiocytes. However, the signaling pathways implicated in the differentiation of LPCs are still incompletely understood. Transcription Factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy, is known to be involved in osteoblast and myeloid differentiation, but its role in lineage commitment in the liver has not been investigated. Here we show that during development and upon regeneration TFEB drives the differentiation status of murine LPCs into the progenitor/cholangiocyte lineage while inhibiting hepatocyte differentiation. Genetic interaction studies show that Sox9, a marker of precursor and biliary cells, is a direct transcriptional target of TFEB and a primary mediator of its effects on liver cell fate. In summary, our findings identify an unexplored pathway that controls liver cell lineage commitment and whose dysregulation may play a role in biliary cancer.

Published
2020

4. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Abbott, Kristin M., Banka, Siddharth, de Boer, Elke, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Denommé-Pichon, Anne-Sophie, Faivre, Laurence, Gilissen, Christian, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jackson, Adam, Kerstjens, Mieke, Kleefstra, Tjitske, Martín, Estrella López, Macek, Milan, Jr., Matalonga, Leslie, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca C., Renieri, Alessandra, Riess, Olaf, Rooryck, Caroline, Ryba, Lukas, Agathe, Jean-Madeleine de Sainte, Santen, Gijs W.E., Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Trimouille, Aurélien, Verloes, Alain, Vissers, Lisenka, Vitobello, Antonio, Votypka, Pavel, Zguro, Kristina, Boer, Elke de, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B.A.W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, ‘t Hoen, Peter A.C., Vissers, Lisenka E.L.M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Başak, Ayşe Nazlı, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A.L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Radio, Francesca Clementina, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, Alembik, Yves, Jean-Marçais, Nolwenn, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Safraou, Hana, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, de Vries, Bert B.A., Willemsen, Marjolein H., and Philippe, Christophe

Published
2023
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5. Nutrient‐sensitive transcription factors TFEB and TFE3 couple autophagy and metabolism to the peripheral clock

Author

Pastore, Nunzia, Vainshtein, Anna, Herz, Niculin J, Huynh, Tuong, Brunetti, Lorenzo, Klisch, Tiemo J, Mutarelli, Margherita, Annunziata, Patrizia, Kinouchi, Kenichiro, Brunetti‐Pierri, Nicola, Sassone‐Corsi, Paolo, and Ballabio, Andrea

Subjects
Genetics, Sleep Research, Nutrition, Neurosciences, 1.1 Normal biological development and functioning, Underpinning research, Animals, Autophagy, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Binding Sites, Cells, Cultured, Circadian Clocks, Circadian Rhythm, Energy Metabolism, Gene Expression Regulation, HEK293 Cells, Humans, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Nuclear Receptor Subfamily 1, Group D, Member 1, Nutrients, Transcription Factors, circadian rhythm, gene oscillation, MiT-TFE, REV-ERB alpha, MiT‐TFE, REV‐ERBα, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Autophagy and energy metabolism are known to follow a circadian pattern. However, it is unclear whether autophagy and the circadian clock are coordinated by common control mechanisms. Here, we show that the oscillation of autophagy genes is dependent on the nutrient-sensitive activation of TFEB and TFE3, key regulators of autophagy, lysosomal biogenesis, and cell homeostasis. TFEB and TFE3 display a circadian activation over the 24-h cycle and are responsible for the rhythmic induction of genes involved in autophagy during the light phase. Genetic ablation of TFEB and TFE3 in mice results in deregulated autophagy over the diurnal cycle and altered gene expression causing abnormal circadian wheel-running behavior. In addition, TFEB and TFE3 directly regulate the expression of Rev-erbα (Nr1d1), a transcriptional repressor component of the core clock machinery also involved in the regulation of whole-body metabolism and autophagy. Comparative analysis of the cistromes of TFEB/TFE3 and REV-ERBα showed an extensive overlap of their binding sites, particularly in genes involved in autophagy and metabolic functions. These data reveal a direct link between nutrient and clock-dependent regulation of gene expression shedding a new light on the crosstalk between autophagy, metabolism, and circadian cycles.

Published
2019

6. Milder presentation of TELO2-related syndrome in two sisters homozygous for the p.Arg609His pathogenic variant

Author

Torella, Annalaura, Cappuccio, Gerarda, Musacchia, Francesco, Mutarelli, Margherita, Carrella, Diego, Vitiello, Giuseppina, Parenti, Giancarlo, Capra, Valeria, Leuzzi, Vincenzo, Selicorni, Angelo, Maitz, Silvia, Brunetti-Pierri, Nicola, Banfi, Sandro, Zollino, Marcella, Montomoli, Martino, Milani, Donatella, Romano, Corrado, Tummolo, Albina, De Brasi, Daniele, Coppola, Antonietta, Santoro, Claudia, Ciaccio, Claudia, Duga, Valentina, Pantaleoni, Chiara, Esposito, Silvia, Moroni, Isabella, Pinelli, Michele, Castello, Raffaele, Nigro, Vincenzo, Chiapparini, Luisa, and D'Arrigo, Stefano

Published
2021
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11. TFEB and TFE3 control glucose homeostasis by regulating insulin gene expression

Author

Pasquier, Adrien, primary, Pastore, Nunzia, additional, D'Orsi, Luca, additional, Colonna, Rita, additional, Esposito, Alessandra, additional, Maffia, Veronica, additional, De Cegli, Rossella, additional, Mutarelli, Margherita, additional, Ambrosio, Susanna, additional, Tufano, Gennaro, additional, Grimaldi, Antonio, additional, Cesana, Marcella, additional, Cacchiarelli, Davide, additional, Delalleau, Nathalie, additional, Napolitano, Gennaro, additional, and Ballabio, Andrea, additional

Published
2023
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12. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Denommé-Pichon, Anne-Sophie, Matalonga, Leslie, de Boer, Elke, Jackson, Adam, Benetti, Elisa, Banka, Siddharth, Bruel, Ange-Line, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Duffourd, Yannis, Ellwanger, Kornelia, Fallerini, Chiara, Gilissen, Christian, Graessner, Holm, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jean-Marçais, Nolwenn, Kleefstra, Tjitske, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Pizzi, Simone, Posada, Manuel, Radio, Francesca Clementina, Renieri, Alessandra, Rooryck, Caroline, Ryba, Lukas, Safraou, Hana, Schwarz, Martin, Tartaglia, Marco, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, Trimouille, Aurélien, Votypka, Pavel, de Vries, Bert B. A., Willemsen, Marjolein H., Zurek, Birte, Verloes, Alain, Philippe, Christophe, Abbott, Kristin M., Faivre, Laurence, Kerstjens, Mieke, Martín, Estrella López, Macek Jr., Milan, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Radio, Francesca C., Riess, Olaf, Agathe, Jean-Madeleine De Sainte, Santen, Gijs W. E., Thauvin, Christel, Torella, Annalaura, Vissers, Lisenka, Vitobello, Antonio, Zguro, Kristina, Boer, Elke De, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B. A. W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, `t Hoen, Peter A. C., Vissers, Lisenka E. L. M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris Te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Li\vsková, Petra, Dole\vzalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A. L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, Alembik, Yves, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Denommé-Pichon, Anne-Sophie, Matalonga, Leslie, de Boer, Elke, Jackson, Adam, Benetti, Elisa, Banka, Siddharth, Bruel, Ange-Line, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Duffourd, Yannis, Ellwanger, Kornelia, Fallerini, Chiara, Gilissen, Christian, Graessner, Holm, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jean-Marçais, Nolwenn, Kleefstra, Tjitske, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Pizzi, Simone, Posada, Manuel, Radio, Francesca Clementina, Renieri, Alessandra, Rooryck, Caroline, Ryba, Lukas, Safraou, Hana, Schwarz, Martin, Tartaglia, Marco, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, Trimouille, Aurélien, Votypka, Pavel, de Vries, Bert B. 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W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, `t Hoen, Peter A. C., Vissers, Lisenka E. L. M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris Te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Li\vsková, Petra, Dole\vzalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A. L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, and Alembik, Yves

Abstract

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock.

Published
2023

13. Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Yaldiz, Burcu, Kucuk, Erdi, Hampstead, Juliet, Hofste, Tom, Pfundt, Rolph, Corominas Galbany, Jordi, Rinne, Tuula, Yntema, Helger G., Hoischen, Alexander, Nelen, Marcel, Gilissen, Christian, consortium, Solve-R. D., Riess, Olaf, Haack, Tobias B., Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, Hoen, Peter A. C. T, Vissers, Lisenka E. L. M., Steyaert, Wouter, Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, te Paske, Iris, Janssen, Erik, de Boer, Elke, Steehouwer, Marloes, Kleefstra, Tjitske, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Töpf, Ana, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Clayton-Smith, Jill, Banka, Siddharth, Alexander, Elizabeth, Jackson, Adam, Faivre, Laurence, Thauvin, Christel, Vitobello, Antonio, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Matalonga, Leslie, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Paramonov, Ida, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Nelson, Isabelle, Yaou, Rabah Ben, Metay, Corinne, Eymard, Bruno, Cohen, Enzo, Atalaia, Antonio, Stojkovic, Tanya, Macek, Milan, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robinson, Peter, Danis, Daniel, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Vandrovcova, Jana, Efthymiou, Stephanie, Morsy, Heba, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Morleo, Manuela, Pinelli, Michele, Varavallo, Alessandra, Banfi, Sandro, Torella, Annalaura, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Velde, Joeri K., van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Abbott, Kristin M., Frederikse, Wilhemina Skerstjens, Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Verloes, Alain, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, de Sainte Agathe, Jean-Madeleine, Rooryck, Caroline, Lacombe, Didier, Trimouille, Aurelien, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Martín, Estrella López, Delgado, Beatriz Martínez, de la Rosa, F. Javier Alonso García, Ciolfi, Andrea, Dallapiccola, Bruno, Pizzi, Simone, Radio, Francesca Clementina, Tartaglia, Marco, Renieri, Alessandra, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Balicza, Peter, Molnar, Maria Judit, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Osorio, Andrés Nascimento, de Benito, Daniel Natera, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Beeson, David, Cossins, Judith, Hackman, Peter, Johari, Mridul, Savarese, Marco, Udd, Bjarne, Horvath, Rita, Chinnery, Patrick F., Ratnaike, Thiloka, Gao, Fei, Schon, Katherine, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Schröck, Evelin, Rump, Andreas, Başak, Ayşe Nazlı, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Claeys, Kristl, Santen, Gijs W. E., Bijlsma, Emilia K., Hoffer, Mariette J. V., Ruivenkamp, Claudia A. L., Boztug, Kaan, Haimel, Matthias, Maystadt, Isabelle, Cordts, Isabelle, Deschauer, Marcus, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Depienne, Christel, Roos, Andreas, May, Patrick, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Yaldiz, Burcu, Kucuk, Erdi, Hampstead, Juliet, Hofste, Tom, Pfundt, Rolph, Corominas Galbany, Jordi, Rinne, Tuula, Yntema, Helger G., Hoischen, Alexander, Nelen, Marcel, Gilissen, Christian, consortium, Solve-R. D., Riess, Olaf, Haack, Tobias B., Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, Hoen, Peter A. C. T, Vissers, Lisenka E. L. M., Steyaert, Wouter, Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, te Paske, Iris, Janssen, Erik, de Boer, Elke, Steehouwer, Marloes, Kleefstra, Tjitske, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Töpf, Ana, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Clayton-Smith, Jill, Banka, Siddharth, Alexander, Elizabeth, Jackson, Adam, Faivre, Laurence, Thauvin, Christel, Vitobello, Antonio, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Matalonga, Leslie, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Paramonov, Ida, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Nelson, Isabelle, Yaou, Rabah Ben, Metay, Corinne, Eymard, Bruno, Cohen, Enzo, Atalaia, Antonio, Stojkovic, Tanya, Macek, Milan, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robinson, Peter, Danis, Daniel, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Vandrovcova, Jana, Efthymiou, Stephanie, Morsy, Heba, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Morleo, Manuela, Pinelli, Michele, Varavallo, Alessandra, Banfi, Sandro, Torella, Annalaura, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Velde, Joeri K., van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Abbott, Kristin M., Frederikse, Wilhemina Skerstjens, Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Verloes, Alain, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, de Sainte Agathe, Jean-Madeleine, Rooryck, Caroline, Lacombe, Didier, Trimouille, Aurelien, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Martín, Estrella López, Delgado, Beatriz Martínez, de la Rosa, F. Javier Alonso García, Ciolfi, Andrea, Dallapiccola, Bruno, Pizzi, Simone, Radio, Francesca Clementina, Tartaglia, Marco, Renieri, Alessandra, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Balicza, Peter, Molnar, Maria Judit, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Osorio, Andrés Nascimento, de Benito, Daniel Natera, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Beeson, David, Cossins, Judith, Hackman, Peter, Johari, Mridul, Savarese, Marco, Udd, Bjarne, Horvath, Rita, Chinnery, Patrick F., Ratnaike, Thiloka, Gao, Fei, Schon, Katherine, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Schröck, Evelin, Rump, Andreas, Başak, Ayşe Nazlı, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Claeys, Kristl, Santen, Gijs W. E., Bijlsma, Emilia K., Hoffer, Mariette J. V., Ruivenkamp, Claudia A. L., Boztug, Kaan, Haimel, Matthias, Maystadt, Isabelle, Cordts, Isabelle, Deschauer, Marcus, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Depienne, Christel, Roos, Andreas, and May, Patrick

Abstract

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.

Published
2023

14. Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Author

Yaldiz, Burcu, Kucuk, Erdi, Hampstead, Juliet, Hofste, Tom, Pfundt, Rolph, Corominas Galbany, Jordi, Rinne, Tuula, Yntema, Helger G., Hoischen, Alexander, Nelen, Marcel, Gilissen, Christian, consortium, Solve-R. D., Riess, Olaf, Haack, Tobias B., Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, Hoen, Peter A. C. T, Vissers, Lisenka E. L. M., Steyaert, Wouter, Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, te Paske, Iris, Janssen, Erik, de Boer, Elke, Steehouwer, Marloes, Kleefstra, Tjitske, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Töpf, Ana, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Clayton-Smith, Jill, Banka, Siddharth, Alexander, Elizabeth, Jackson, Adam, Faivre, Laurence, Thauvin, Christel, Vitobello, Antonio, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Matalonga, Leslie, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Paramonov, Ida, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Nelson, Isabelle, Yaou, Rabah Ben, Metay, Corinne, Eymard, Bruno, Cohen, Enzo, Atalaia, Antonio, Stojkovic, Tanya, Macek, Milan, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robinson, Peter, Danis, Daniel, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Vandrovcova, Jana, Efthymiou, Stephanie, Morsy, Heba, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Morleo, Manuela, Pinelli, Michele, Varavallo, Alessandra, Banfi, Sandro, Torella, Annalaura, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Velde, Joeri K., van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Abbott, Kristin M., Frederikse, Wilhemina Skerstjens, Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Verloes, Alain, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, de Sainte Agathe, Jean-Madeleine, Rooryck, Caroline, Lacombe, Didier, Trimouille, Aurelien, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Martín, Estrella López, Delgado, Beatriz Martínez, de la Rosa, F. Javier Alonso García, Ciolfi, Andrea, Dallapiccola, Bruno, Pizzi, Simone, Radio, Francesca Clementina, Tartaglia, Marco, Renieri, Alessandra, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Balicza, Peter, Molnar, Maria Judit, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Osorio, Andrés Nascimento, de Benito, Daniel Natera, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Beeson, David, Cossins, Judith, Hackman, Peter, Johari, Mridul, Savarese, Marco, Udd, Bjarne, Horvath, Rita, Chinnery, Patrick F., Ratnaike, Thiloka, Gao, Fei, Schon, Katherine, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Schröck, Evelin, Rump, Andreas, Başak, Ayşe Nazlı, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Claeys, Kristl, Santen, Gijs W. E., Bijlsma, Emilia K., Hoffer, Mariette J. V., Ruivenkamp, Claudia A. L., Boztug, Kaan, Haimel, Matthias, Maystadt, Isabelle, Cordts, Isabelle, Deschauer, Marcus, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Depienne, Christel, Roos, Andreas, May, Patrick, and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Multidisciplinary, general & others [D99] [Human health sciences]
Abstract

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.

Published
2023

16. EGR1 drives cell proliferation by directly stimulating TFEB transcription in response to starvation

Author

Cesana, Marcella, primary, Tufano, Gennaro, additional, Panariello, Francesco, additional, Zampelli, Nicolina, additional, Ambrosio, Susanna, additional, De Cegli, Rossella, additional, Mutarelli, Margherita, additional, Vaccaro, Lorenzo, additional, Ziller, Micheal J., additional, Cacchiarelli, Davide, additional, Medina, Diego L., additional, and Ballabio, Andrea, additional

Published
2023
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17. Effect of CB2 Stimulation on Gene Expression in Pediatric B-Acute Lymphoblastic Leukemia: New Possible Targets

Author

Punzo, Francesca, primary, Argenziano, Maura, additional, Tortora, Chiara, additional, Di Paola, Alessandra, additional, Mutarelli, Margherita, additional, Pota, Elvira, additional, Di Martino, Martina, additional, Di Pinto, Daniela, additional, Marrapodi, Maria Maddalena, additional, Roberti, Domenico, additional, and Rossi, Francesca, additional

Published
2022
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18. MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy

Author

Piccolo, Pasquale, Attanasio, Sergio, Secco, Ilaria, Sangermano, Riccardo, Strisciuglio, Caterina, Limongelli, Giuseppe, Miele, Erasmo, Mutarelli, Margherita, Banfi, Sandro, Nigro, Vincenzo, Pons, Tirso, Valencia, Alfonso, Zentilin, Lorena, Campione, Severo, Nardone, Gerardo, Lynnes, Ty C., Celestino-Soper, Patricia B.S., Spoonamore, Katherine G., D’Armiento, Francesco P., Giacca, Mauro, Staiano, Annamaria, Vatta, Matteo, Collesi, Chiara, and Brunetti-Pierri, Nicola

Published
2017
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20. Tracing back the origin of cell-cell communication: Hydra vulgaris releases extracellular vesicles delivering regulators of head and foot regeneration

Author

Moros, Maria, primary, Fergola, Eugenio, additional, Marchesano, Valentina, additional, Mutarelli, Margherita, additional, Tommasini, Giuseppina, additional, Miedziak, Beata, additional, Palumbo, Giuliana, additional, Ambrosone, Alfredo, additional, Tino, Angela, additional, and Tortiglione, Claudia, additional

Published
2021
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22. SB4ER: an ELIXIR Service Bundle for Epidemic Response

Author

SAVOJARDO, CASTRENSE, primary, Martelli, Pier Luigi, additional, Babbi, Giulia, additional, Anteghini, Marco, additional, Manfredi, Matteo, additional, Madeo, Giovanni, additional, Capriotti, Emidio, additional, Bayjanov, Jumamurat R., additional, Mutarelli, Margherita, additional, and Casadio, Rita, additional

Published
2021
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23. Milder presentation of TELO2-related syndrome in two sisters homozygous for the p.Arg609His pathogenic variant

Author

Ciaccio, Claudia, primary, Duga, Valentina, additional, Pantaleoni, Chiara, additional, Esposito, Silvia, additional, Moroni, Isabella, additional, Pinelli, Michele, additional, Castello, Raffaele, additional, Nigro, Vincenzo, additional, Chiapparini, Luisa, additional, D'Arrigo, Stefano, additional, Torella, Annalaura, additional, Cappuccio, Gerarda, additional, Musacchia, Francesco, additional, Mutarelli, Margherita, additional, Carrella, Diego, additional, Vitiello, Giuseppina, additional, Parenti, Giancarlo, additional, Capra, Valeria, additional, Leuzzi, Vincenzo, additional, Selicorni, Angelo, additional, Maitz, Silvia, additional, Brunetti-Pierri, Nicola, additional, Banfi, Sandro, additional, Zollino, Marcella, additional, Montomoli, Martino, additional, Milani, Donatella, additional, Romano, Corrado, additional, Tummolo, Albina, additional, De Brasi, Daniele, additional, Coppola, Antonietta, additional, and Santoro, Claudia, additional

Published
2021
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24. YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation

Author

Passaro, Fabiana, primary, De Martino, Ilaria, additional, Zambelli, Federico, additional, Di Benedetto, Giorgia, additional, Barbato, Matteo, additional, D’Erchia, Anna Maria, additional, Manzari, Caterina, additional, Pesole, Graziano, additional, Mutarelli, Margherita, additional, Cacchiarelli, Davide, additional, Antonini, Dario, additional, Parisi, Silvia, additional, and Russo, Tommaso, additional

Published
2021
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25. Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells

Author

Grober Olì MV, Ferraro Lorenzo, Cicatiello Luigi, Mutarelli Margherita, Ravo Maria, Facchiano Angelo M, Angelini Claudia, and Weisz Alessandro

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a ‘molecular picture’ of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where time influences gene activity and expression. The potential use of the statistical analysis of microarray data in time series has not been fully exploited so far, due to the fact that only few methods are available which take into proper account temporal relationships between samples. Results We compared here four different methods to analyze data derived from a time course mRNA expression profiling experiment which consisted in the study of the effects of estrogen on hormone-responsive human breast cancer cells. Gene expression was monitored with the innovative Illumina BeadArray platform, which includes an average of 30-40 replicates for each probe sequence randomly distributed on the chip surface. We present and discuss the results obtained by applying to these datasets different statistical methods for serial gene expression analysis. The influence of the normalization algorithm applied on data and of different parameter or threshold choices for the selection of differentially expressed transcripts has also been evaluated. In most cases, the selection was found fairly robust with respect to changes in parameters and type of normalization. We then identified which genes showed an expression profile significantly affected by the hormonal treatment over time. The final list of differentially expressed genes underwent cluster analysis of functional type, to identify groups of genes with similar regulation dynamics. Conclusions Several methods for processing time series gene expression data are presented, including evaluation of benefits and drawbacks of the different methods applied. The resulting protocol for data analysis was applied to characterization of the gene expression changes induced by estrogen in human breast cancer ZR-75.1 cells over an entire cell cycle.

Published
2008
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26. De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides–Baraitser syndrome

Author

Cappuccio, Gerarda, primary, Sayou, Camille, additional, Tanno, Pauline Le, additional, Tisserant, Emilie, additional, Bruel, Ange-Line, additional, Kennani, Sara El, additional, Sá, Joaquim, additional, Low, Karen J., additional, Dias, Cristina, additional, Havlovicová, Markéta, additional, Hančárová, Miroslava, additional, Eichler, Evan E., additional, Devillard, Françoise, additional, Moutton, Sébastien, additional, Van-Gils, Julien, additional, Dubourg, Christèle, additional, Odent, Sylvie, additional, Gerard, Bénédicte, additional, Piton, Amélie, additional, Yamamoto, Toshiyuki, additional, Okamoto, Nobuhiko, additional, Firth, Helen, additional, Metcalfe, Kay, additional, Moh, Anna, additional, Chapman, Kimberly A., additional, Aref-Eshghi, Erfan, additional, Kerkhof, Jennifer, additional, Torella, Annalaura, additional, Nigro, Vincenzo, additional, Perrin, Laurence, additional, Piard, Juliette, additional, Le Guyader, Gwenaël, additional, Jouan, Thibaud, additional, Thauvin-Robinet, Christel, additional, Duffourd, Yannis, additional, George-Abraham, Jaya K., additional, Buchanan, Catherine A., additional, Williams, Denise, additional, Kini, Usha, additional, Wilson, Kate, additional, Brunetti-Pierri, Nicola, additional, Casari, Giorgio, additional, Cappuccio, Gerarda, additional, Pinelli, Michele, additional, Musacchia, Francesco, additional, Mutarelli, Margherita, additional, Carrella, Diego, additional, Vitiello, Giuseppina, additional, Capra, Valeria, additional, Parenti, Giancarlo, additional, Leuzzi, Vincenzo, additional, Selicorni, Angelo, additional, Maitz, Silvia, additional, Banfi, Sandro, additional, Zollino, Marcella, additional, Montomoli, Mario, additional, Milani, Donatelli, additional, Romano, Corrado, additional, Tummolo, Albina, additional, De Brasi, Daniele, additional, Coppola, Antonietta, additional, Santoro, Claudia, additional, Peron, Angela, additional, Pantaleoni, Chiara, additional, Castello, Raffaele, additional, D’Arrigo, Stefano, additional, Sousa, Sérgio B., additional, Hennekam, Raoul C.M., additional, Sadikovic, Bekim, additional, Thevenon, Julien, additional, Govin, Jérôme, additional, and Vitobello, Antonio, additional

Published
2020
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27. Altered PTPRD DNA methylation associates with restricted adipogenesis in healthy first-degree relatives of Type 2 diabetes subjects

Author

Parrillo, Luca, primary, Spinelli, Rosa, additional, Longo, Michele, additional, Desiderio, Antonella, additional, Mirra, Paola, additional, Nigro, Cecilia, additional, Fiory, Francesca, additional, Hedjazifar, Shahram, additional, Mutarelli, Margherita, additional, Carissimo, Annamaria, additional, Formisano, Pietro, additional, Miele, Claudia, additional, Smith, Ulf, additional, Raciti, Gregory Alexander, additional, and Beguinot, Francesco, additional

Published
2020
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29. The ADAMTS18 gene is responsible for autosomal recessive early onset severe retinal dystrophy

Author

Peluso Ivana, Conte Ivan, Testa Francesco, Dharmalingam Gopuraja, Pizzo Mariateresa, Collin Rob WJ, Meola Nicola, Barbato Sara, Mutarelli Margherita, Ziviello Carmela, Barbarulo Anna Maria, Nigro Vincenzo, Melone Mariarosa AB, Simonelli Francesca, and Banfi Sandro

Subjects
Inherited retinal dystrophies, ADAMTS18, Exome, Homozygosity mapping, Medaka fish, Knobloch syndrome, Medicine
Abstract

Abstract Background Inherited retinal dystrophies, including Retinitis Pigmentosa and Leber Congenital Amaurosis among others, are a group of genetically heterogeneous disorders that lead to variable degrees of visual deficits. They can be caused by mutations in over 100 genes and there is evidence for the presence of as yet unidentified genes in a significant proportion of patients. We aimed at identifying a novel gene for an autosomal recessive form of early onset severe retinal dystrophy in a patient carrying no previously described mutations in known genes. Methods An integrated strategy including homozygosity mapping and whole exome sequencing was used to identify the responsible mutation. Functional tests were performed in the medaka fish (Oryzias latipes) model organism to gain further insight into the pathogenic role of the ADAMTS18 gene in eye and central nervous system (CNS) dysfunction. Results This study identified, in the analyzed patient, a homozygous missense mutation in the ADAMTS18 gene, which was recently linked to Knobloch syndrome, a rare developmental disorder that affects the eye and the occipital skull. In vivo gene knockdown performed in medaka fish confirmed both that the mutation has a pathogenic role and that the inactivation of this gene has a deleterious effect on photoreceptor cell function. Conclusion This study reveals that mutations in the ADAMTS18 gene can cause a broad phenotypic spectrum of eye disorders and contribute to shed further light on the complexity of retinal diseases.

Published
2013
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30. Myopalladin promotes muscle growth through modulation of the serum response factor pathway

Author

Filomena, Maria Carmela, primary, Yamamoto, Daniel L., additional, Caremani, Marco, additional, Kadarla, Vinay K., additional, Mastrototaro, Giuseppina, additional, Serio, Simone, additional, Vydyanath, Anupama, additional, Mutarelli, Margherita, additional, Garofalo, Arcamaria, additional, Pertici, Irene, additional, Knöll, Ralph, additional, Nigro, Vincenzo, additional, Luther, Pradeep K., additional, Lieber, Richard L., additional, Beck, Moriah R., additional, Linari, Marco, additional, and Bang, Marie‐Louise, additional

Published
2019
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31. Nutrient‐sensitive transcription factorsTFEBandTFE3 couple autophagy and metabolism to the peripheral clock

Author

Pastore, Nunzia, primary, Vainshtein, Anna, additional, Herz, Niculin J, additional, Huynh, Tuong, additional, Brunetti, Lorenzo, additional, Klisch, Tiemo J, additional, Mutarelli, Margherita, additional, Annunziata, Patrizia, additional, Kinouchi, Kenichiro, additional, Brunetti‐Pierri, Nicola, additional, Sassone‐Corsi, Paolo, additional, and Ballabio, Andrea, additional

Published
2019
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32. Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

Author

Papa Maria, Nassa Giovanni, Ferraro Lorenzo, De Filippo Maria, Cicatiello Luigi, Ravo Maria, Giurato Giorgio, Mutarelli Margherita, Grober Oli MV, Paris Ornella, Tarallo Roberta, Luo Shujun, Schroth Gary P, Benes Vladimir, and Weisz Alessandro

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Estrogen receptors alpha (ERα) and beta (ERβ) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found co-expressed and play specific, often opposite, roles, with ERβ being able to modulate the effects of ERα on gene transcription and cell proliferation. ERβ is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERβ in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Results Expression of full-length ERβ in hormone-responsive, ERα-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERβ and 6024 ERα binding sites in estrogen-stimulated cells, comprising sites occupied by either ERβ, ERα or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERβ+ vs ERβ- cells, 424 showed one or more ERβ site within 10 kb. These putative primary ERβ target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERβ binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Conclusions Results indicate that the vast majority of the genomic targets of ERβ can bind also ERα, suggesting that the overall action of ERβ on the genome of hormone-responsive BC cells depends mainly on the relative concentration of both ERs in the cell.

Published
2011
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33. BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments

Author

Mutarelli Margherita, De Canditiis Daniela, Cutillo Luisa, Angelini Claudia, and Pensky Marianna

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach which allows one to identify differentially expressed genes in a 'one-sample' time-course microarray experiment, to rank them and to estimate their expression profiles. The method is based on explicit expressions for calculations and, hence, very computationally efficient. Results The software package BATS (Bayesian Analysis of Time Series) presented here implements the methodology described above. It allows an user to automatically identify and rank differentially expressed genes and to estimate their expression profiles when at least 5–6 time points are available. The package has a user-friendly interface. BATS successfully manages various technical difficulties which arise in time-course microarray experiments, such as a small number of observations, non-uniform sampling intervals and replicated or missing data. Conclusion BATS is a free user-friendly software for the analysis of both simulated and real microarray time course experiments. The software, the user manual and a brief illustrative example are freely available online at the BATS website: http://www.na.iac.cnr.it/bats

Published
2008
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34. An atlas of gene expression and gene co-regulation in the human retina

Author

Pinelli, Michele, Carissimo, Annamaria, Cutillo, Luisa, Lai, Ching Hung, Mutarelli, Margherita, Moretti, Maria Nicoletta, Singh, Marwah Veer, Karali, Marianthi, Carrella, Diego, Pizzo, Mariateresa, Russo, Francesco, Ferrari, Stefano, Ponzin, Diego, Angelini, Claudia, Banfi, Sandro, Di Bernardo, Diego, Pinelli, Michele, Carissimo, Annamaria, Cutillo, Luisa, Lai, Ching Hung, Mutarelli, Margherita, Moretti, Maria Nicoletta, Singh, Marwah Veer, Karali, Marianthi, Carrella, Diego, Pizzo, Mariateresa, Russo, Francesco, Ferrari, Stefano, Ponzin, Diego, Angelini, Claudia, Banfi, Sandro, DI BERNARDO, Diego, and Di Bernardo, Diego

Subjects
0301 basic medicine, Gene isoform, Adult, Male, retina, gene co-regulation, Network, rna-seq, retina, Network, Biology, Genome, Transcriptome, Mitochondrial Proteins, 03 medical and health sciences, Exon, Atlases as Topic, Gene expression, Genetics, Humans, Protein Isoforms, Gene Regulatory Networks, Eye Proteins, Gene, Aged, Genome, Human, Gene Expression Profiling, Alternative splicing, Web tools, pipeline, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Genomics, Exons, Middle Aged, Gene expression profiling, Alternative Splicing, 030104 developmental biology, Gene Ontology, Gene Network, rna-seq, Female
Abstract

The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it).

Published
2016
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35. Autophagosome–lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL

Author

De Leo, Maria Giovanna, Staiano, Leopoldo, Vicinanza, Mariella, Luciani, Alessandro, Carissimo, Annamaria, Mutarelli, Margherita, Di Campli, Antonella, Polishchuk, Elena, Di Tullio, Giuseppe, Morra, Valentina, Levtchenko, Elena, Oltrabella, Francesca, Starborg, Tobias, Santoro, Michele, Devuyst, Olivier, Lowe, Martin, Medina, Diego L., BALLABIO, ANDREA, DE MATTEIS, Maria Antonietta, MEDINA SANABRIA, Diego Luis, DI BERNARDO, DIEGO, University of Zurich, De Leo, Maria Giovanna, Staiano, Leopoldo, Vicinanza, Mariella, Luciani, Alessandro, Carissimo, Annamaria, Mutarelli, Margherita, Di Campli, Antonella, Polishchuk, Elena, Di Tullio, Giuseppe, Morra, Valentina, Levtchenko, Elena, Oltrabella, Francesca, Starborg, Tobia, Santoro, Michele, DI BERNARDO, Diego, Devuyst, Olivier, Lowe, Martin, Medina, Diego L., Ballabio, Andrea, DE MATTEIS, Maria Antonietta, MEDINA SANABRIA, Diego Luis, and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Phosphatidylinositol 4,5-Diphosphate, Oculocerebrorenal syndrome, Phosphatase, 610 Medicine & health, Biology, medicine.disease_cause, Phosphatidylinositols, Cell Line, 10052 Institute of Physiology, 1307 Cell Biology, 03 medical and health sciences, medicine, Autophagy, Animals, Humans, Receptor, Zebrafish, Mutation, Autophagosomes Autophagy Lysosomes, Kinase, Calcium channel, Autophagosomes, Cell Biology, News and Commentary, medicine.disease, Phosphoric Monoester Hydrolases, Cell biology, Lowe syndrome, 030104 developmental biology, Oculocerebrorenal Syndrome, Toll-Like Receptor 9, lysosome, 570 Life sciences, biology, OCRL, Lysosomes
Abstract

Phosphoinositides (PtdIns) control fundamental cell processes, and inherited defects of PtdIns kinases or phosphatases cause severe human diseases, including Lowe syndrome due to mutations in OCRL, which encodes a PtdIns(4,5)P2 5-phosphatase. Here we unveil a lysosomal response to the arrival of autophagosomal cargo in which OCRL plays a key part. We identify mitochondrial DNA and TLR9 as the cargo and the receptor that triggers and mediates, respectively, this response. This lysosome-cargo response is required to sustain the autophagic flux and involves a local increase in PtdIns(4,5)P2 that is confined in space and time by OCRL. Depleting or inhibiting OCRL leads to an accumulation of lysosomal PtdIns(4,5)P2, an inhibitor of the calcium channel mucolipin-1 that controls autophagosome-lysosome fusion. Hence, autophagosomes accumulate in OCRL-depleted cells and in the kidneys of Lowe syndrome patients. Importantly, boosting the activity of mucolipin-1 with selective agonists restores the autophagic flux in cells from Lowe syndrome patients.

Published
2016
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36. The genetic basis of undiagnosed muscular dystrophies and myopathies

Author

Savarese, Marco, Di Fruscio, Giuseppina, Torella, Annalaura, Fiorillo, Chiara, Magri, Francesca, Fanin, Marina, Ruggiero, Lucia, Ricci, Giulia, Astrea, Guja, Passamano, Luigia, Ruggieri, Alessandra, Ronchi, Dario, Tasca, Giorgio, D'Amico, Adele, Janssens, Sandra, Farina, Olimpia, Mutarelli, Margherita, Marwah, Veer Singh, Garofalo, Arcomaria, Giugliano, Teresa, Sanpaolo, Simone, Del Vecchio Blanco, Francesca, Esposito, Gaia, Piluso, Giulio, D'Ambrosio, Paola, Petillo, Roberta, Musumeci, Olimpia, Rodolico, Carmelo, Messina, Sonia, Evilä, Anni, Hackman, Peter, Filosto, Massimiliano, Di Iorio, Giuseppe, Siciliano, Gabriele, Mora, Marina, Maggi, Lorenzo, Minetti, Carlo, Sacconi, Sabrina, Santoro, Lucio, Claes, Kathleen, Vercelli, Liliana, Mongini, Tiziana, Ricci, Enzo, Gualandi, Francesca, Tupler, Rossella, De Bleecker, Jan, Udd, Bjarne, Toscano, Antonio, Moggio, Maurizio, Pegoraro, Elena, Bertini, Enrico, Mercuri, Eugenio, Angelini, Corrado, Santorelli, Filippo Maria, Politano, Luisa, Bruno, Claudio, Comi, Giacomo Pietro, Nigro, Vincenzo, Savarese, Marco, Di Fruscio, Giuseppina, Torella, Annalaura, Fiorillo, Chiara, Magri, Francesca, Fanin, Marina, Ruggiero, Lucia, Ricci, Giulia, Astrea, Guja, Passamano, Luigia, Ruggieri, Alessandra, Ronchi, Dario, Tasca, Giorgio, D'Amico, Adele, Janssens, Sandra, Farina, Olimpia, Mutarelli, Margherita, Marwah, Veer Singh, Garofalo, Arcomaria, Giugliano, Teresa, Sanpaolo, Simone, Del Vecchio Blanco, Francesca, Esposito, Gaia, Piluso, Giulio, D'Ambrosio, Paola, Petillo, Roberta, Musumeci, Olimpia, Rodolico, Carmelo, Messina, Sonia, Evilä, Anni, Hackman, Peter, Filosto, Massimiliano, Di Iorio, Giuseppe, Siciliano, Gabriele, Mora, Marina, Maggi, Lorenzo, Minetti, Carlo, Sacconi, Sabrina, Santoro, Lucio, Claes, Kathleen, Vercelli, Liliana, Mongini, Tiziana, Ricci, Enzo, Gualandi, Francesca, Tupler, Rossella, De Bleecker, Jan, Udd, Bjarne, Toscano, Antonio, Moggio, Maurizio, Pegoraro, Elena, Bertini, Enrico, Mercuri, Eugenio, Angelini, Corrado, Santorelli, Filippo Maria, Politano, Luisa, Bruno, Claudio, Comi, Giacomo Pietro, and Nigro, Vincenzo

Subjects
Male, Genetic Variation, Cohort Studies, Diagnosis, Differential, Female, Humans, Italy, Muscular Dystrophies, Sequence Analysis, Neurology (clinical), Settore MED/26 - NEUROLOGIA, Diagnosis, Differential
Published
2016

37. Myopalladin promotes muscle growth through modulation of the serum response factor pathway.

Author

Filomena, Maria Carmela, Yamamoto, Daniel L., Caremani, Marco, Kadarla, Vinay K., Mastrototaro, Giuseppina, Serio, Simone, Vydyanath, Anupama, Mutarelli, Margherita, Garofalo, Arcamaria, Pertici, Irene, Knöll, Ralph, Nigro, Vincenzo, Luther, Pradeep K., Lieber, Richard L., Beck, Moriah R., Linari, Marco, and Bang, Marie‐Louise

Subjects
MUSCLE growth, SERUM response factor, NEMALINE myopathy, MOLECULAR motor proteins, MYOBLASTS, TRANSCRIPTION factors, MUSCLE weakness
Abstract

Background: Myopalladin (MYPN) is a striated muscle‐specific, immunoglobulin‐containing protein located in the Z‐line and I‐band of the sarcomere as well as the nucleus. Heterozygous MYPN gene mutations are associated with hypertrophic, dilated, and restrictive cardiomyopathy, and homozygous loss‐of‐function truncating mutations have recently been identified in patients with cap myopathy, nemaline myopathy, and congenital myopathy with hanging big toe. Methods: Constitutive MYPN knockout (MKO) mice were generated, and the role of MYPN in skeletal muscle was studied through molecular, cellular, biochemical, structural, biomechanical, and physiological studies in vivo and in vitro. Results: MKO mice were 13% smaller compared with wild‐type controls and exhibited a 48% reduction in myofibre cross‐sectional area (CSA) and significantly increased fibre number. Similarly, reduced myotube width was observed in MKO primary myoblast cultures. Biomechanical studies showed reduced isometric force and power output in MKO mice as a result of the reduced CSA, whereas the force developed by each myosin molecular motor was unaffected. While the performance by treadmill running was similar in MKO and wild‐type mice, MKO mice showed progressively decreased exercise capability, Z‐line damage, and signs of muscle regeneration following consecutive days of downhill running. Additionally, MKO muscle exhibited progressive Z‐line widening starting from 8 months of age. RNA‐sequencing analysis revealed down‐regulation of serum response factor (SRF)‐target genes in muscles from postnatal MKO mice, important for muscle growth and differentiation. The SRF pathway is regulated by actin dynamics as binding of globular actin to the SRF‐cofactor myocardin‐related transcription factor A (MRTF‐A) prevents its translocation to the nucleus where it binds and activates SRF. MYPN was found to bind and bundle filamentous actin as well as interact with MRTF‐A. In particular, while MYPN reduced actin polymerization, it strongly inhibited actin depolymerization and consequently increased MRTF‐A‐mediated activation of SRF signalling in myogenic cells. Reduced myotube width in MKO primary myoblast cultures was rescued by transduction with constitutive active SRF, demonstrating that MYPN promotes skeletal muscle growth through activation of the SRF pathway. Conclusions: Myopalladin plays a critical role in the control of skeletal muscle growth through its effect on actin dynamics and consequently the SRF pathway. In addition, MYPN is important for the maintenance of Z‐line integrity during exercise and aging. These results suggest that muscle weakness in patients with biallelic MYPN mutations may be associated with reduced myofibre CSA and SRF signalling and that the disease phenotype may be aggravated by exercise. [ABSTRACT FROM AUTHOR]

Published
2020
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38. Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics

Author

Giulitti, Stefano, primary, Pellegrini, Marco, additional, Zorzan, Irene, additional, Martini, Paolo, additional, Gagliano, Onelia, additional, Mutarelli, Margherita, additional, Ziller, Michael Johannes, additional, Cacchiarelli, Davide, additional, Romualdi, Chiara, additional, Elvassore, Nicola, additional, and Martello, Graziano, additional

Published
2018
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39. Triple Vectors Expand AAV Transfer Capacity in the Retina

Author

Maddalena, Andrea, primary, Tornabene, Patrizia, additional, Tiberi, Paola, additional, Minopoli, Renato, additional, Manfredi, Anna, additional, Mutarelli, Margherita, additional, Rossi, Settimio, additional, Simonelli, Francesca, additional, Naggert, Jurgen K., additional, Cacchiarelli, Davide, additional, and Auricchio, Alberto, additional

Published
2018
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41. Clinical and Genetic Evaluation of a Cohort of Pediatric Patients with Severe Inherited Retinal Dystrophies

Author

Di Iorio, Valentina, primary, Karali, Marianthi, additional, Brunetti-Pierri, Raffaella, additional, Filippelli, Mariaelena, additional, Di Fruscio, Giuseppina, additional, Pizzo, Mariateresa, additional, Mutarelli, Margherita, additional, Nigro, Vincenzo, additional, Testa, Francesco, additional, Banfi, Sandro, additional, and Simonelli, Francesca, additional

Published
2017
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42. Chromatin conformation of muscle stem cells in physiological and pathological muscular aging.

Author

Santarelli, Philina, di Patrizio Soldateschi, Emanuele, Lucini, Federica, Mutarelli, Margherita, Rosti, Valentina, Petrini, Cristiano, Salviato, Elisa, Ferrari, Francesco, and Lanzuolo, Chiara

Subjects
STEM cells, MUSCLE cells, CHROMATIN, CELLULAR aging, MUSCLE aging
Abstract

The correct 3D organization of the genome is known to influence the spatiotemporal expression of lineagespecific genes during stem cell differentiation and aging processes. We introduce a novel evolution of the SAMMY-seq technique to precisely map genomic regions separated by their biochemical properties. This single-handedly technique enables the identification of heterochromatic and euchromatic domains and their compartmentalization in the nuclear space. Crucial practical advantages of this method include: its applicability on as little as 10K cells; reduced costs; few manipulation steps and short execution time. In postnatal Muscle Stem Cells (MuSCs) we observed a reproducible distribution of euchromatic and heterochromatic genomic domains, in line with known epigenetic signatures. Our findings highlight how MuSCs over life exhibit a global steady chromatin organization, accompanied by solubility changes that favour processes such as MuSCs activation but may become obstacles during aging for proper pool maintenance. Still, we describe environmental alterations of the muscle niche, emphasizing a supportive population of MuSCs, namely FAPs, which exhibit dramatic transcriptional alterations during aging. Our extensive characterization of the environment and chromatin organization in MuSCs expands our understanding of quiescence, activation and aging processes, laying the groundwork for the study of the role of the epigenome in pathological conditions. [ABSTRACT FROM AUTHOR]

Published
2023
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43. Autophagosome-lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL.

Author

UCL - SSS/IREC/NEFR - Pôle de Néphrologie, UCL - (SLuc) Service de néphrologie, De Leo, Maria Giovanna, Staiano, Leopoldo, Vicinanza, Mariella, Luciani, Alessandro, Carissimo, Annamaria, Mutarelli, Margherita, Di Campli, Antonella, Polishchuk, Elena, Di Tullio, Giuseppe, Morra, Valentina, Levtchenko, Elena, Oltrabella, Francesca, Starborg, Tobias, Santoro, Michele, di Bernardo, Diego, Devuyst, Olivier, Lowe, Martin, Medina, Diego L, Ballabio, Andrea, De Matteis, Maria Antonietta, UCL - SSS/IREC/NEFR - Pôle de Néphrologie, UCL - (SLuc) Service de néphrologie, De Leo, Maria Giovanna, Staiano, Leopoldo, Vicinanza, Mariella, Luciani, Alessandro, Carissimo, Annamaria, Mutarelli, Margherita, Di Campli, Antonella, Polishchuk, Elena, Di Tullio, Giuseppe, Morra, Valentina, Levtchenko, Elena, Oltrabella, Francesca, Starborg, Tobias, Santoro, Michele, di Bernardo, Diego, Devuyst, Olivier, Lowe, Martin, Medina, Diego L, Ballabio, Andrea, and De Matteis, Maria Antonietta

Abstract

Phosphoinositides (PtdIns) control fundamental cell processes, and inherited defects of PtdIns kinases or phosphatases cause severe human diseases, including Lowe syndrome due to mutations in OCRL, which encodes a PtdIns(4,5)P2 5-phosphatase. Here we unveil a lysosomal response to the arrival of autophagosomal cargo in which OCRL plays a key part. We identify mitochondrial DNA and TLR9 as the cargo and the receptor that triggers and mediates, respectively, this response. This lysosome-cargo response is required to sustain the autophagic flux and involves a local increase in PtdIns(4,5)P2 that is confined in space and time by OCRL. Depleting or inhibiting OCRL leads to an accumulation of lysosomal PtdIns(4,5)P2, an inhibitor of the calcium channel mucolipin-1 that controls autophagosome-lysosome fusion. Hence, autophagosomes accumulate in OCRL-depleted cells and in the kidneys of Lowe syndrome patients. Importantly, boosting the activity of mucolipin-1 with selective agonists restores the autophagic flux in cells from Lowe syndrome patients.

Published
2016

44. MIB2variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy

Author

Piccolo, Pasquale, primary, Attanasio, Sergio, additional, Secco, Ilaria, additional, Sangermano, Riccardo, additional, Strisciuglio, Caterina, additional, Limongelli, Giuseppe, additional, Miele, Erasmo, additional, Mutarelli, Margherita, additional, Banfi, Sandro, additional, Nigro, Vincenzo, additional, Pons, Tirso, additional, Valencia, Alfonso, additional, Zentilin, Lorena, additional, Campione, Severo, additional, Nardone, Gerardo, additional, Lynnes, Ty C., additional, Celestino-Soper, Patricia B.S., additional, Spoonamore, Katherine G., additional, D’Armiento, Francesco P., additional, Giacca, Mauro, additional, Staiano, Annamaria, additional, Vatta, Matteo, additional, Collesi, Chiara, additional, and Brunetti-Pierri, Nicola, additional

Published
2016
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45. Computational drugs repositioning identifies inhibitors of oncogenic PI3K/AKT/P70S6K-dependent pathways among FDA-approved compounds

Author

Carrella, Diego, primary, Manni, Isabella, additional, Tumaini, Barbara, additional, Dattilo, Rosanna, additional, Papaccio, Federica, additional, Mutarelli, Margherita, additional, Sirci, Francesco, additional, Amoreo, Carla A., additional, Mottolese, Marcella, additional, Iezzi, Manuela, additional, Ciolli, Laura, additional, Aria, Valentina, additional, Bosotti, Roberta, additional, Isacchi, Antonella, additional, Loreni, Fabrizio, additional, Bardelli, Alberto, additional, Avvedimento, Vittorio E., additional, di Bernardo, Diego, additional, and Cardone, Luca, additional

Published
2016
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46. Autophagosome–lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL

Author

De Leo, Maria Giovanna, primary, Staiano, Leopoldo, additional, Vicinanza, Mariella, additional, Luciani, Alessandro, additional, Carissimo, Annamaria, additional, Mutarelli, Margherita, additional, Di Campli, Antonella, additional, Polishchuk, Elena, additional, Di Tullio, Giuseppe, additional, Morra, Valentina, additional, Levtchenko, Elena, additional, Oltrabella, Francesca, additional, Starborg, Tobias, additional, Santoro, Michele, additional, di Bernardo, Diego, additional, Devuyst, Olivier, additional, Lowe, Martin, additional, Medina, Diego L., additional, Ballabio, Andrea, additional, and De Matteis, Maria Antonietta, additional

Published
2016
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47. The genetic basis of undiagnosed muscular dystrophies and myopathies

Author

Savarese, Marco, primary, Di Fruscio, Giuseppina, additional, Torella, Annalaura, additional, Fiorillo, Chiara, additional, Magri, Francesca, additional, Fanin, Marina, additional, Ruggiero, Lucia, additional, Ricci, Giulia, additional, Astrea, Guja, additional, Passamano, Luigia, additional, Ruggieri, Alessandra, additional, Ronchi, Dario, additional, Tasca, Giorgio, additional, D'Amico, Adele, additional, Janssens, Sandra, additional, Farina, Olimpia, additional, Mutarelli, Margherita, additional, Marwah, Veer Singh, additional, Garofalo, Arcomaria, additional, Giugliano, Teresa, additional, Sanpaolo, Simone, additional, Del Vecchio Blanco, Francesca, additional, Esposito, Gaia, additional, Piluso, Giulio, additional, D'Ambrosio, Paola, additional, Petillo, Roberta, additional, Musumeci, Olimpia, additional, Rodolico, Carmelo, additional, Messina, Sonia, additional, Evilä, Anni, additional, Hackman, Peter, additional, Filosto, Massimiliano, additional, Di Iorio, Giuseppe, additional, Siciliano, Gabriele, additional, Mora, Marina, additional, Maggi, Lorenzo, additional, Minetti, Carlo, additional, Sacconi, Sabrina, additional, Santoro, Lucio, additional, Claes, Kathleen, additional, Vercelli, Liliana, additional, Mongini, Tiziana, additional, Ricci, Enzo, additional, Gualandi, Francesca, additional, Tupler, Rossella, additional, De Bleecker, Jan, additional, Udd, Bjarne, additional, Toscano, Antonio, additional, Moggio, Maurizio, additional, Pegoraro, Elena, additional, Bertini, Enrico, additional, Mercuri, Eugenio, additional, Angelini, Corrado, additional, Santorelli, Filippo Maria, additional, Politano, Luisa, additional, Bruno, Claudio, additional, Comi, Giacomo Pietro, additional, and Nigro, Vincenzo, additional

Published
2016
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48. High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs

Author

Karali, Marianthi, primary, Persico, Maria, additional, Mutarelli, Margherita, additional, Carissimo, Annamaria, additional, Pizzo, Mariateresa, additional, Singh Marwah, Veer, additional, Ambrosio, Concetta, additional, Pinelli, Michele, additional, Carrella, Diego, additional, Ferrari, Stefano, additional, Ponzin, Diego, additional, Nigro, Vincenzo, additional, di Bernardo, Diego, additional, and Banfi, Sandro, additional

Published
2016
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49. Microdeletion of pseudogene chr14.232.a affects LRFN5expression in cells of a patient with autism spectrum disorder

Author

Cappuccio, Gerarda, Attanasio, Sergio, Alagia, Marianna, Mutarelli, Margherita, Borzone, Roberta, Karali, Marianthi, Genesio, Rita, Mormile, Angela, Nitsch, Lucio, Imperati, Floriana, Esposito, Annalisa, Banfi, Sandro, Giudice, Ennio, and Brunetti-Pierri, Nicola

Abstract

We identified a 14q21.2 microdeletion in a 16-year-old boy with autism spectrum disorder (ASD), IQ in the lower part of normal range but high-functioning memory skills. The deletion affects a gene desert, and the non-deleted gene closest to the microdeletion boundaries is LRFN5, which encodes a protein involved in synaptic plasticity and implicated in neuro-psychiatric disorders. LRFN5expression was significantly decreased in the proband’s skin fibroblasts. The deleted region includes the pseudogene chr14.232.a, which is transcribed into a long non-coding RNA (lncLRFN5-10), whose levels were also significantly reduced in the proband’s fibroblasts compared to controls. Transfection of the patient’s fibroblasts with a plasmid expressing chr14.232.a significantly increased LRFN5expression, while siRNA targeting chr14.232.a-derived lncLRFN5-10 reduced LRFN5levels. In summary, we report on an individual with ASD carrying a microdeletion encompassing the pseudogene chr14.232.a encoding for lncLRFN5-10, which was found to affect the expression levels of the nearby, non-deleted LRFN5. This case illustrates the potential role of long non-coding RNAs in regulating expression of neighbouring genes with a functional role in ASD pathogenesis.

Published
2019
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