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1. LINE-1 regulates cortical development by acting as long non-coding RNAs

Author

Damiano Mangoni, Alessandro Simi, Pierre Lau, Alexandros Armaos, Federico Ansaloni, Azzurra Codino, Devid Damiani, Lavinia Floreani, Valerio Di Carlo, Diego Vozzi, Francesca Persichetti, Claudio Santoro, Luca Pandolfini, Gian Gaetano Tartaglia, Remo Sanges, and Stefano Gustincich

Subjects
Science
Abstract

Abstract Long Interspersed Nuclear Elements-1s (L1s) are transposable elements that constitute most of the genome’s transcriptional output yet have still largely unknown functions. Here we show that L1s are required for proper mouse brain corticogenesis operating as regulatory long non-coding RNAs. They contribute to the regulation of the balance between neuronal progenitors and differentiation, the migration of post-mitotic neurons and the proportions of different cell types. In cortical cultured neurons, L1 RNAs are mainly associated to chromatin and interact with the Polycomb Repressive Complex 2 (PRC2) protein subunits enhancer of Zeste homolog 2 (Ezh2) and suppressor of zeste 12 (Suz12). L1 RNA silencing influences PRC2’s ability to bind a portion of its targets and the deposition of tri-methylated histone H3 (H3K27me3) marks. Our results position L1 RNAs as crucial signalling hubs for genome-wide chromatin remodelling, enabling the fine-tuning of gene expression during brain development and evolution.

Published
2023
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2. P756: IMPAIRED MITOCHONDRIAL FUNCTION AND MARROW FAILURE IN PATIENTS CARRYING A MUTATION ON SRSF4 GENE

Author

Maurizio Miano, Nadia Bertola, Alice Grossi, Gianluca Dell’orso, Stefano Regis, Francesca Fioredda, Michela Lupia, Marina Lanciotti, Elena Palmisani, Maria Carla Giarratana, Luca Arcuri, Fabio Corsolini, Marta Rusmini, Paolo Uva, Diego Vozzi, Isabella Ceccherini, Silvia Ravera, Enrico Cappelli, and Carlo Dufour

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Published
2023
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3. Impaired Mitochondrial Function and Marrow Failure in Patients Carrying a Variant of the SRSF4 Gene

Author

Maurizio Miano, Nadia Bertola, Alice Grossi, Gianluca Dell’Orso, Stefano Regis, Marta Rusmini, Paolo Uva, Diego Vozzi, Francesca Fioredda, Elena Palmisani, Michela Lupia, Marina Lanciotti, Federica Grilli, Fabio Corsolini, Luca Arcuri, Maria Carla Giarratana, Isabella Ceccherini, Carlo Dufour, Enrico Cappelli, and Silvia Ravera

Subjects
marrow failure, mitochondria, SRSF4, mTOR, CLUH, DRP1, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

Serine/arginine-rich splicing factors (SRSFs) are a family of proteins involved in RNA metabolism, including pre-mRNA constitutive and alternative splicing. The role of SRSF proteins in regulating mitochondrial activity has already been shown for SRSF6, but SRSF4 altered expression has never been reported as a cause of bone marrow failure. An 8-year-old patient admitted to the hematology unit because of leukopenia, lymphopenia, and neutropenia showed a missense variant of unknown significance of the SRSF4 gene (p.R235W) found via whole genome sequencing analysis and inherited from the mother who suffered from mild leuko-neutropenia. Both patients showed lower SRSF4 protein expression and altered mitochondrial function and energetic metabolism in primary lymphocytes and Epstein–Barr-virus (EBV)-immortalized lymphoblasts compared to healthy donor (HD) cells, which appeared associated with low mTOR phosphorylation and an imbalance in the proteins regulating mitochondrial biogenesis (i.e., CLUH) and dynamics (i.e., DRP1 and OPA1). Transfection with the wtSRSF4 gene restored mitochondrial function. In conclusion, this study shows that the described variant of the SRSF4 gene is pathogenetic and causes reduced SRSF4 protein expression, which leads to mitochondrial dysfunction. Since mitochondrial function is crucial for hematopoietic stem cell maintenance and some genetic bone marrow failure syndromes display mitochondrial defects, the SRSF4 mutation could have substantially contributed to the clinical phenotype of our patient.

Published
2024
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4. Case Report: Whole Exome Sequencing Revealed Disease-Causing Variants in Two Genes in a Patient With Autism Spectrum Disorder, Intellectual Disability, Hyperactivity, Sleep and Gastrointestinal Disturbances

Author

Maria Cerminara, Giovanni Spirito, Livia Pisciotta, Margherita Squillario, Martina Servetti, Maria Teresa Divizia, Margherita Lerone, Bianca Berloco, Silvia Boeri, Lino Nobili, Diego Vozzi, Remo Sanges, Stefano Gustincich, and Aldamaria Puliti

Subjects
autism spectrum disorder, attention deficit disorder and hyperactivity, whole exome sequencing, sleep disturbance, oligenic disease, ORVAL, Genetics, QH426-470
Abstract

Autism Spectrum Disorder (ASD) refers to a broad range of conditions characterized by difficulties in communication, social interaction and behavior, and may be accompanied by other medical or psychiatric conditions. Patients with ASD and comorbidities are often difficult to diagnose because of the tendency to consider the multiple symptoms as the presentation of a complicated syndromic form. This view influences variant filtering which might ignore causative variants for specific clinical features shown by the patient. Here we report on a male child diagnosed with ASD, showing cognitive and motor impairments, stereotypies, hyperactivity, sleep, and gastrointestinal disturbances. The analysis of whole exome sequencing (WES) data with bioinformatic tools for oligogenic diseases helped us to identify two major previously unreported pathogenetic variants: a maternally inherited missense variant (p.R4122H) in HUWE1, an ubiquitin protein ligase associated to X-linked intellectual disability and ASD; and a de novo stop variant (p.Q259X) in TPH2, encoding the tryptophan hydroxylase 2 enzyme involved in serotonin synthesis and associated with susceptibility to attention deficit-hyperactivity disorder (ADHD). TPH2, expressed in central and peripheral nervous tissues, modulates various physiological functions, including gut motility and sleep. To the best of our knowledge, this is the first case presenting with ASD, cognitive impairment, sleep, and gastrointestinal disturbances linked to both HUWE1 and TPH2 genes. Our findings could contribute to the existing knowledge on clinical and genetic diagnosis of patients with ASD presentation with comorbidities.

Published
2021
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5. Type I interferon-mediated autoinflammation due to DNase II deficiency

Author

Mathieu P. Rodero, Alessandra Tesser, Eva Bartok, Gillian I. Rice, Erika Della Mina, Marine Depp, Benoit Beitz, Vincent Bondet, Nicolas Cagnard, Darragh Duffy, Michael Dussiot, Marie-Louise Frémond, Marco Gattorno, Flavia Guillem, Naoki Kitabayashi, Fabrice Porcheray, Frederic Rieux-Laucat, Luis Seabra, Carolina Uggenti, Stefano Volpi, Leo A H. Zeef, Marie-Alexandra Alyanakian, Jacques Beltrand, Anna Monica Bianco, Nathalie Boddaert, Chantal Brouzes, Sophie Candon, Roberta Caorsi, Marina Charbit, Monique Fabre, Flavio Faletra, Muriel Girard, Annie Harroche, Evelyn Hartmann, Dominique Lasne, Annalisa Marcuzzi, Bénédicte Neven, Patrick Nitschke, Tiffany Pascreau, Serena Pastore, Capucine Picard, Paolo Picco, Elisa Piscianz, Michel Polak, Pierre Quartier, Marion Rabant, Gabriele Stocco, Andrea Taddio, Florence Uettwiller, Erica Valencic, Diego Vozzi, Gunther Hartmann, Winfried Barchet, Olivier Hermine, Brigitte Bader-Meunier, Alberto Tommasini, and Yanick J. Crow

Subjects
Science
Abstract

Nucleic acid sensing is important to ensure that an innate immune response is only mounted against microbial nucleic acid. Here, the authors identify loss-of-function mutations in the DNASE2 gene that cause type I interferon-mediated autoinflammation due to enhanced systemic interferon signaling.

Published
2017
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6. Proceedings of the 23rd Paediatric Rheumatology European Society Congress: part one

Author

F. De Benedetti, J. Anton, M. Gattorno, H. Lachmann, I. Kone-Paut, S. Ozen, J. Frenkel, A. Simon, A. Zeft, E. Ben-Chetrit, H. M. Hoffman, Y. Joubert, K. Lheritier, A. Speziale, J. Guido, Roberta Caorsi, Federica Penco, Alice Grossi, Antonella Insalaco, Maria Alessio, Giovanni Conti, Federico Marchetti, Alberto Tommasini, Silvana Martino, Romina Gallizzi, Annalisa Salis, Francesca Schena, Francesco Caroli, Alberto Martini, Gianluca Damonte, Isabella Ceccherini, Marco Gattorno, Marie-Louise Frémond, Carolina Uggenti, Lien Van Eyck, Isabelle Melki, Darragh Duffy, Vincent Bondet, Yoann Rose, Bénédicte Neven, Yanick Crow, Mathieu P. Rodero, Yvonne Kusche, Johannes Roth, Katarzyna Barczyk-Kahlert, Giovanna Ferrara, Annalisa Chiocchetti, Silvio Polizzi, Josef Vuch, Diego Vozzi, Anna Mondino, Erica Valencic, Serena Pastore, Andrea Taddio, Flavio Faletra, Umberto Dianzani, Ugo Ramenghi, Qing Zhou, Xiaomin Yu, Erkan Demirkaya, Natalie Deuitch, Deborah Stone, Wanxia Tsai, Amanda Ombrello, Tina Romeo, Elaine F. Remmers, JaeJin Chae, Massimo Gadina, Steven Welch, Seza Ozen, Rezan Topaloglu, Mario Abinun, Daniel L. Kastner, Ivona Aksentijevich, Donatella Vairo, Rosalba Monica Ferraro, Giulia Zani, Jessica Galli, Micaela De Simone, Marco Cattalini, Elisa Fazzi, Silvia Giliani, Ebun Omoyinmi, Ariane Standing, Dorota Rowczenio, Annette Keylock, Sonia Melo Gomes, Fiona Price-Kuehne, Sira Nanthapisal, Claire Murphy, Thomas Cullup, Lucy Jenkins, Kimberly Gilmour, Despina Eleftheriou, Helen Lachmann, Philip Hawkins, Nigel Klein, Paul Brogan, Anita Dhanrajani, Mercedes Chan, Stephanie Pau, Janet Ellsworth, Jaime Guzman, Florence A. Aeschlimann, Marinka Twilt, Simon W. Eng, Shehla Sheikh, Ronald M. Laxer, Diane Hebert, Damien Noone, Christian Pagnoux, Susanne M. Benseler, Rae S. Yeung, Christoph Kessel, Katrin Lippitz, Toni Weinhage, Claas Hinze, Helmut Wittkowski, Dirk Holzinger, Niklas Grün, Dirk Föll, Pieter Van Dijkhuizen, Federica Del Chierico, Clara Malattia, Alessandra Russo, Denise Pires Marafon, Nienke M. ter Haar, Silvia Magni-Manzoni, Sebastiaan J. Vastert, Bruno Dallapiccola, Berent Prakken, Fabrizio De Benedetti, Lorenza Putignani, Berna Eren Fidanci, Kenan Barut, Serap Arıcı, Dogan Simsek, Mustafa Cakan, Ezgi D. Batu, Sezgin Şahin, Ayşenur Kısaarslan, Ebru Yilmaz, Özge Basaran, Ferhat Demir, Kubra Ozturk, Zübeyde Gunduz, Betül Sozeri, Balahan Makay, Nuray Ayaz, Onder Yavascan, Ozlem Aydog, Yelda Bilginer, Zelal Ekinci, Dilek Yıldız, Faysal Gök, Muferret Erguven, Erbil Unsal, Ozgur Kasapcopur, For the FMF Arthritis Vasculitis and Orphan Disease Research in Paediatric Rheumatology (FAVOR), Hafize E. Sönmez, Betül Sözeri, Yonatan Butbul, Seza Özen, Claudia Bracaglia, Giusi Prencipe, Manuela Pardeo, Geneviève Lapeyre, Emiliano Marasco, Walter Ferlin, Robert Nelson, Cristina de Min, N. Ruperto, H. I. Brunner, P. Quartier, T. Constantin, E. Alexeeva, K. Marzan, N. Wulffraat, R. Schneider, S. Padeh, V. Chasnyk, C. Wouters, J. B. Kuemmerle-Deschner, T. Kallinich, B. Lauwerys, E. Haddad, E. Nasonov, M. Trachana, O. Vougiouka, K. Leon, E. Vritzali, A. Martini, D. Lovell, PRINTO/PRCSG, Stefano Volpi, Claudia Pastorino, Francesca Kalli, Alessia Omenetti, Sabrina Chiesa, Arinna Bertoni, Paolo Picco, Gilberto Filaci, Elisabetta Traggiai, Marie-Louise Fremond, Naoki Kitabayashi, Olivero Sacco, Isabelle Meyts, Marie-Anne Morren, Carine Wouters, Eric Legius, Isabelle Callebaut, Christine Bodemer, Frederic Rieux-Laucat, Mathieu Rodero, Nadia Jeremiah, Alexandre Belot, Eric Jeziorski, Didier Bessis, Guilhem Cros, Gillian I. Rice, Bruno Charbit, Anne Hulin, Nihel Khoudour, Consuelo Modesto Caballero, Monique Fabre, Laureline Berteloot, Muriel Le Bourgeois, Philippe Reix, Thierry Walzer, Despina Moshous, Stéphane Blanche, Alain Fischer, Brigitte Bader-Meunier, Frédéric Rieux-Laucat, K. Annink, N. ter Haar, S. Al-Mayouf, G. Amaryan, K. Barron, S. Benseler, P. Brogan, L. Cantarini, M. Cattalini, A. Cochino, F. Dedeoglu, A. De Jesus, O. Dellacasa, E. Demirkaya, P. Dolezalova, K. Durrant, G. Fabio, R. Gallizzi, R. Goldbach-Mansky, E. Hachulla, V. Hentgen, T. Herlin, M. Hofer, H. Hoffman, A. Insalaco, A. Jansson, I. Koné-Paut, A. Kozlova, J. Kuemmerle-Deschner, R. Laxer, S. Nielsen, I. Nikishina, A. Ombrello, E. Papadopoulou-Alataki, A. Ravelli, D. Rigante, R. Russo, Y. Uziel, Nienke ter Haar, Jerold Jeyaratnam, Anna Simon, Matteo Doglio, Jordi Anton, Consuelo Modesto, Pierre Quartier, Esther Hoppenreijs, Luca Cantarini, Loredana Lepore, Inmaculada Calvo Penades, Christina Boros, Rita Consolini, Donato Rigante, Ricardo Russo, Jana Pachlopnik Schmid, Thirusha Lane, Nicolino Ruperto, Joost Frenkel, Chiara Passarelli, Elisa Pisaneschi, Virginia Messia, Antonio Novelli, Fabrizio Debenedetti, P. A. Brogan, X. Wei, Martina Finetti, Francesca Orlando, Elisabetta Cortis, Angela Miniaci, Nicola Ruperto, Charlotte Eijkelboom, Pavla Dolezalova, Isabelle Koné-Paut, Marija Jelusic-Drazic, Liliana Bezrodnik, Mari Carmen Pinedo, Valda Stanevicha, Marielle van Gijn, Silvia Federici, Hermann Girschick, Gerd Ganser, Susan Nielsen, Troels Herlin, Sulaiman Mohammed Al-Mayouf, Michael Hofer, Jasmin Kuemmerle-Deschner, Susanne Schalm, Annette Jansson, on behalf of PRINTO and Eurofever registry, Marta Marchi, Chiara Marini, Angelo Ravelli, Alberto Garaventa, Sonia Carta, Enrica Balza, Patrizia Castellani, Caterina Pellecchia, Silvia Borghini, Maria Libera Trotta, Anna Rubartelli, Andrew Henrey, Thomas Loughin, Roberta Berard, Natalie Shiff, Roman Jurencak, Susanne Benseler, Lori Tucker, on behalf of ReACCh-Out Investigators, Charalampia Papadopoulou, Ying Hong, Petra Krol, Yiannis Ioannou, Clarissa Pilkington, Hema Chaplin, Stephania Simou, Marietta Charakida, Lucy Wedderburn, Lynn R. Spiegel, Sara Ahola Kohut, Jennifer Stinson, Paula Forgeron, Miriam Kaufman, Nadia Luca, Khush Amaria, Mary Bell, J Swart, F. Boris, E. Castagnola, A. Groll, G. Giancane, G. Horneff, H. I. Huppertz, T. Wolfs, E. Alekseeva, V. Panaviene, F. Uettwiller, V. Stanevicha, L. M. Ailioaie, E. Tsitami, S. Kamphuis, G. Susic, F. Sztajnbok, B. Flato, A. Pistorio, Stephanie J. W. Shoop, Suzanne M. M. Verstappen, Janet E. McDonagh, Wendy Thomson, Kimme L. Hyrich, CAPS, Maarit Tarkiainen, Pirjo Tynjala, Pekka Lahdenne, Janne Martikainen, Acute-JIA Study Group, Meredyth Wilkinson, Christopher Piper, Georg Otto, Claire T. Deakin, Stefanie Dowle, Stefania Simou, Daniel Kelberman, Claudia Mauri, Elizabeth Jury, David Isenberg, Lucy R. Wedderburn, Kiran Nistala, I. Foeldvari, D. J. Lovell, G. Simonini, M. Bereswill, J. Kalabic, Kiem Oen, Brian M. Feldman, Brenden Dufault, Jennifer Lee, Karen Watanabe Duffy, Ciaran Duffy, ReACCh-Out Investigators, N. Tzaribachev, G. Vega-Cornejo, I. Louw, A. Berman, I. Calvo, R. Cuttica, F. Avila-Zapata, R. Cimaz, E. Solau-Gervais, R. Joos, G. Espada, X. Li, M. Nys, R. Wong, S. Banerjee, For Pediatric Rheumatology International Trials Organization (PRINTO)/Pediatric Rheumatology Collaborative Study Group (PRCSG), Rebecca Nicolai, Margherita Verardo, Adele D’Amico, Luisa Bracci-Laudiero, Gian Marco Moneta, Gillian Rice, Anne-Laure Mathieu, Sulliman O. Omarjee, Tracy A. Briggs, James O’Sullivan, Simon Williams, Rolando Cimaz, Eve Smith, Michael W. Beresford, Yanick J. Crow, GENIAL Investigators, UK JSLE Study Group, Madeleine Rooney, Nick Bishop, joyce davidson, Clarissa pilkington, Michael Beresford, Jacqui Clinch, Rangaraj Satyapal, Helen Foster, Janet Gardner Medwin, Janet McDonagh, Sue Wyatt, On Behalf of the British Society for Paediatric and Adolescent Rheumatology, Valentina Litta Modignani, Francesco Baldo, Stefano Lanni, Alessandro Consolaro, Giovanni Filocamo, Helen J. Lachmann, on behalf of Eurofever Registry, Gianmarco Moneta, Camilla Celani, Bilade Cherqaoui, Linda Rossi-Semerano, Perrine Dusser, Véronique Hentgen, Claire Grimwood, Linda Rossi, Isabelle Kone Paut, Veronique Hentgen, Denise Lasigliè, Denise Ferrera, Giulia Amico, Marco Di Duca, Laura Obici, Roberto Ravazzolo, Ryuta Nishikomori, Juan Arostegui, Andrea Petretto, Chiara Lavarello, Elvira Inglese, Federica Vanoni, Michaël Hofer, on behalf of EUROFEVER PROJECT, P. N. Hawkins, T. van der Poll, U. A. Walker, H. H. Tilson, Pascal N. Tyrrell, Raphaela Goldbach-Mansky, Norbert Blank, Hal M. Hoffman, Elisabeth Weissbarth-Riedel, Boris Huegle, Tilmann Kallinich, Ahmet Gul, Marlen Oswald, Fatma Dedeoglu, Aki Hanaya, Takako Miyamae, Manabu Kawamoto, Yumi Tani, Takuma Hara, Yasushi Kawaguchi, Satoru Nagata, Hisashi Yamanaka, Almira Ćosićkić, Fahrija Skokić, Belkisa Čolić, Sanimir Suljendić, Anna Kozlova, Irina Mersiyanova, Mariya Panina, Lily Hachtryan, Vasiliy Burlakov, Elena Raikina, Alexey Maschan, Anna Shcherbina, Banu Acar, Meryem Albayrak, Betul Sozeri, Sezgin Sahin, Amra Adrovic, Nese Inan, Serhan Sevgi, Caroline M. Andreasen, Anne Grethe Jurik, Mia B. Glerup, Christian Høst, Birgitte T. Mahler, Ellen-Margrethe Hauge, Cecilia Lazea, Laura Damian, Calin Lazar, Rodica Manasia, Chloe M. Stephenson, Vimal Prajapati, Paivi M. Miettunen, Dilek Yılmaz, Yavuz Tokgöz, Yasin Bulut, Harun Çakmak, Ferah Sönmez, Elif Comak, Gülşah Kaya Aksoy, Mustafa Koyun, Sema Akman, Yunus Arıkan, Ender Terzioğlu, Osman Nidai Özdeş, İbrahim Keser, Hüseyin Koçak, Ayşen Bingöl, Aygen Yılmaz, Reha Artan, X. Xu, Fatemeh F. Mehregan, Vahid Ziaee, Mohammad H. Moradinejad, Francesco La Torre, Clotilde Alizzi, Pio D’Adamo, G. Junge, J. Gregson, Hasmik Sargsyan, Hulya Zengin, Berna E. Fidanci, Cagla Kaymakamgil, Dilek Konukbay, Dilek Yildiz, Faysal Gok, Iris Stoler, Judith Freytag, Banu Orak, Christine Seib, Lars Esmann, Eva Seipelt, Faekah Gohar, Dirk Foell, Ismail Dursun, Sebahat Tulpar, Sibel Yel, Demet Kartal, Murat Borlu, Funda Bastug, Hakan Poyrazoglu, Zubeyde Gunduz, Kader Kose, Mehmet E. Yuksel, Abdullah Calıskan, Ahmet B. Cekgeloglu, Ruhan Dusunsel, Katerina Bouchalova, Jana Franova, Marcel Schuller, Marie Macku, Katerina Theodoropoulou, Raffaella Carlomagno, Annette von Scheven-Gête, Claudia Poloni, Laura O. Damian, Dan Cosma, Amanda Radulescu, Dan Vasilescu, Liliana Rogojan, Simona Rednic, Mihaela Lupse, Lien De Somer, Pierre Moens, Rocio Galindo Zavala, Laura Martín Pedraz, Esmeralda Núñez Cuadros, Gisela Díaz-Cordovés Rego, Antonio L. Urda Cardona, Ilaria Dal Forno, Sara Pieropan, Ombretta Viapiana, Davide Gatti, Gloria Dallagiacoma, Paola Caramaschi, Domenico Biasi, Daniel Windschall, Ralf Trauzeddel, Hartwig Lehmann, Rainer Berendes, Maria Haller, Manuela Krumrey-Langkammerer, Antje Nimtz-Talaska, Philipp Schoof, Ralf Felix Trauzeddel, Christine Nirschl, Estefania Quesada-Masachs, Carla Aguilar Blancafort, Sara Marsal Barril, Francisca Aguiar, Rita Fonseca, Duarte Alves, Ana Vieira, Alberto Vieira, Jorge A. Dias, Iva Brito, Gordana Susic, Vera Milic, Goran Radunovic, Ivan Boricic, Pauline Marteau, Catherine Adamsbaum, Michel De Bandt, Irène Lemelle, Chantal Deslandre, Tu Anh Tran, Anne Lohse, Elisabeth Solau-Gervais, Pascal Pillet, Julien Wipff, Cécile Gaujoux-Viala, Sylvain Breton, Valérie Devauchelle-Pensec, Sandra Gran, Olesja Fehler, Stefanie Zenker, Michael Schäfers, Thomas Vogl, Severine Guillaume Czitrom, EH Pieter Van Dijkhuizen, Silvia Magni Manzoni, Francesca Magnaguagno, Laura Tanturri de Horatio, Nienke M. Ter Haar, Annemieke S. Littooij, Vitor A. Teixeira, Raquel Campanilho-Marques, Ana F. Mourão, Filipa O. Ramos, Manuela Costa, Wafa A. Madan, Orla G. Killeen, Adriana Rodriguez Vidal, Diana Sueiro Delgado, Maria Isabel Gonzalez Fernandez, Berta Lopez Montesinos, Aleksey Kozhevnikov, Nina Pozdeeva, Mikhail Konev, Evgeniy Melchenko, Vladimir Kenis, Gennadiy Novik, Aysenur Pac Kısaarslan, Butsabong Lerkvaleekul, Suphaneewan Jaovisidha, Witaya Sungkarat, Niyata Chitrapazt, Praman Fuangfa, Thumanoon Ruangchaijatuporn, Soamarat Vilaiyuk, Dan Ø. Pradsgaard, Arne Hørlyck, Anne H. Spannow, Carsten W. Heuck, Talia Diaz, Fernando Garcia, Lorenia De La Cruz, Nadina Rubio, Joanna Świdrowska-Jaros, Elzbieta Smolewska, Mirta Lamot, Lovro Lamot, Mandica Vidovic, Edi Paleka Bosak, Ivana Rados, Miroslav Harjacek, Nikolay Tzaribachev, Polymnia Louka, Romiesa Hagoug, Chiara Trentin, Olga Kubassova, Mark Hinton, Mikael Boesen, Olena A. Oshlianska, Illya A. Chaikovsky, G. Mjasnikov, A. Kazmirchyk, Umberto Garagiola, Irene Borzani, Paolo Cressoni, Fabrizia Corona, Eszter Dzsida, Giampietro Farronato, Antonella Petaccia, Alenka Gagro, Agneza Marija Pasini, Goran Roic, Ozren Vrdoljak, Lucija Lujic, Matija Zutelija-Fattorini, Monika M. Esser, Deepthi R. Abraham, Craig Kinnear, Glenda Durrheim, Mike Urban, Eileen Hoal, Victoria B. Nikolayenko, Kubilay Şahin, Yasar Karaaslan, Adele Civino, Giovanni Alighieri, Sergio Davì, Roberto Rondelli, Andrea Magnolato, Francesca Ricci, Alma Olivieri, Valeria Gerloni, Bianca Lattanzi, Francesca Soscia, Alessandro De Fanti, Stefania Citiso, Lorenzo Quartulli, Maria Cristina Maggio, Manuela Marsili, Maria Antonietta Pelagatti, Valentino Conter, Franca Fagioli, Andrea Pession, Marco Garrone, Mariangela Rinaldi, Jaime De Inocencio, Stella Garay, Daniel J. Lovell, Berit Flato, EPOCA Study Group, Angela Aquilani, Simona Cascioli, Ivan Caiello, Denise Pires-Marafón, Rita Carsetti, Emily Robinson, Salvatore Albani, Wilco de Jager, Sytze de Roock, Trang Duong, Justine Ellis, Kimme Hyrich, Laetitia Jervis, Daniel Lovell, Lucy Marshall, Elizabeth D. Mellins, Kirsten Minden, Jane Munro, Peter A. Nigrovic, Jason Palman, Sunil Sampath, Laura E. Schanberg, Susan D. Thompson, Richard Vesely, Chris Wallace, Chris Williams, Qiong Wu, Nico Wulffraat, Rae S. M. Yeung, M. B. Seyger, D. Arikan, J. K. Anderson, A. Lazar, D. A. Williams, C. Wang, R. Tarzynski-Potempa, J. S. Hymans, Gabriele Simonini, Erika Scoccimarro, Irene Pontikaki, Teresa Giani, Alessandro Ventura, Pier Luigi Meroni, Gaetana Minnone, Marzia Soligo, Luigi Manni, Luisa Bracci Laudiero, Noortje Groot, I. Grein, N. M. Wulffraat, R. Schepp, G. Berbers, C. C. Barbosa Sandoval de Souza, V. Paes Leme Ferriani, G. Pileggi, S. de Roock, Ingrid H. R. Grein, Silvia Scala, Elisa Patrone, Casper Schoemaker, on behalf of Dutch JIA patient organization, Wendy Costello, on behalf of ENCA, Suzanne Parsons, Jean-David Cohen, Damien Bentayou, Marc-Antoine Bernard Brunel, Sonia Trope, Jens Klotsche, Miriam Listing, Martina Niewerth, Gerd Horneff, Angelika Thon, Hans-Iko Huppertz, Kirsten Mönkemöller, Ivan Foeldvari, ICON study group, Achille Marino, Stefano Stagi, Niccolò Carli, Federico Bertini, Adriana S. Díaz-Maldonado, Sally Pino, Pilar Guarnizo, Alfonso Ragnar Torres-Jimenez, Berenice Sanchez-Jara, Eunice Solis-Vallejo, Adriana Ivonne Cespedes-Cruz, Maritza Zeferino-Cruz, Julia Veronica Ramirez-Miramontes, Ankur Kumar, Anju Gupta, Deepti Suri, Amit Rawat, Nandita Kakkar, Surjit Singh, Özge A. Gücenmez, Erbil Ünsal, Bo Magnusson, Karina Mördrup, Anna Vermé, Christina Peterson, Board of the Swedish Pediatric Rheumatology Registry, Caroline Freychet, Jean Louis Stephan, Cathryn E. Harkness, Leanne Foster, Emma Henry, Pauline Taggart, Coskun F. Ozkececi, Esra Kurt, Gokalp Basbozkurt, Daiva Gorczyca, Jacek Postępski, Aleksandra Czajkowska, Bogumiła Szponar, Mariola Paściak, Anna Gruenpeter, Iwona Lachór-Motyka, Daria Augustyniak, Edyta Olesińska, Emediong S. Asuka, Tatyana Golovko, Samuel U. Aliejim, Emilio Inarejos Clemente, Estibaliz Iglesias Jimenez, Joan Calzada Hernandez, Sergi Borlan Fernandez, Clara Gimenez Roca, David Moreno Romo, Natalia Rodriguez Nieva, Juan Manuel Mosquera Angarita, Jordi Anton Lopez, Esmeralda Nuñez-Cuadros, Gisela Diaz-Cordovés, Rocío Galindo-Zavala, Antonio Urda-Cardona, Antonio Fernández-Nebro, Daniel Álvarez de la Sierra, Marina Garcia Prat, Mónica Martínez Gallo, Ricardo Pujol Borrell, Ana M. Marín Sánchez, Etienne Merlin, Sylvie Fraitag, Jean-Louis Stephan, Federico Annoni, Giancarla Di Landro, Sofia Torreggiani, Marta Torcoletti, Georgina Tiller, Jo Buckle, Angela Cox, Peter Gowdie, Roger C. Allen, Jonathan D. Akikusa, Hayde G. Hernández-Huirache, Edel R. Rodea-Montero, William Fahy, Christelle Sordet, Karin B. Berggren, Johanna T. Kembe, Joyce Bos, Wineke Armbrust, Marco van Brussel, Jeanette Cappon, Pieter Dijkstra, Jan Geertzen, Elizabeth Legger, Marion van Rossum, Pieter Sauer, Otto Lelieveld, Levent Buluc, Gur Akansel, Bahar Muezzinoglu, Ljubov Rychkova, Tatyana Knyazeva, Anna Pogodina, Tatyana Belova, Tamara Mandzyak, Ekaterina Kulesh, Alessandro Cafarotti, Cosimo Giannini, Roberta Salvatore, Giuseppe Lapergola, Caterina Di Battista, Maria Loredana Marcovecchio, Raffaella Basilico, Piernicola Pelliccia, Francesco Chiarelli, Luciana Breda, Beverley Almeida, Sarah Tansley, Harsha Gunawardena, Neil McHugh, Juvenile Dermatomyositis Research Group (JDRG), Jessie Aouizerate, Marie De Antonio, Christine Barnerias, Guillaume Bassez, Isabelle Desguerre, Romain Gherardi, Jean-Luc Charuel, François-Jérôme Authier, Cyril Gitiaux, C. H. Spencer, Rabheh Abdul Aziz, Chack-Yung Yu, Brent Adler, Sharon Bout-Tabaku, Katherine Lintner, Melissa Moore-Clingenpeel, Liza McCann, Nicola Ambrose, Mario Cortina-Borja, Juvenile Dermatomyositis Cohort and Biomarker Study (JCDBS), Prasad T. Oommen, Fabian Speth, Johannes-Peter Haas, Working Group “Juvenile Dermatomyositis” of the German Society for Paediatric and Adolescent Rheumatology (GKJR), Claudio Lavarello, Gabriella Giancane, Angela Pistorio, Lisa Rider, Rohit Aggarwal, Sheila K. Oliveira, Ruben Cuttica, Michel Fischbach, Gary Sterba, Karine Brochard, Frank Dressler, Patrizia Barone, Ruben Burgos-Vargas, Elizabeth Candell Chalom, Marine Desjonqueres, Graciela Espada, Anders Fasth, Stella Maris Garay, Rose-Marie Herbigneaux, Claire Hoyoux, Chantal Job Deslandre, Frederick W. Miller, Jiri Vencovsky, Erdal Sag, Gulsev Kale, Haluk Topaloglu, Beril Talim, Francesco Zulian, Tadej Avcin, Roberto Marini, Anne Pagnier, Michel Rodiere, Christine Soler, Rebecca Ten Cate, Yosef Uziel, Jelena Vojinovic, Ana V. Villarreal, Nydia Acevedo, Yuridiana Ramirez, Enrique Faugier, Rocio Maldonado, Bita Arabshahi, John H. Lee, Ian Leibowitz, Lawrence O. Okong’o, Jo Wilmshurst, Monika Esser, Christiaan Scott, Ezgi Deniz Batu, Nagehan Emiroglu, Hafize Emine Sonmez, Gokcen Dilsa Tugcu, Zehra Serap Arici, Ebru Yalcin, Deniz Dogru, Ugur Ozcelik, Mithat Haliloglu, Nural Kiper, Masato Yashiro, Mutsuko Yamada, Toshihiko Yabuuchi, Tomonobu Kikkawa, Nobuyuki Nosaka, Yosuke Fujii, Yukie Saito, Hirokazu Tsukahara, Sulaiman M. Al-Mayouf, Nora AlMutiari, Mohammed Muzaffer, Rawiah shehata, Adel Al-Wahadneh, Reem Abdwani, Safia Al-Abrawi, Mohammed Abu-shukair, Zeyad El-Habahbeh, Abdullah Alsonbul, Aleksandra Szabat, Monika Chęć, Violetta Opoka-Winiarska, Biman Saikia, Ranjana W. Minz, Christine Arango, Clara Malagon, Maria D. P. Gomez, Angela C. Mosquera, Ricardo Yepez, Tatiana Gonzalez, Camilo Vargas, GRIP study group, Marta Balzarin, Biagio Castaldi, Elena Reffo, Francesca Sperotto, Giorgia Martini, Alessandra Meneghel, Ornella Milanesi, Ozgur Kasapçopur, Maria Teresa Terreri, Ekaterina Alexeeva, Maria Katsicas, Mikhail Kostik, Thomas Lehman, W.-Alberto Sifuentes-Giraldo, Vanessa Smith, Flavio Sztajnbok, Tadey Avcin, Maria Jose Santos, Dana Nemcova, Cristina Battagliotti, Liora Harel, Mahesh Janarthanan, Kathryn Torok, Nicola Helmus, Eileen Baildem, Michael Blakley, Kim Fligelstone, Antonia Kienast, Clare Pain, Amanda Saracino, Gabriele Simoni, Lisa Weibel, Maria K. Osminina, Nathalia A. Geppe, Olga V. Niconorova, Olesya V. Karashtina, Oksana V. Abbyasova, Olga V. Shpitonkova, Sinem Durmus, Hafize Uzun, Angela Mauro, Eleonora Fanti, Fabio Voller, Franca Rusconi, Fernando Garcia-Rodriguez, Ana V. Villarreal-Treviño, Angel J. Flores-Pineda, Paola B. Lara-Herrea, Diego R. Salinas-Encinas, Talia Diaz-Prieto, Maria R. Maldonado-Velazquez, Sarbelio Moreno-Espinosa, Enrique Faugier-Fuentes, Mirella Crapanzano, Ilaria Parissenti, Man S. Parihar, Pandiarajan Vignesh, ManojKumar Rohit, Kavitha Gopalan, Savita V. Attri, Alan Salama, David Jayne, Mark Little, Yulia Kostina, Galina Lyskina, Olga Shpitonkova, Alena Torbyak, Olga Shirinsky, Maria Francesca Gicchino, Maria Cristina Smaldone, Mario Diplomatico, Alma Nunzia Olivieri, C H. Spencer, Richard McClead, Hiren Patel, Chung-Yung Yu, Dita Cebecauerová, Tomáš Dallos, Edita Kabíčková, Martin Kynčl, Daniela Chroustová, Jozef Hoza, Dana Němcová, Vladimír Tesař, Pavla Doležalová, Tuncay Hazirolan, Fatih Ozaltin, Fabiola Almeida, Isabela H. Faria de Paula, Maíra M. Sampaio, Fernando N. Arita, Andressa G. Alves, Maria Carolina Santos, Eunice M. Okuda, Silvana B. Sacchetti, Fernanda Falcini, Marini Francesca, Gemma Lepri, Marco Matucci-Cerinic, Maria Luisa Brandi, Hakan Kisaoglu, Sema Misir, Selim Demir, Yuksel Aliyazicioglu, Mukaddes Kalyoncu, Carlos Eduardo Ramalho, Fabiola D. Almeida, Joan Calzada-Hernández, Rosa Bou, Estíbaliz Iglesias, Judith Sánchez-Manubens, Fredy Hermógenes Prada Martínez, Clara Giménez Roca, Sergi Borlan Fernández, Marek Bohm, Kamran Mahmood, Valentina Leone, Mark Wood, Ken-Ichi Yamaguchi, Satoshi Fujikawa, Working Group of Behçet’s Disease, Pediatric Rheumatology Association of Japan (PRAJ), Kyu Yeun Kim, Do Young Kim, Dong Soo Kim, Maka Ioseliani, Ivane Chkhaidze, Maia Lekishvili, Nana Tskhakaia, Shorena Tvalabeishvili, Aleksandre Kajrishvili, Maiko Takakura, Masaki Shimizu, Natsumi Inoue, Mao Mizuta, Akihiro Yachie, Giovanni Corsello, Maryam Piram, Carla Maldini, Sandra Biscardi, Nathalie Desuremain, Catherine Orzechowski, Emilie Georget, Delphine Regnard, Isabelle Kone-Paut, Alfred Mahr, Mihaela Sparchez, Zeno Sparchez, Nydia Acevedo Silva, Ana V. Villarreal Treviño, Yuridiana Ramirez Loyola, Talia Diaz Prieto, Enrique Faugier Fuentes, Maria D. R. Maldonado Velazquez, Pilar Perez, Sagar Bhattad, Ranjana Minz, Jitendra Shandilya, Pediatric Allergy and Immunology Unit, PGIMER, Chandigarh, Ana Villarreal, Yuridiana Ramírez, Zeynep Birsin Özçakar, Suat Fitoz, Fatos Yalcinkaya, Annacarin Horne, Francesca Minoia, Francesca Bovis, Sergio Davi, Priyankar Pal, Kimo Stein, Sandra Enciso, Michael Jeng, Despoina Maritsi, Randy C. Cron, Anne Thorwarth, Sae Lim von Stuckrad, Angela Rösen-Wolff, Hella Luksch, Patrick Hundsdoerfer, Peter Krawitz, Nuray Aktay Ayaz, Doğan Simsek, Şebnem Sara Kılıc, Emine Sonmez, Aysenur Pac Kisaarslan, Ozge Altug Gucenmez, Z. Serap Arıcı, Fatih Kelesoglu, Zelal Ekinci Ekinci, Maria Miranda-Garcia, Carolin Pretzer, Michael Frosch, F. Gohar, Angela McArdle, Niamh Callan, Belinda Hernandez, Miha Lavric, Oliver FitzGerald, Stephen R. Pennington, Joachim Peitz, Joern Kekow, Ariane Klein, Anna C. Schulz, Frank Weller-Heinemann, Anton Hospach, J-Peter Haas, BIKER collaborative group, Karen Put, Jessica Vandenhaute, Anneleen Avau, Annemarie van Nieuwenhuijze, Ellen Brisse, Tim Dierckx, Omer Rutgeerts, Josselyn E. Garcia-Perez, Jaan Toelen, Mark Waer, Georges Leclercq, An Goris, Johan Van Weyenbergh, Adrian Liston, Patrick Matthys, Carine H. Wouters, Yasuo Nakagishi, Michael J. Ombrello, Victoria Arthur, Anne Hinks, Patricia Woo, International Childhood Arthritis Genetics (INCHARGE) Consortium, Barbara Stanimirovic, Biljana Djurdjevic-Banjac, Olivera Ljuboja, Boris Hugle, MArgarita Onoufriou, Olga Vougiouka, Kenza Bouayed, Sanae El Hani, Imane Hafid, Nabiha Mikou, Nunu Shelia, Mari Laan, Jaanika Ilisson, and Chris Pruunsild

Subjects
Pediatrics, RJ1-570, Diseases of the musculoskeletal system, RC925-935
Published
2017
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7. Linkage study and exome sequencing identify a BDP1 mutation associated with hereditary hearing loss.

Author

Giorgia Girotto, Khalid Abdulhadi, Annalisa Buniello, Diego Vozzi, Danilo Licastro, Angela d'Eustacchio, Dragana Vuckovic, Moza Khalifa Alkowari, Karen P Steel, Ramin Badii, and Paolo Gasparini

Subjects
Medicine, Science
Abstract

Nonsyndromic Hereditary Hearing Loss is a common disorder accounting for at least 60% of prelingual deafness. GJB2 gene mutations, GJB6 deletion, and the A1555G mitochondrial mutation play a major role worldwide in causing deafness, but there is a high degree of genetic heterogeneity and many genes involved in deafness have not yet been identified. Therefore, there remains a need to search for new causative mutations. In this study, a combined strategy using both linkage analysis and sequencing identified a new mutation causing hearing loss. Linkage analysis identified a region of 40 Mb on chromosome 5q13 (LOD score 3.8) for which exome sequencing data revealed a mutation (c.7873 T>G leading to p.*2625Gluext*11) in the BDP1 gene (B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB) in patients from a consanguineous Qatari family of second degree, showing bilateral, post-lingual, sensorineural moderate to severe hearing impairment. The mutation disrupts the termination codon of the transcript resulting in an elongation of 11 residues of the BDP1 protein. This elongation does not contain any known motif and is not conserved across species. Immunohistochemistry studies carried out in the mouse inner ear showed Bdp1 expression within the endothelial cells in the stria vascularis, as well as in mesenchyme-derived cells surrounding the cochlear duct. The identification of the BDP1 mutation increases our knowledge of the molecular bases of Nonsyndromic Hereditary Hearing Loss and provides new opportunities for the diagnosis and treatment of this disease in the Qatari population.

Published
2013
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8. Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures.

Author

Danilo Licastro, Margherita Mutarelli, Ivana Peluso, Kornelia Neveling, Nienke Wieskamp, Rossella Rispoli, Diego Vozzi, Emmanouil Athanasakis, Angela D'Eustacchio, Mariateresa Pizzo, Francesca D'Amico, Carmela Ziviello, Francesca Simonelli, Antonella Fabretto, Hans Scheffer, Paolo Gasparini, Sandro Banfi, and Vincenzo Nigro

Subjects
Medicine, Science
Abstract

Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS) technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25×, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified.

Published
2012
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9. Somatic Double Inactivation of NF1 Associated with NF1-Related Pectus Excavatum Deformity

Author

Cristina Chelleri, Marcello Scala, Patrizia De Marco, Vittorio Guerriero, Marzia Ognibene, Francesca Madia, Sara Guerrisi, Marco Di Duca, Michele Torre, Serena Tamburro, Paolo Scudieri, Gianluca Piccolo, Girolamo Mattioli, Francesca Buffelli, Paolo Uva, Diego Vozzi, Ezio Fulcheri, Pasquale Striano, Maria Cristina Diana, and Federico Zara

Subjects
Article Subject, Genetics, Genetics (clinical)
Abstract

Neurofibromatosis type 1 (NF1) is a neurocutaneous genetic disorder with a broad spectrum of associated signs and symptoms, including skeletal anomalies. The association of NF1 with anterior chest wall deformities has been recently reported, especially the pectus excavatum (PE). Over the years, several authors have suggested loss of heterozygosity (LOH) as the possible pathogenic mechanism underlying the development of the typical NF1 skeletal features. Here, we report a NF1 patient with severe chest deformity and harboring the germline heterozygous pathogenic NF1 variant NM_001042492.3: c.4271delC p.(Ala1424Glufs ∗ 4). Through next-generation sequencing (NGS), we investigated the affected cartilage from the PE deformity and identified the additional frameshift variant NM_001042492.3: c.2953delC p.(Gln985Lysfs ∗ 7), occurring as a somatic NF1 second hit mutation. Exome sequencing confirmed the absence of additional variants of potential pathogenic relevance. Western blot analysis showed the absence of wild-type NF1 protein in the cartilage of the patient, consistent with a somatic double inactivation (SDI) of NF1. Taken together, our findings support the role of SDI in NF1-related PE, widening the spectrum of the pathophysiological mechanisms involved in NF1-related skeletal features.

Published
2023

10. The Pgbd5 DNA transposase is required for mouse cerebral cortex development through DNA double-strand breaks formation

Author

Alessandro Simi, Federico Ansaloni, Devid Damiani, Azzurra Codino, Damiano Mangoni, Pierre Lau, Diego Vozzi, Luca Pandolfini, Remo Sanges, and Stefano Gustincich

Abstract

Transposons are conserved mobile genetic elements and one of the major sources of genetic variability during organisms’ evolution. PiggyBac Transposable Element Derived 5 (Pgbd5), an evolutionarily conserved vertebrate DNA transposase-coding gene, is highly expressed in the central nervous system during development and adult life, suggesting it may play a role in neuronal differentiation and maintenance.Here, we show thatPgbd5controls the expression of pro-neuronal and proliferative genes in a cell autonomous manner, leading to a decreased generation of neurons with altered migration. This activity depends on the induction of endogenous DNA double-strand breaks (DSBs).These results positionPgbd5as a crucial regulator of brain development through its endonuclease activity.One-Sentence SummaryPgbd5regulates cerebral cortex neurogenesis through DNA double-strand breaks modulation.

Published
2023

11. Moyamoya Vasculopathy in Neurofibromatosis Type 1 Pediatric Patients: The Role of Rare Variants of RNF213

Author

Marzia Ognibene, Marcello Scala, Michele Iacomino, Irene Schiavetti, Francesca Madia, Monica Traverso, Sara Guerrisi, Marco Di Duca, Francesco Caroli, Simona Baldassari, Barbara Tappino, Ferruccio Romano, Paolo Uva, Diego Vozzi, Cristina Chelleri, Gianluca Piatelli, Maria Cristina Diana, Federico Zara, Valeria Capra, Marco Pavanello, and Patrizia De Marco

Subjects
Cancer Research, Oncology, neurofibromatosis type 1, Moyamoya, next-generation sequencing (NGS), NF1, RNF213
Abstract

Neurofibromatosis type 1 (NF1) is a neurocutaneous disorder caused by mutations in NF1 gene, coding for neurofibromin 1. NF1 can be associated with Moyamoya disease (MMD), and this association, typical of paediatric patients, is referred to as Moyamoya syndrome (MMS). MMD is a cerebral arteriopathy characterized by the occlusion of intracranial arteries and collateral vessel formation, which increase the risk of ischemic and hemorrhagic events. RNF213 gene mutations have been associated with MMD, so we investigated whether rare variants of RNF213 could act as genetic modifiers of MMS phenotype in a pediatric cohort of 20 MMS children, 25 children affected by isolated MMD and 47 affected only by isolated NF1. By next-generation re-sequencing (NGS) of patients’ DNA and gene burden tests, we found that RNF213 seems to play a role only for MMD occurrence, while it does not appear to be involved in the increased risk of Moyamoya for MMS patients. We postulated that the loss of neurofibromin 1 can be enough for the excessive proliferation of vascular smooth muscle cells, causing Moyamoya arteriopathy associated with NF1. Further studies will be crucial to support these findings and to elucidate the possible role of other genes, enhancing our knowledge about pathogenesis and treatment of MMS.

Published
2023
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12. Type I interferon activation in RAS-associated autoimmune leukoproliferative disease (RALD)

Author

Giovanni Spirito, Roberta Caorsi, Stefano Volpi, Sara Signa, Stefano Gustincich, Remo Sanges, Francesco Pasetti, Francesca Schena, Isabella Ceccherini, Patrizia Barone, Marta Rusmini, Riccardo Papa, Elisabetta Traggiai, Andrea Cavalli, Maria C Coccia, Angelo Ravelli, Giuseppe Santamaria, Diego Vozzi, Serena Arrigo, and Marco Gattorno

Subjects
Neuroblastoma RAS viral oncogene homolog, Adult, Interferon, NRAS, RALD, Regenerative nodular hyperplasia, SLE, Autoimmune Lymphoproliferative Syndrome, GTP Phosphohydrolases, Humans, Interferon Type I, Liver Diseases, Membrane Proteins, Mutation, Immunology, Gene mutation, medicine.disease_cause, Hypogammaglobulinemia, Immunology and Allergy, Medicine, Hepatopulmonary syndrome, Exome sequencing, business.industry, Immune dysregulation, medicine.disease, Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin), KRAS, business, medicine.drug
Abstract

RAS-associated autoimmune leukoproliferative disease (RALD) is a rare immune dysregulation syndrome caused by somatic gain-of-function mutations of either NRAS or KRAS gene in hematopoietic cells. We describe a 27-year-old patient presenting at 5 months of age with recurrent infections and generalized lymphadenopathy who developed a complex multi-organ autoimmune syndrome with hypogammaglobulinemia, partially controlled with oral steroids, hydroxichloroquine, mofetil mycophenolate and IVIG prophylaxis. Activation of type I interferon pathway was observed in peripheral blood. Since 18 years of age, the patient developed regenerative nodular hyperplasia of the liver evolving into hepatopulmonary syndrome. Whole exome sequencing analysis of the peripheral blood DNA showed the NRAS p.Gly13Asp mutation validated as somatic. Our report highlights the possibility of detecting somatic NRAS gene mutations in patients with inflammatory immune dysregulation and type I interferon activation.

Published
2021

13. AB1105 A NOVEL AUTOINFLAMMATORY AND LYMPHOPROLIFERATIVE SYNDROME ASSOCIATED WITH PIM1 MUTATIONS

Author

Paola Tomietto, Elisa Piscianz, Flavio Faletra, Serena Pastore, Andrea Taddio, Giovanna Ferrara, Diego Vozzi, Alessia Pin, Erica Valencic, Silvio Polizzi, Alberto Tommasini, Umberto Dianzani, Annalisa Chiocchetti, and Josef Vuch

Subjects
Mutation, Oncogene, business.industry, medicine.medical_treatment, Inflammation, medicine.disease, medicine.disease_cause, Cytokine, Immunology, medicine, Missense mutation, Sarcoidosis, medicine.symptom, business, Exome sequencing, Extracellular matrix organization
Abstract

Background Whole exome sequencing can allow genetic diagnosis in subjects with long lasting clinical stories not supporting any well-defined disorder. A 35-year-old man was referred to ophthalmologist’s evaluation for blurry vision in his left eye. The fundus examination showed choroidal lesions in both eyes. His past medical history was relevant for celiac disease, recurrent episodes of fever and skin rashes with leukocytoclastic vasculitis, inflammatory lesions of the osteoarticular and muscular system, one episode of aseptic meningitis, an intracranial granuloma and two episodes of anterior uveitis. He had also splenomegaly with non-caseating granulomas. Brain TC founded multiple lytic and sclerotic skull lesions. He was diagnosed with atypical sarcoidosis and treated with oral steroid and methotrexate. Laboratory data always showed elevated erythrocyte sedimentation rate, strong positive C-reactive protein and polyclonal gammopathy. Objectives To describe functional and genetic data supporting the role of a PIM1 mutation in the multisystemic inflammation and lymphoproliferation of the patient. Methods Whole exome sequencing (WES) analysis. Flow-cytometry to evaluate Pim1 expression, Bad phosphorylation (target of Pim1 kinase) and the effect of PIM inhibitor on peripheral blood mononuclear cell (PBMC) viability. RNAseq was on primary fibroblasts from the patient and from healthy donors. Cloning of the mutated gene in a vector for further functional studies. Results WES analysis revealed the de novo heterozygous missense variation c.C1132A (p.H378N) in PIM1 gene. This variation was never described in on-line database and was predicted as damaging by various bioinformatic tools. Preliminary functional investigations in fibroblasts showed normal expression of Pim1, but higher phosphorylation of BAD protein was measured in cells from the patient. Moreover, PBMC from the patient displayed a lower sensitivity to the PIM inhibitor PIM447. RNAseq showed an altered expression profile in genes involved in the extracellular matrix organization. Conclusion PIM1 is an oncogene that encodes a protein kinase and, indeed, somatic gain of function mutations can be found in cancers. Preliminary data obtained from our patient suggest a gain of function effect of the p.H378N variant. The lymphoproliferative disorder may be sustained by the anti-apoptotic action of phosphorylated BAD. Recent data correlated hyperactive PIM1 in tumors with high degree of inflammatory infiltration accompanied by NFAT and mTOR activation and IL6 expression. A role of this cytokine also in our patient was coherent with a good clinical response to a treatment with tocilizumab, targeting IL-6. Although these results are supportive of a role of mutated PIM1 in the observed phenotype, we cannot still claim that this is causative of a novel syndrome. The detection of further cases and functional studies on cells transfected with mutated PIM1 will help shedding more light on this inflammatory and lymphoproliferative disorder. Disclosure of Interests None declared

Published
2019

14. Next-generation sequencing identified SPATC1L as a possible candidate gene for both early-onset and age-related hearing loss

Author

Navaneethakrishnan Krishnamoorthy, Elisa Rubinato, Martina La Bianca, Paolo Gasparini, Umberto Ambrosetti, Diego Vozzi, Annamaria Franzè, Dragana Vuckovic, Giorgia Girotto, Mariateresa Di Stazio, Pierangela Castorina, Stefania Cappellani, Anna Morgan, Morgan, A, Vuckovic, D, Krishnamoorthy, N, Rubinato, E, Ambrosetti, U, Castorina, P, Franze', Annamaria, Vozzi, D, La Bianca, M, Cappellani, S, Di Stazio, M, Gasparini, P, Girotto, G, Morgan, Anna, Vuckovic, Dragana, Krishnamoorthy, Navaneethakrishnan, Rubinato, Elisa, Ambrosetti, Umberto, Castorina, Pierangela, Franzè, Annamaria, Vozzi, Diego, La Bianca, Martina, Cappellani, Stefania, Di Stazio, Mariateresa, Gasparini, Paolo, and Girotto, Giorgia

Subjects
Male, Candidate gene, Next-generation Sequencing, Hearing loss, Hearing Loss, SPATC1L, Population, Mutation, Missense, Biology, Article, Frameshift mutation, 03 medical and health sciences, Mice, Genetics, medicine, otorhinolaryngologic diseases, Missense mutation, Animals, Humans, Allele, education, Hearing Lo, Genetics (clinical), Exome sequencing, Genetic association, Genetics & Heredity, 0604 Genetics, 0303 health sciences, education.field_of_study, Protein Stability, 030305 genetics & heredity, Middle Aged, Cytoskeletal Proteins, HEK293 Cells, Codon, Nonsense, Female, medicine.symptom
Abstract

Hereditary hearing loss (HHL) and age-related hearing loss (ARHL) are two major sensory diseases affecting millions of people worldwide. Despite many efforts, additional HHL-genes and ARHL genetic risk factors still need to be identified. To fill this gap a large genomic screening based on next-generation sequencing technologies was performed. Whole exome sequencing in a 3-generation Italian HHL family and targeted re-sequencing in 464 ARHL patients were performed. We detected three variants in SPATC1L: a nonsense allele in an HHL family and a frameshift insertion and a missense variation in two unrelated ARHL patients. In silico molecular modelling of all variants suggested a significant impact on the structural stability of the protein itself, likely leading to deleterious effects and resulting in truncated isoforms. After demonstrating Spatc1l expression in mice inner ear, in vitro functional experiments were performed confirming the results of the molecular modelling studies. Finally, a candidate-gene population-based statistical study in cohorts from Caucasus and Central Asia revealed a statistically significant association of SPATC1L with normal hearing function at low and medium hearing frequencies. Overall, the amount of different genetic data presented here (variants with early-onset and late-onset hearing loss in addition to genetic association with normal hearing function), together with relevant functional evidence, likely suggest a role of SPATC1L in hearing function and loss.

Published
2019

15. TBL1Y: a new gene involved in syndromic hearing loss

Author

Paolo Gasparini, Michael P. Myers, Anna Morgan, Pio Adamo D′Adamo, Wei Liu, Diego Vozzi, Mauro Giacca, Giorgia Girotto, Chiara Collesi, Elisa Rubinato, Mariateresa Di Stazio, DI STAZIO, Mariateresa, Collesi, Chiara, Vozzi, Diego, Liu, Wei, Myers, Mike, Morgan, Anna, D'Adamo, ADAMO PIO, Girotto, Giorgia, Rubinato, Elisa, Giacca, Mauro, and Gasparini, Paolo

Subjects
Adult, Male, medicine.medical_specialty, Adolescent, TBL1X, Hearing loss, Mutation, Missense, TBL1Y, Cochlea, Y-linked Disease, Syndromic hearing loss, Prostatic hyperplasia, Biology, medicine.disease_cause, Article, 03 medical and health sciences, Genetics, medicine, Homologous chromosome, Missense mutation, Humans, Transducin, Hearing Loss, Gene, Genetics (clinical), Exome sequencing, Aged, Aged, 80 and over, 0303 health sciences, Mutation, Protein Stability, 030305 genetics & heredity, Syndromic hearing lo, Prostate, Genetic Diseases, Y-Linked, Syndrome, Middle Aged, Pedigree, Medical genetics, Female, medicine.symptom
Abstract

Hereditary hearing loss (HHL) is an extremely heterogeneous disorder with autosomal dominant, recessive, and X-linked forms. Here, we described an Italian pedigree affected by HHL but also prostate hyperplasia and increased ratio of the free/total PSA levels, with the unusual and extremely rare Y-linked pattern of inheritance. Using exome sequencing we found a missense variant (r.206A>T leading to p.Asp69Val) in the TBL1Y gene. TBL1Y is homologous of TBL1X, whose partial deletion has described to be involved in X-linked hearing loss. Here, we demonstrate that it has a restricted expression in adult human cochlea and prostate and the variant identified induces a lower protein stability caused by misfolded mutated protein that impairs its cellular function. These findings indicate that TBL1Y could be considered a novel candidate for HHL.

Published
2019

16. Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders

Author

Symen Ligthart, Ahmad Vaez, Urmo Võsa, Maria G. Stathopoulou, Paul S. de Vries, Bram P. Prins, Peter J. Van der Most, Toshiko Tanaka, Elnaz Naderi, Lynda M. Rose, Ying Wu, Robert Karlsson, Maja Barbalic, Honghuang Lin, René Pool, Gu Zhu, Aurélien Macé, Carlo Sidore, Stella Trompet, Massimo Mangino, Maria Sabater-Lleal, John P. Kemp, Ali Abbasi, Tim Kacprowski, Niek Verweij, Albert V. Smith, Tao Huang, Carola Marzi, Mary F. Feitosa, Kurt K. Lohman, Marcus E. Kleber, Yuri Milaneschi, Christian Mueller, Mahmudul Huq, Efthymia Vlachopoulou, Leo-Pekka Lyytikäinen, Christopher Oldmeadow, Joris Deelen, Markus Perola, Jing Hua Zhao, Bjarke Feenstra, Marzyeh Amini, Jari Lahti, Katharina E. Schraut, Myriam Fornage, Bhoom Suktitipat, Wei-Min Chen, Xiaohui Li, Teresa Nutile, Giovanni Malerba, Jian’an Luan, Tom Bak, Nicholas Schork, Fabiola Del Greco M., Elisabeth Thiering, Anubha Mahajan, Riccardo E. Marioni, Evelin Mihailov, Joel Eriksson, Ayse Bilge Ozel, Weihua Zhang, Maria Nethander, Yu-Ching Cheng, Stella Aslibekyan, Wei Ang, Ilaria Gandin, Loïc Yengo, Laura Portas, Charles Kooperberg, Edith Hofer, Kumar B. Rajan, Claudia Schurmann, Wouter den Hollander, Tarunveer S. Ahluwalia, Jing Zhao, Harmen H.M. Draisma, Ian Ford, Nicholas Timpson, Alexander Teumer, Hongyan Huang, Simone Wahl, YongMei Liu, Jie Huang, Hae-Won Uh, Frank Geller, Peter K. Joshi, Lisa R. Yanek, Elisabetta Trabetti, Benjamin Lehne, Diego Vozzi, Marie Verbanck, Ginevra Biino, Yasaman Saba, Ingrid Meulenbelt, Jeff R. O’Connell, Markku Laakso, Franco Giulianini, Patrik K.E. Magnusson, Christie M. Ballantyne, Jouke Jan Hottenga, Grant W. Montgomery, Fernando Rivadineira, Rico Rueedi, Maristella Steri, Karl-Heinz Herzig, David J. Stott, Cristina Menni, Mattias Frånberg, Beate St. Pourcain, Stephan B. Felix, Tune H. Pers, Stephan J.L. Bakker, Peter Kraft, Annette Peters, Dhananjay Vaidya, Graciela Delgado, Johannes H. Smit, Vera Großmann, Juha Sinisalo, Ilkka Seppälä, Stephen R. Williams, Elizabeth G. Holliday, Matthijs Moed, Claudia Langenberg, Katri Räikkönen, Jingzhong Ding, Harry Campbell, Michele M. Sale, Yii-Der I. Chen, Alan L. James, Daniela Ruggiero, Nicole Soranzo, Catharina A. Hartman, Erin N. Smith, Gerald S. Berenson, Christian Fuchsberger, Dena Hernandez, Carla M.T. Tiesler, Vilmantas Giedraitis, David Liewald, Krista Fischer, Dan Mellström, Anders Larsson, Yunmei Wang, William R. Scott, Matthias Lorentzon, John Beilby, Kathleen A. Ryan, Craig E. Pennell, Dragana Vuckovic, Beverly Balkau, Maria Pina Concas, Reinhold Schmidt, Carlos F. Mendes de Leon, Erwin P. Bottinger, Margreet Kloppenburg, Lavinia Paternoster, Michael Boehnke, A.W. Musk, Gonneke Willemsen, David M. Evans, Pamela A.F. Madden, Mika Kähönen, Zoltán Kutalik, Magdalena Zoledziewska, Ville Karhunen, Stephen B. Kritchevsky, Naveed Sattar, Genevieve Lachance, Robert Clarke, Tamara B. Harris, Olli T. Raitakari, John R. Attia, Diana van Heemst, Eero Kajantie, Rossella Sorice, Giovanni Gambaro, Robert A. Scott, Andrew A. Hicks, Luigi Ferrucci, Marie Standl, Cecilia M. Lindgren, John M. Starr, Magnus Karlsson, Lars Lind, Jun Z. Li, John C. Chambers, Trevor A. Mori, Eco J.C.N. de Geus, Andrew C. Heath, Nicholas G. Martin, Juha Auvinen, Brendan M. Buckley, Anton J.M. de Craen, Melanie Waldenberger, Konstantin Strauch, Thomas Meitinger, Rodney J. Scott, Mark McEvoy, Marian Beekman, Cristina Bombieri, Paul M. Ridker, Karen L. Mohlke, Nancy L. Pedersen, Alanna C. Morrison, Dorret I. Boomsma, John B. Whitfield, David P. Strachan, Albert Hofman, Peter Vollenweider, Francesco Cucca, Marjo-Riitta Jarvelin, J. Wouter Jukema, Tim D. Spector, Anders Hamsten, Tanja Zeller, André G. Uitterlinden, Matthias Nauck, Vilmundur Gudnason, Lu Qi, Harald Grallert, Ingrid B. Borecki, Jerome I. Rotter, Winfried März, Philipp S. Wild, Marja-Liisa Lokki, Michael Boyle, Veikko Salomaa, Mads Melbye, Johan G. Eriksson, James F. Wilson, Brenda W.J.H. Penninx, Diane M. Becker, Bradford B. Worrall, Greg Gibson, Ronald M. Krauss, Marina Ciullo, Gianluigi Zaza, Nicholas J. Wareham, Albertine J. Oldehinkel, Lyle J. Palmer, Sarah S. Murray, Peter P. Pramstaller, Stefania Bandinelli, Joachim Heinrich, Erik Ingelsson, Ian J. Deary, Reedik Mägi, Liesbeth Vandenput, Pim van der Harst, Karl C. Desch, Jaspal S. Kooner, Claes Ohlsson, Caroline Hayward, Terho Lehtimäki, Alan R. Shuldiner, Donna K. Arnett, Lawrence J. Beilin, Antonietta Robino, Philippe Froguel, Mario Pirastu, Tine Jess, Wolfgang Koenig, Ruth J.F. Loos, Denis A. Evans, Helena Schmidt, George Davey Smith, P. Eline Slagboom, Gudny Eiriksdottir, Andrew P. Morris, Bruce M. Psaty, Russell P. Tracy, Ilja M. Nolte, Eric Boerwinkle, Sophie Visvikis-Siest, Alex P. Reiner, Myron Gross, Joshua C. Bis, Lude Franke, Oscar H. Franco, Emelia J. Benjamin, Daniel I. Chasman, Josée Dupuis, Harold Snieder, Abbas Dehghan, Behrooz Z. Alizadeh, H. Marike Boezen, Gerjan Navis, Marianne Rots, Morris Swertz, Bruce H.R. Wolffenbuttel, Cisca Wijmenga, Emelia Benjamin, Tarunveer Singh Ahluwalia, James Meigs, Russell Tracy, Josh Bis, Nathan Pankratz, Alex Rainer, James G. Wilson, Josee Dupuis, Bram Prins, Urmo Vaso, Maria Stathopoulou, Terho Lehtimaki, Yalda Jamshidi, Sophie Siest, Andre G. Uitterlinden, Mohammadreza Abdollahi, Renate Schnabel, Ursula M. Schick, Aldi Kraja, Yi-Hsiang Hsu, Daniel S. Tylee, Alyson Zwicker, Rudolf Uher, George Davey-Smith, Andrew Hicks, Cornelia M. van Duijn, Cavin Ward-Caviness, J. Rotter, Ken Rice, Leslie Lange, Eco de Geus, Kari Matti Makela, David Stacey, Johan Eriksson, Tim M. Frayling, Eline P. Slagboom, Erasmus University Medical Center [Rotterdam] (Erasmus MC), University Medical Center Groningen [Groningen] (UMCG), University of Isfahan, University of Tartu, Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire (IGE-PCV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), The University of Texas Health Science Center at Houston (UTHealth), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Brigham and Women's Hospital [Boston], University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], University of Split, Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Process & Energy Laboratory, Delft University of Technology (TU Delft), Grand Lyon : communauté urbaine de Lyon, Interuniversity Cardiology Institute Netherlands, Department of Twin Research and Genetic Epidemiology, King's College London, London, Huazhong University of Science and Technology [Wuhan] (HUST), Division of Statistical Genomics, Washington University School of Medicine, Department of Psychiatry, VU University Medical Center [Amsterdam], Institut fuer Theoretische Physik (Institut fuer Theoretische Physik), Universität Heidelberg [Heidelberg] = Heidelberg University, Molecular Epidemiology, MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Mahidol University [Bangkok], Northwest A and F University, Laboratoire d'Optimisation des Systèmes Industriels (LOSI), Institut Charles Delaunay (ICD), Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS), Institute of Genetics and Biophysics, CNR, Naples, Università degli studi di Verona = University of Verona (UNIVR), Department of Molecular Medicine [Scripps Research Institute], The Scripps Research Institute [La Jolla, San Diego], Department of Physics, Indian Institute of Technology Kanpur (IIT Kanpur), Deptartment of Medical Biochemistry and Microbiology, Uppsala University, Department of Electrical and Computer Engineering [Waterloo] (ECE), University of Waterloo [Waterloo], University of Maryland School of Medicine, University of Maryland System, Institut National de l'Environnement Industriel et des Risques (INERIS), Institute of Pop. Genetics, CNR, Sassari, Interfaculty Institute for Genetics and Functional Genomics, Universität Greifswald - University of Greifswald, IT University of Copenhagen (ITU), Robertson Centre for Biostatistics, University of Glasgow, Centre for Causal Analyses in Translational Epidemiology, University of Bristol [Bristol]-Medical Research Council, King‘s College London, Jinan University [Guangzhou], Institute of Oceanology [China], School Medicine, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), General Internal Medicine, Johns Hopkins School of Medicine, Johns Hopkins University School of Medicine [Baltimore], Shardna life science Pula Cagliari, Section Molecular Epidemiology, Leiden University Medical Center (LUMC), Department of Medicine, University of Eastern Finland-Kuopio University Hospital, Medstar Research Institute, Department of Cardiology, Ernst-Moritz-Arndt University, Center for Biological Sequence Analysis [Lyngby], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Department of Internal Medicine, University of Groningen and University Medical Center Groningen, Department of Epidemiology, Harvard School of Public Health, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Metacohorts Consortium, INEOS Technologies (SWITZERLAND), MRC Epidemiology Unit, University of Cambridge [UK] (CAM)-Institute of Metabolic Science, University of Edinburgh, School of Population Health [Crawley, Western Australia], The University of Western Australia (UWA), Institute of Genetics and Biophysics, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), The Scripps Translational Science Institute and Scripps Health, Tulane Center for Cardiovascular Health, Tulane University Health Sciences Center, Centre for Population Health Sciences, Genomic Research Laboratory, Service of Infectious Disease, Hôpitaux Universitaires de Genève (HUG), Infectious diseases division, Department of internal medicine, Washington University in Saint Louis (WUSTL), Luleå University of Technology (LUT), Recherche en épidémiologie et biostatistique, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Austrian Institute of Technology [Vienna] (AIT), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Department of Rheumatology and Clinical Epidemiology, Leiden University Medical Center (LUMC), Department of Rheumatology and Clinical Epidemiology [Leiden University Medical Center] (LUMC), Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden-Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Department of Biostatistics and Center for Statistical Genetics, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of Virginia, Tampere University Hospital, Department of Medical Genetics, Université de Lausanne = University of Lausanne (UNIL), Department of Pathological Biochemistry, Royal Infirmary, Oxford University, University of Oxford, University of Newcastle [Callaghan, Australia] (UoN), Department of neurology, Institute of Metabolic Science, MRC, The Wellcome Trust Centre for Human Genetics [Oxford], Uppsala Universitet [Uppsala], QIMR Berghofer Medical Research Institute, Institute of Genetic Epidemiology [Neuherberg, Germany], Institute of Human Genetics, Helmholtz Zentrum München = German Research Center for Environmental Health, Schizophrenia Research Institute [Sydney], Department of Genetics, University of North Carolina System (UNC)-University of North Carolina System (UNC), Vrije Universiteit Brussel (VUB), Population Health Sciences and Education, St George's University of London, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Institute of Health Sciences and Biocenter Oulu, University of Oulu, Medizinische Klinik und Poliklinik, Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Institute of Clinical Chemistry and Laboratory Medicine, Icelandic Heart Association, Heart Preventive Clinic and Research Institute, Departments of Epidemiology and Nutrition, Institute of Epidemiology [Neuherberg] (EPI), Medical University Graz, Transplantation Laboratory [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Chronic Disease Prevention, National Institute for Health and Welfare [Helsinki], Dept. of Epidemiology Research, Statens Serum Institut [Copenhagen], CLinical Psychology, Genetics and Pathology, Geriatric Rehabilitation Unit, Azienda Sanitaria Firenze, Center For Narcolepsy, Stanford University, Centre for Bone and Arthritis Research, University of Gothenburg (GU)-Institute of Medicine, MRC Human Gentics Unit, Inst Genet and Mol Med, Western General Hospital, Edinburgh, University of Maryland School of Medicine [Baltimore, MD, USA], Génétique des maladies multifactorielles (GMM), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Stockholm], Stockholm University, University of Bristol [Bristol], Universiteit Leiden, Department of Epidemiology, University of Washington, University of Washington [Seattle], Department of Epidemiology [Rotterdam], University of Groningen [Groningen], Dutch Initiative on Crohn and Colitis (ICC), Icelandic Heart Association [Kopavogur, Iceland] (IHA), Department of Physiology and Biophysics [Jackson, MS, USA], University of Southern Mississippi (USM), Human Genetics Branch, National Institutes of Health [Bethesda] (NIH)-National Institute of Mental Health (NIMH), Faculty of Medicine and Life Sciences [Tampere], University of Tampere [Finland], German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), MRC Centre for Neuropsychiatric Genetics and Genomics, Medical Research Council-Cardiff University, Department of Social Medicine, School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Department of Medicine [Aurora, CO, USA], University of Colorado [Denver], Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Mathematical Institute [Oxford] (MI), Institute of Psychiatry, Psychology & Neuroscience, King's College London, LifeLines Cohort Study, CHARGE Inflammation Working Group, Ligthart, S., Vaez, A., Vosa, U., Stathopoulou, M. G., de Vries, P. S., Prins, B. P., Van der Most, P. J., Tanaka, T., Naderi, E., Rose, L. M., Wu, Y., Karlsson, R., Barbalic, M., Lin, H., Pool, R., Zhu, G., Mace, A., Sidore, C., Trompet, S., Mangino, M., Sabater-Lleal, M., Kemp, J. P., Abbasi, A., Kacprowski, T., Verweij, N., Smith, A. V., Huang, T., Marzi, C., Feitosa, M. F., Lohman, K. K., Kleber, M. E., Milaneschi, Y., Mueller, C., Huq, M., Vlachopoulou, E., Lyytikainen, L. -P., Oldmeadow, C., Deelen, J., Perola, M., Zhao, J. H., Feenstra, B., Alizadeh, B. Z., Boezen, H. M., Franke, L., van der Harst, P., Navis, G., Rots, M., Snieder, H., Swertz, M., Wolffenbuttel, B. H. R., Wijmenga, C., Amini, M., Benjamin, E., Chasman, D. I., Dehghan, A., Ahluwalia, T. S., Meigs, J., Tracy, R., Bis, J., Eiriksdottir, G., Pankratz, N., Gross, M., Rainer, A., Wilson, J. G., Psaty, B. M., Dupuis, J., Prins, B., Vaso, U., Stathopoulou, M., Lehtimaki, T., Koenig, W., Jamshidi, Y., Siest, S., Uitterlinden, A. G., Abdollahi, M., Schnabel, R., Schick, U. M., Nolte, I. M., Kraja, A., Hsu, Y. -H., Tylee, D. S., Zwicker, A., Uher, R., Davey-Smith, G., Morrison, A. C., Hicks, A., van Duijn, C. M., Ward-Caviness, C., Boerwinkle, E., Rotter, J., Rice, K., Lange, L., de Geus, E., Morris, A. P., Makela, K. M., Stacey, D., Eriksson, J., Frayling, T. M., Slagboom, E. P., Lahti, J., Schraut, K. E., Fornage, M., Suktitipat, B., Chen, W. -M., Li, X., Nutile, T., Malerba, G., Luan, J., Bak, T., Schork, N., Del Greco, M. F., Thiering, E., Mahajan, A., Marioni, R. E., Mihailov, E., Ozel, A. B., Zhang, W., Nethander, M., Cheng, Y. -C., Aslibekyan, S., Ang, W., Gandin, I., Yengo, L., Portas, L., Kooperberg, C., Hofer, E., Rajan, K. B., Schurmann, C., den Hollander, W., Zhao, J., Draisma, H. H. M., Ford, I., Timpson, N., Teumer, A., Huang, H., Wahl, S., Liu, Y., Huang, J., Uh, H. -W., Geller, F., Joshi, P. K., Yanek, L. R., Trabetti, E., Lehne, B., Vozzi, D., Verbanck, M., Biino, G., Saba, Y., Meulenbelt, I., O'Connell, J. R., Laakso, M., Giulianini, F., Magnusson, P. K. E., Ballantyne, C. M., Hottenga, J. J., Montgomery, G. W., Rivadineira, F., Rueedi, R., Steri, M., Herzig, K. -H., Stott, D. J., Menni, C., Franberg, M., S, t. Pourcain B., Felix, S. B., Pers, T. H., Bakker, S. J. L., Kraft, P., Peters, A., Vaidya, D., Delgado, G., Smit, J. H., Grossmann, V., Sinisalo, J., Seppala, I., Williams, S. R., Holliday, E. G., Moed, M., Langenberg, C., Raikkonen, K., Ding, J., Campbell, H., Sale, M. M., Chen, Y. -D. I., James, A. L., Ruggiero, D., Soranzo, N., Hartman, C. A., Smith, E. N., Berenson, G. S., Fuchsberger, C., Hernandez, D., Tiesler, C. M. T., Giedraitis, V., Liewald, D., Fischer, K., Mellstrom, D., Larsson, A., Wang, Y., Scott, W. R., Lorentzon, M., Beilby, J., Ryan, K. A., Pennell, C. E., Vuckovic, D., Balkau, B., Concas, M. P., Schmidt, R., Mendes de Leon, C. F., Bottinger, E. P., Kloppenburg, M., Paternoster, L., Boehnke, M., Musk, A. W., Willemsen, G., Evans, D. M., Madden, P. A. F., Kahonen, M., Kutalik, Z., Zoledziewska, M., Karhunen, V., Kritchevsky, S. B., Sattar, N., Lachance, G., Clarke, R., Harris, T. B., Raitakari, O. T., Attia, J. R., van Heemst, D., Kajantie, E., Sorice, R., Gambaro, G., Scott, R. A., Hicks, A. A., Ferrucci, L., Standl, M., Lindgren, C. M., Starr, J. M., Karlsson, M., Lind, L., Li, J. Z., Chambers, J. C., Mori, T. A., de Geus, E. J. C. N., Heath, A. C., Martin, N. G., Auvinen, J., Buckley, B. M., de Craen, A. J. M., Waldenberger, M., Strauch, K., Meitinger, T., Scott, R. J., Mcevoy, M., Beekman, M., Bombieri, C., Ridker, P. M., Mohlke, K. L., Pedersen, N. L., Boomsma, D. I., Whitfield, J. B., Strachan, D. P., Hofman, A., Vollenweider, P., Cucca, F., Jarvelin, M. -R., Jukema, J. W., Spector, T. D., Hamsten, A., Zeller, T., Nauck, M., Gudnason, V., Qi, L., Grallert, H., Borecki, I. B., Rotter, J. I., Marz, W., Wild, P. S., Lokki, M. -L., Boyle, M., Salomaa, V., Melbye, M., Eriksson, J. G., Wilson, J. F., Penninx, B. W. J. H., Becker, D. M., Worrall, B. B., Gibson, G., Krauss, R. M., Ciullo, M., Zaza, G., Wareham, N. J., Oldehinkel, A. J., Palmer, L. J., Murray, S. S., Pramstaller, P. P., Bandinelli, S., Heinrich, J., Ingelsson, E., Deary, I. J., Magi, R., Vandenput, L., Desch, K. C., Kooner, J. S., Ohlsson, C., Hayward, C., Shuldiner, A. R., Arnett, D. K., Beilin, L. J., Robino, A., Froguel, P., Pirastu, M., Jess, T., Loos, R. J. F., Evans, D. A., Schmidt, H., Slagboom, P. E., Tracy, R. P., Visvikis-Siest, S., Reiner, A. P., Bis, J. C., Franco, O. H., Benjamin, E. J., AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, Graduate School, Epidemiology, Internal Medicine, Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Cardiovascular Centre (CVC), Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Stem Cell Aging Leukemia and Lymphoma (SALL), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), VU University medical center, Psychiatry, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Mental Health, APH - Methodology, APH - Digital Health, Biological Psychology, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, Universität Heidelberg [Heidelberg], University of Verona (UNIVR), Department of Molecular and Experimental Medicine, The Scripps Research Institute, The Scripps Research Institute, Université Grenoble Alpes - UFR Sciences de l'Homme et de la Société (UGA UFR SHS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), IT University of Copenhagen, Technical University of Denmark [Lyngby] (DTU), Consiglio Nazionale delle Ricerche (CNR), University of Virginia [Charlottesville], Université de Lausanne (UNIL), University of Oxford [Oxford], University of Newcastle [Australia] (UoN), Centre d'économie industrielle i3 (CERNA i3), Centre National de la Recherche Scientifique (CNRS)-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Helmholtz-Zentrum München (HZM), Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Universitätsmedizin der Johannes-Gutenberg Universität Mainz, University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Cardiff University-Medical Research Council, University of California-University of California, and DE CARVALHO, Philippe

Subjects
0301 basic medicine, Male, Netherlands Twin Register (NTR), Bipolar Disorder, LD SCORE REGRESSION, [SDV]Life Sciences [q-bio], Genome-wide association study, [SDV.GEN] Life Sciences [q-bio]/Genetics, Body Mass Index, inflammatory disorder, 80 and over, WIDE ASSOCIATION, EPIDEMIOLOGY, ta318, International HapMap Project, Child, Genetics (clinical), 2. Zero hunger, Genetics, Genetics & Heredity, Aged, 80 and over, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, C-reactive proteingenome-wide association studyinflammationMendelian randomizationinflammatory disordersDEPICTcoronary artery diseaseschizophreniasystem biology, system biology, DEPICT, Mendelian Randomization Analysis, 11 Medical And Health Sciences, Middle Aged, C-reactive protein, coronary artery disease, genome-wide association study, inflammation, inflammatory disorders, Mendelian randomization, schizophrenia, Adolescent, Adult, Aged, Biomarkers, C-Reactive Protein, Female, Genetic Loci, Genome-Wide Association Study, Humans, Inflammation, Liver, Metabolic Networks and Pathways, Schizophrenia, Young Adult, 3. Good health, [SDV] Life Sciences [q-bio], Medical genetics, Biomarker (medicine), Life Sciences & Biomedicine, Human, medicine.medical_specialty, CHARGE Inflammation Working Group, Biology, IMMUNITY, ta3111, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, medicine, CORONARY-HEART-DISEASE, Mendelian Randomization Analysi, 1000 Genomes Project, METAANALYSIS, Genetic association, [SDV.GEN]Life Sciences [q-bio]/Genetics, Science & Technology, ta1184, Metabolic Networks and Pathway, Biomarker, INSTRUMENTS, 06 Biological Sciences, 030104 developmental biology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, LifeLines Cohort Study
Abstract

International audience; C-reactive protein (CRP) is a sensitive biomarker of chronic low-grade inflammation and is associated with multiple complex diseases. The genetic determinants of chronic inflammation remain largely unknown, and the causal role of CRP in several clinical outcomes is debated. We performed two genome-wide association studies (GWASs), on HapMap and 1000 Genomes imputed data, of circulating amounts of CRP by using data from 88 studies comprising 204,402 European individuals. Additionally, we performed in silico functional analyses and Mendelian randomization analyses with several clinical outcomes. The GWAS meta-analyses of CRP revealed 58 distinct genetic loci (p < 5 × 10-8). After adjustment for body mass index in the regression analysis, the associations at all except three loci remained. The lead variants at the distinct loci explained up to 7.0% of the variance in circulating amounts of CRP. We identified 66 gene sets that were organized in two substantially correlated clusters, one mainly composed of immune pathways and the other characterized by metabolic pathways in the liver. Mendelian randomization analyses revealed a causal protective effect of CRP on schizophrenia and a risk-increasing effect on bipolar disorder. Our findings provide further insights into the biology of inflammation and could lead to interventions for treating inflammation and its clinical consequences.Copyright © 2018 American Society of Human Genetics. All rights reserved.

Published
2018

17. Type I interferon-mediated autoinflammation due to DNase II deficiency

Author

Flavio Faletra, Gabriele Stocco, Evelyn Hartmann, Chantal Brouzes, Flavia Guillem, Fabrice Porcheray, Florence Uettwiller, Carolina Uggenti, Diego Vozzi, Marion Rabant, Capucine Picard, Nicolas Cagnard, Elisa Piscianz, Olivier Hermine, Andrea Taddio, Sophie Candon, Gunther Hartmann, Leo A. H. Zeef, Pierre Quartier, Marie Alexandra Alyanakian, Brigitte Bader-Meunier, Benoit Beitz, Gillian I. Rice, Muriel Girard, Monique Fabre, Alberto Tommasini, Dominique Lasne, Marine Depp, Nathalie Boddaert, Mathieu P Rodero, Stefano Volpi, Marco Gattorno, Yanick J. Crow, Eva Bartok, Michael Dussiot, Michel Polak, Tiffany Pascreau, Roberta Caorsi, Erika Della Mina, Naoki Kitabayashi, Annalisa Marcuzzi, Vincent Bondet, Paolo Picco, Luis Seabra, Jacques Beltrand, Erica Valencic, Marie-Louise Frémond, Bénédicte Neven, Frédéric Rieux-Laucat, Darragh Duffy, Alessandra Tesser, Patrick Nitschke, Anna Monica Bianco, Marina Charbit, Annie Harroche, Serena Pastore, Winfried Barchet, Laboratory of neurogenetics and neuroinflammation (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Trieste, University of Bonn, Academic Unit of Medical Genetic, University of Manchester [Manchester], Microbiology Technology Institute, BIOASTER Microbiology Technology Institute [Lyon], Immunobiologie des Cellules dendritiques, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Structure Fédérative de Recherche Necker (SFR Necker - UMS 3633 / US24), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Giannina Gaslini Institute, Istituto Giannina Gaslini, Genova, Immunologia Clinica e Sperimentale, Service d'immuno-hématologie pédiatrique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Radiologie et imagerie médicale [CHU Necker], Laboratory of molecular mechanisms of hematologic disorders and therapeutic implications (ERL 8254 - Equipe Inserm U1163), Service de néphrologie pédiatrique [CHU Necker], Hôpital Bicêtre, Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Plate Forme Paris Descartes de Bioinformatique (BIP-D), Université Paris Descartes - Paris 5 (UPD5), Centre d'étude des Déficits Immunitaires, Service d'endocrinologie, gynécologie et diabétologie pédiatriques [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Life Sciences, Institute of Clinical Chemistry and Pharmacology, Center for Integrated Oncology, University Hospital of Bonn, Service d'Hématologie Adulte, IRCCS Burlo Garofolo, Inst Maternal & Child Hlth, Trieste, Italy, Y.J.C. acknowledges the European Research Council (GA 309449), and a state subsidymanaged by the National Research Agency (France) under the 'Investments for the Future'program bearing the reference ANR-10-IAHU-01. We thank ImmunoQure AGfor sharing of antibodies used to assess interferon alpha protein levels in the Simoa assay.M.-L.F. is supported by the Institut National de la Santé et de la Recherche Médicale(Grant number 000427993). A.T. and M.G. acknowledge the Italian Telethon (Grant no.GGP15241A). A.T. acknowledges the Institute for Maternal and Child Health-IRCCS'Burlo Garofolo' (RC 17/2014 funded by Italian Ministry of Health, art 12 and 12bis D.lgs 502/92), the 'Associazione Azzurra Malattie Rare'and the 'Beneficientia Stiftung in Vaduz'. We would like to thank Olivier pellet and Jerome Megret from theflow cytometry platform at SFR Necker (INSERM US24-CNRS UMS 3633) for their help withperipheral blood mononuclear cell subset isolation. We would like to thank the Geno-mics Platform, INSERM UMR1163 for whole-exome sequencing. E.B., G.H., and W.B.acknowledge DZIF funding and German Research Foundation (DFG) grants EXC1023:ImmunoSensation, CRCs 670 and 704, ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), European Project: 309449,EC:FP7:ERC,ERC-2012-StG_20111109,T1-IFN(2013), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), BIOASTER, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Università degli studi di Trieste = University of Trieste, Universität Bonn = University of Bonn, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University Hospital Bonn, Vougny, Marie-Christine, Instituts Hospitalo-Universitaires - Institut Hospitalo-Universitaire Imagine - - Imagine2010 - ANR-10-IAHU-0001 - IAHU - VALID, Definition and characterization of type I interferonopathies - T1-IFN - - EC:FP7:ERC2013-03-01 - 2018-02-28 - 309449 - VALID, Rodero, Mathieu P., Tesser, Alessandra, Bartok, Eva, Rice, Gillian I., Della Mina, Erika, Depp, Marine, Beitz, Benoit, Bondet, Vincent, Cagnard, Nicola, Duffy, Darragh, Dussiot, Michael, Frã©mond, Marie-Louise, Gattorno, Marco, Guillem, Flavia, Kitabayashi, Naoki, Porcheray, Fabrice, Rieux-Laucat, Frederic, Seabra, Lui, Uggenti, Carolina, Volpi, Stefano, Zeef, Leo A. H., Alyanakian, Marie-Alexandra, Beltrand, Jacque, Bianco, Anna Monica, Boddaert, Nathalie, Brouzes, Chantal, Candon, Sophie, Caorsi, Roberta, Charbit, Marina, Fabre, Monique, Faletra, Flavio, Girard, Muriel, Harroche, Annie, Hartmann, Evelyn, Lasne, Dominique, Marcuzzi, Annalisa, Neven, Bã©nã©dicte, Nitschke, Patrick, Pascreau, Tiffany, Pastore, Serena, Picard, Capucine, Picco, Paolo, Piscianz, Elisa, Polak, Michel, Quartier, Pierre, Rabant, Marion, Stocco, Gabriele, Taddio, Andrea, Uettwiller, Florence, Valencic, Erica, Vozzi, Diego, Hartmann, Gunther, Barchet, Winfried, Hermine, Olivier, Bader-Meunier, Brigitte, Tommasini, Alberto, and Crow, Yanick J.

Subjects
Genetics and Molecular Biology (all), Male, 0301 basic medicine, Erythroblasts, [SDV]Life Sciences [q-bio], DNASE2, type I interferon, autoinflammation, exome sequencing, Up-Regulation/drug effects, General Physics and Astronomy, Erythroblasts/immunology, DNASE2, type I interferon, autoinflammation, exome sequencing, Biochemistry, LS3_11, 0302 clinical medicine, Interferon, Interferon-alpha/blood, Membranoproliferative glomerulonephritis, STAT1, Phosphorylation, lcsh:Science, Child, ComputingMilieux_MISCELLANEOUS, Deoxyribonucleases, Multidisciplinary, biology, RNA, Messenger/analysis, Chemistry (all), Endodeoxyribonucleases/deficiency, Up-Regulation, 3. Good health, STAT1 Transcription Factor, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, STAT1 Transcription Factor/metabolism, Antibody, Signal Transduction, medicine.drug, STAT3 Transcription Factor, [SDV.IMM] Life Sciences [q-bio]/Immunology, Adolescent, Science, Alpha interferon, Antiviral Agents/pharmacology, Hematopoiesis/immunology, Antiviral Agents, Article, General Biochemistry, Genetics and Molecular Biology, Deoxyribonucleases/deficiency, NO, Physics and Astronomy (all), 03 medical and health sciences, Downregulation and upregulation, medicine, Humans, RNA, Messenger, Signal Transduction/immunology, Endodeoxyribonucleases, Innate immune system, Sequence Analysis, RNA, Gene Expression Profiling, Hereditary Autoinflammatory Diseases, Interferon-alpha, General Chemistry, medicine.disease, Hematopoiesis, 030104 developmental biology, STAT3 Transcription Factor/metabolism, Hereditary Autoinflammatory Diseases/blood, Mutation, Immunology, biology.protein, Nucleic acid, lcsh:Q, Biochemistry, Genetics and Molecular Biology (all), 030215 immunology
Abstract

Microbial nucleic acid recognition serves as the major stimulus to an antiviral response, implying a requirement to limit the misrepresentation of self nucleic acids as non-self and the induction of autoinflammation. By systematic screening using a panel of interferon-stimulated genes we identify two siblings and a singleton variably demonstrating severe neonatal anemia, membranoproliferative glomerulonephritis, liver fibrosis, deforming arthropathy and increased anti-DNA antibodies. In both families we identify biallelic mutations in DNASE2, associated with a loss of DNase II endonuclease activity. We record increased interferon alpha protein levels using digital ELISA, enhanced interferon signaling by RNA-Seq analysis and constitutive upregulation of phosphorylated STAT1 and STAT3 in patient lymphocytes and monocytes. A hematological disease transcriptomic signature and increased numbers of erythroblasts are recorded in patient peripheral blood, suggesting that interferon might have a particular effect on hematopoiesis. These data define a type I interferonopathy due to DNase II deficiency in humans., Nucleic acid sensing is important to ensure that an innate immune response is only mounted against microbial nucleic acid. Here, the authors identify loss-of-function mutations in the DNASE2 gene that cause type I interferon-mediated autoinflammation due to enhanced systemic interferon signaling.

Published
2017

18. The Challenge of Next Generation Sequencing in a Boy With Severe Mononucleosis and EBV-related Lymphoma

Author

Nagua Giurici, Annalisa Marcuzzi, Alberto Tommasini, Flavio Faletra, Federico Verzegnassi, Diego Vozzi, Valentina Kiren, Anna Monica Bianco, Erica Valencic, Verzegnassi, F., Valencic, E., Kiren, V., Giurici, N., Bianco, A. M., Marcuzzi, A., Vozzi, D., Tommasini, A., and Faletra, F.

Subjects
0301 basic medicine, Male, Herpesvirus 4, Human, Mononucleosis, Adolescent, Lymphoma, Infectious Mononucleosi, medicine.disease_cause, NO, whole exome sequencing, CTPS2, 03 medical and health sciences, 0302 clinical medicine, Epstein Barr virus, hemophagocytic lymphohistiocytosis, lymphoma, Humans, Exome, High-Throughput Nucleotide Sequencing, Infectious Mononucleosis, Mutation, hemophagocytic lymphohistiocytosi, medicine, Exome sequencing, Hemophagocytic lymphohistiocytosis, business.industry, Herpesvirus 4, Hematology, medicine.disease, Penetrance, Epstein–Barr virus, 030104 developmental biology, Oncology, Epstein Barr viru, Pediatrics, Perinatology and Child Health, Immunology, Primary immunodeficiency, business, 030215 immunology, Human
Abstract

A severe course of infectious mononucleosis should always lead up to the suspicion of a primary immunodeficiency. We describe the case of a boy with severe mononucleosis accompanied by the development of hemophagocytic lymphohistiocytosis and lymphoma. By whole exome sequencing, we identified a mutation of uncertain significance in CTPS2, a gene closely related to CTPS1, which is involved in a primary immune deficiency with susceptibility to herpesviruses. We discuss the challenge of a correct interpretation of data from whole exome sequencing, questioning whether the CTPS2 variant found in our patient is just an incidental finding or a mutation with variable penetrance.

Published
2017

19. Novel NOD2 Mutation in Early-Onset Inflammatory Bowel Phenotype

Author

Costantino De Giacomo, Diego Vozzi, Gabriele Baj, Eva Decleva, Alessia Pin, E.F. Stacul, Martina Girardelli, Anna Monica Bianco, Claudia Loganes, Alberto Tommasini, Girardelli, M., Loganes, C., Pin, A., Stacul, E., Decleva, Eva, Vozzi, D., Baj, G., De Giacomo, C., Tommasini, A., and Bianco, A. M.

Subjects
0301 basic medicine, Male, Chemokine, medicine.medical_treatment, Nod2 Signaling Adaptor Protein, HEK293 Cell, NOD2, Immunology and Allergy, Missense mutation, Age of Onset, Caco-2 Cell, Synovitis, biology, cytokines profile, EO-IBD, rare disease, WES, Arthritis, Caco-2 Cells, Cytokines, Genetic Predisposition to Disease, HEK293 Cells, Homozygote, Humans, Infant, Inflammatory Bowel Diseases, Intestines, Mutation, Missense, Phenotype, Uveitis, Gastroenterology, Intestine, Cytokine, Synoviti, Tumor necrosis factor alpha, Arthriti, Human, Sarcoidosis, 03 medical and health sciences, medicine, Blau syndrome, Innate immune system, Inflammatory Bowel Disease, medicine.disease, Molecular biology, digestive system diseases, 030104 developmental biology, Mutation, biology.protein, Missense
Abstract

BACKGROUND: Nucleotide-binding oligomerization domain 2 (NOD2) is a key intracellular protein of the innate immune system. NOD2 variants are associated with inflammatory bowel disease (IBD) and other inflammatory phenotypes. We described the case of a baby with a very early-onset IBD who is characterized by a rare homozygous variant in NOD2, found through whole-exome sequencing, Its pathogenic effect was investigated through bioinformatics and functional studies. METHODS: The microbicide activity of the patient's phagocytes was analyzed using Escherichia coli. HEK293 and Caco2 cell lines were transfected with wild-type and mutated NOD2 cDNA to evaluate the NF-kB activity and the protein distribution. The functionality of the NOD2 pathway was assessed through analysis of the expression of tumor nectrosis factor alpha (TNFα) on monocytes. The levels of various cytokines were quantified in the patient plasma by a multiplex suspension array. RESULTS: A missense NOD2 mutation, c.G1277A; p.R426H in homozygosis, was found. The patient's microbicide activity was comparable to that observed in controls. HEK293 cells transfected with the mutated cDNA showed a 20-fold increase of NF-kB activation in basal condition. Moreover, Caco2 immunostaining revealed a different cytoplasmic distribution of the mutated protein compared with wild-type. A higher production of TNFα by monocytes and elevated levels of plasmatic cytokines and chemokines were evidenced in the patient. CONCLUSIONS: This homozygous mutation is functionally relevant and shows a different NOD2 involvement in the IBD phenotype. In our patient, this mutation caused a gain of function typical of the Blau syndrome phenotype, manifesting, however, an IBD-like phenotype.

Published
2017

20. Targeted sequencing identifies novel variants involved in autosomal recessive hereditary hearing loss in Qatari families

Author

Giorgia Girotto, Navaneethakrishnan Krishnamoorthy, Ilaria Gandin, Shruti Bhagat, Yousra Hayder, Ramin Badii, Anna Morgan, Diego Vozzi, Nehal Najjar, Khalid Abdulhadi, Paolo Gasparini, Moza Khalifa Alkowari, Barathy W. Logendra, Alkowari, Moza K, Vozzi, Diego, Bhagat, Shruti, Krishnamoorthy, Navaneethakrishnan, Morgan, Anna, Hayder, Yousra, Logendra, Barathy, Najjar, Nehal, Gandin, Ilaria, Gasparini, Paolo, Badii, Ramin, Girotto, Giorgia, and Abdulhadi, Khalid

Subjects
Male, Models, Molecular, 0301 basic medicine, Adolescent, Protein Conformation, Hearing loss, Hearing Loss, Sensorineural, Health, Toxicology and Mutagenesis, Genetic counseling, Population, Cadherin Related Proteins, GPI-Linked Proteins, Connexins, 03 medical and health sciences, Hereditary Hearing Loss, Genetics, OTOF, medicine, Humans, Hereditary Hearing Lo, Allele, Child, education, Molecular Biology, Qatar, Alleles, education.field_of_study, Targeted Sequencing, Myosin Heavy Chains, biology, Genetic heterogeneity, Infant, Membrane Proteins, Sequence Analysis, DNA, Cadherins, Molecular diagnostics, Pedigree, Connexin 26, 030104 developmental biology, Child, Preschool, Mutation, biology.protein, Female, medicine.symptom, GJB6
Abstract

Hereditary hearing loss is characterized by a very high genetic heterogeneity. In the Qatari population the role of GJB2, the worldwide HHL major player, seems to be quite limited compared to Caucasian populations. In this study we analysed 18 Qatari families affected by non-syndromic hearing loss using a targeted sequencing approach that allowed us to analyse 81 genes simultaneously. Thanks to this approach, 50% of these families (9 out of 18) resulted positive for the presence of likely causative alleles in 6 different genes: CDH23, MYO6, GJB6, OTOF, TMC1 and OTOA. In particular, 4 novel alleles were detected while the remaining ones were already described to be associated to HHL in other ethnic groups. Molecular modelling has been used to further investigate the role of novel alleles identified in CDH23 and TMC1 genes demonstrating their crucial role in Ca2+ binding and therefore possible functional role in proteins. Present study showed that an accurate molecular diagnosis based on next generation sequencing technologies might largely improve molecular diagnostics outcome leading to benefits for both genetic counseling and definition of recurrence risk.

Published
2017

21. Alagille Syndrome: A New Missense Mutation Detected by Whole-Exome Sequencing in a Case Previously Found to Be Negative by DHPLC and MLPA

Author

Emmanouil Athanasakis, Paolo Gasparini, Danilo Licastro, Antonella Fabretto, S. Martelossi, Diego Vozzi, Vozzi, D., Licastro, D., Martelossi, S., Athanasakis, E., Gasparini, P., and Fabretto, A.

Subjects
Proband, Genetics, JAG1, education.field_of_study, Population, Case Report, Alagille syndrome, Biology, medicine.disease, Genetic, Whole-exome sequencing, medicine, Missense mutation, Genetics (clinical), Multiplex ligation-dependent probe amplification, education, Haploinsufficiency, Exome sequencing
Abstract

Alagille syndrome (ALGS, MIM 118450) is an autosomal dominant, multisystem disorder with high variability. Two genes have been described: JAG1 and NOTCH2. The population prevalence is 1:70,000 based on the presence of neonatal liver disease. The majority of cases (∼97%) are caused by haploinsufficiency of the JAG1 gene on 20p11.2p12, either due to mutations or deletions at the locus. Less than 1% of cases are caused by mutations in NOTCH2. The most widely used methods for mutational screening include denaturing high-performance liquid chromatography (DHPLC) and multiplex ligation-dependent probe amplification (MLPA). Very recently, whole-exome sequencing (WES) has become technically feasible due to the recent advances in next-generation sequencing technologies, therefore offering new opportunities for mutations/genes identification. A proband and its family, negative for the presence of mutations in JAG1 and NOTCH2 genes by neither DHPLC nor MLPA, were analyzed by WES. A missense mutation, not previously described, in JAG1 gene was identified. This result shows an improvement in the mutation detection rate due to novel sequencing technology suggesting the strong need to reanalyze all negative cases.

Published
2013

22. Genetic variants linked to education predict longevity

Author

Chris Power, Gail Davies, Ilaria Gandin, Panagiotis Deloukas, Jennifer E. Huffman, Pascal Timshel, Albert V. Smith, A. Kong, Paul Lichtenstein, Joseph K. Pickrell, Philipp Koellinger, P. L. De Jager, Reedik Mägi, G. B. Chen, Neil Pendleton, B. V. Halldórsson, George Dedoussis, Antti-Pekka Sarin, Natalia Pervjakova, Veikko Salomaa, Simona Vaccargiu, Ozren Polasek, K. H. Jöckel, Elisabeth Steinhagen-Thiessen, Y. Milaneschi, Jessica D. Faul, Patricia A. Boyle, Patrik K. E. Magnusson, Igor Rudan, Christopher P. Nelson, Vilmundur Gudnason, John Attia, Jürgen Wellmann, Kristi Läll, Konstantin Strauch, Stuart J. Ritchie, Markus Perola, Nicola Pirastu, Klaus Bønnelykke, Robert Karlsson, R. de Vlaming, Liisa Keltigangas-Jarvinen, Thomas Meitinger, Riccardo E. Marioni, Anu Loukola, Barbera Franke, Reinhold Schmidt, Maël Lebreton, Sven Oskarsson, E. Mihailov, Harm-Jan Westra, David R. Weir, Aldi T. Kraja, Niek Verweij, Peter M. Visscher, Hans-Jörgen Grabe, Johannes H. Brandsma, Mark Adams, R. J. Scott, G. Thorleifsson, Tõnu Esko, Mika Kähönen, Saskia P. Hagenaars, Patrick Turley, Johannes Waage, Peter Lichtner, Dragana Vuckovic, Antonietta Robino, Henry Völzke, Lydia Quaye, C. de Leeuw, Marika Kaakinen, Wei Zhao, Abdel Abdellaoui, Reka Nagy, Pedro Marques-Vidal, Johan G. Eriksson, Alan F. Wright, Andres Metspalu, Lavinia Paternoster, Momoko Horikoshi, Jan A. Staessen, Tarunveer S. Ahluwalia, Tian Liu, Martin Kroh, Aldo Rustichini, Giorgia Girotto, Cristina Venturini, Lili Milani, Jennifer A. Smith, Ginevra Biino, Tessel E. Galesloot, Michael A. Horan, Gerardus A. Meddens, James F. Wilson, Francesco Cucca, Peter Vollenweider, Erika Salvi, P. J. van der Most, Jari Lahti, Campbell A, David Laibson, Andrew Bakshi, Wolfgang Hoffmann, Tomi Mäki-Opas, Andreas J. Forstner, C M van Duijn, Nicholas G. Martin, Jonathan Marten, Ute Bültmann, Olli T. Raitakari, David A. Bennett, A.G. Uitterlinden, J. E. De Neve, Ingrid B. Borecki, WD Hill, Bo Jacobsson, Antti Latvala, Katri Räikkönen, Michael B. Miller, Jonathan P. Beauchamp, S. J. van der Lee, Ilja Demuth, Stavroula Kanoni, Veronique Vitart, Elina Hyppönen, N. Eklund, Francesco P. Cappuccio, Robert F. Krueger, Maria Pina Concas, Jaime Derringer, F. J.A. Van Rooij, Helena Schmidt, Patrick J. F. Groenen, Valur Emilsson, Rico Rueedi, Aysu Okbay, Georg Homuth, Edith Hofer, W. E. R. Ollier, Hannah Campbell, Paolo Gasparini, Mark Alan Fontana, Magnus Johannesson, Seppo Koskinen, Christopher F. Chabris, Jouke-Jan Hottenga, Christine Meisinger, Kari Stefansson, Jun Ding, Tia Sorensen, Brenda W.J.H. Penninx, Michelle N. Meyer, James J. Lee, Diego Vozzi, Gonneke Willemsen, K. Petrovic, Sarah E. Medland, Mary F. Feitosa, Henning Tiemeier, L. J. Launer, William G. Iacono, Massimo Mangino, Tune H. Pers, S. E. Baumeister, Christopher Oldmeadow, Grant W. Montgomery, Marjo-Riitta Järvelin, Jaakko Kaprio, Catharine R. Gale, S.F.W. Meddens, Kevin Thom, Klaus Berger, Pablo V. Gejman, Lude Franke, Gyda Bjornsdottir, Daniel J. Benjamin, Steven F. Lehrer, Krista Fischer, Alan R. Sanders, S. Ulivi, Katharina E. Schraut, Tim D. Spector, Amy Hofman, Matt McGue, Terho Lehtimäki, D. C. Liewald, Hans Bisgaard, L. Eisele, Astanand Jugessur, George Davey Smith, T.B. Harris, A.R. Thurik, Cornelius A. Rietveld, David Schlessinger, Z. Kutalik, David J. Porteous, Lynne J. Hocking, N J Timpson, A. Palotie, Lambertus A. Kiemeney, Ian J. Deary, Sharon L.R. Kardia, Peter K. Joshi, Nilesh J. Samani, Michael A. Province, Börge Schmidt, Richa Gupta, Carmen Amador, Erin B. Ware, Joyce Y. Tung, Ioanna-Panagiota Kalafati, Lars Bertram, Caroline Hayward, P. van der Harst, Penelope A. Lind, Kadri Kaasik, N.A. Furlotte, Sarah E. Harris, B. St Pourcain, Susan M. Ring, Zhihong Zhu, Alexander Teumer, Behrooz Z. Alizadeh, Judith M. Vonk, Blair H. Smith, A Payton, Wouter J. Peyrot, Jacob Gratten, Douglas F. Levinson, C Gieger, Leanne M. Hall, Andrew Heath, Mario Pirastu, Peter Eibich, Nancy L. Pedersen, Ronny Myhre, Antonio Terracciano, David M. Evans, Raymond A. Poot, Uwe Völker, Dorret I. Boomsma, Clemens Baumbach, Unnur Thorsteinsdottir, Ivana Kolcic, Jia-Shu Yang, Dalton Conley, A. A. Vinkhuyzen, Danielle Posthuma, Karl-Oskar Lindgren, Olga Rostapshova, Jonas Bacelis, Daniele Cusi, Yong Qian, Bjarni Gunnarsson, George McMahon, Elizabeth G. Holliday, Pamela A. F. Madden, David A. Hinds, David Cesarini, Jianxin Shi, Najaf Amin, Dale R. Nyholt, Applied Economics, Epidemiology, Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Groningen Research Institute for Asthma and COPD (GRIAC), Aletta Jacobs School of Public Health, Public Health Research (PHR), Stem Cell Aging Leukemia and Lymphoma (SALL), Cardiovascular Centre (CVC), Amsterdam Neuroscience - Complex Trait Genetics, Psychiatry, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, EMGO - Mental health, Complex Trait Genetics, Biological Psychology, Marioni, RE, Ritchie, SJ, Joshi, PK, Hagenaars, SP, Hypponen, E, Benjamin, DJ, Social Science Genetic Association Consortium, Marioni, Re, Ritchie, Sj, Joshi, Pk, Hagenaars, Sp, Okbay, A, Fischer, K, Adams, Mj, Hill, Wd, Davies, G, Nagy, R, Amador, C, Läll, K, Metspalu, A, Liewald, Dc, Campbell, A, Wilson, Jf, Hayward, C, Esko, T, Porteous, Dj, Gale, Cr, Deary, Ij, Beauchamp, Jp, Fontana, Ma, Lee, Jj, Pers, Th, Rietveld, Ca, Turley, P, Chen, Gb, Emilsson, V, Meddens, Sf, Oskarsson, S, Pickrell, Jk, Thom, K, Timshel, P, de Vlaming, R, Abdellaoui, A, Ahluwalia, T, Bacelis, J, Baumbach, C, Bjornsdottir, G, Brandsma, Jh, Concas, MARIA PINA, Derringer, J, Furlotte, Na, Galesloot, Te, Girotto, Giorgia, Gupta, R, Hall, Lm, Harris, Se, Hofer, E, Horikoshi, M, Huffman, Je, Kaasik, K, Kalafati, Ip, Karlsson, R, Kong, A, Lahti, J, van der Lee, Sj, de Leeuw, C, Lind, Pa, Lindgren, Ko, Liu, T, Mangino, M, Marten, J, Mihailov, E, Miller, Mb, van der Most, Pj, Oldmeadow, C, Payton, A, Pervjakova, N, Peyrot, Wj, Qian, Y, Raitakari, O, Rueedi, R, Salvi, E, Schmidt, B, Schraut, Ke, Shi, J, Smith, Av, Poot, Ra, St Pourcain, B, Teumer, A, Thorleifsson, G, Verweij, N, Vuckovic, Dragana, Wellmann, J, Westra, Hj, Yang, J, Zhao, W, Zhu, Z, Alizadeh, Bz, Amin, N, Bakshi, A, Baumeister, Se, Biino, G, Bønnelykke, K, Boyle, Pa, Campbell, H, Cappuccio, Fp, De Neve, Je, Deloukas, P, Demuth, I, Ding, J, Eibich, P, Eisele, L, Eklund, N, Evans, Dm, Faul, Jd, Feitosa, Mf, Forstner, Aj, Gandin, Ilaria, Gunnarsson, B, Halldórsson, Bv, Harris, Tb, Heath, Ac, Hocking, Lj, Holliday, Eg, Homuth, G, Horan, Ma, Hottenga, Jj, de Jager, Pl, Jugessur, A, Kaakinen, Ma, Kähönen, M, Kanoni, S, Keltigangas Järvinen, L, Kiemeney, La, Kolcic, I, Koskinen, S, Kraja, At, Kroh, M, Kutalik, Z, Latvala, A, Launer, Lj, Lebreton, Mp, Levinson, Df, Lichtenstein, P, Lichtner, P, Loukola, A, Madden, Pa, Mägi, R, Mäki Opas, T, Marques Vidal, P, Meddens, Ga, Mcmahon, G, Meisinger, C, Meitinger, T, Milaneschi, Y, Milani, L, Montgomery, Gw, Myhre, R, Nelson, Cp, Nyholt, Dr, Ollier, We, Palotie, A, Paternoster, L, Pedersen, Nl, Petrovic, Ke, Räikkönen, K, Ring, Sm, Robino, Antonietta, Rostapshova, O, Rudan, I, Rustichini, A, Salomaa, V, Sanders, Ar, Sarin, Ap, Schmidt, H, Scott, Rj, Smith, Bh, Smith, Ja, Staessen, Ja, Steinhagen Thiessen, E, Strauch, K, Terracciano, A, Tobin, Md, Ulivi, Sheila, Vaccargiu, S, Quaye, L, van Rooij, Fj, Venturini, C, Vinkhuyzen, Aa, Völker, U, Völzke, H, Vonk, Jm, Vozzi, Diego, Waage, J, Ware, Eb, Willemsen, G, Attia, Jr, Bennett, Da, Berger, K, Bertram, L, Bisgaard, H, Boomsma, Di, Borecki, Ib, Bultmann, U, Chabris, Cf, Cucca, F, Cusi, D, Dedoussis, Gv, van Duijn, Cm, Eriksson, Jg, Franke, B, Franke, L, Gasparini, Paolo, Gejman, Pv, Gieger, C, Grabe, Hj, Gratten, J, Groenen, Pj, Gudnason, V, van der Harst, P, Hinds, Da, Hoffmann, W, Iacono, Wg, Jacobsson, B, Järvelin, Mr, Jöckel, Kh, Kaprio, J, Kardia, Sl, Lehtimäki, T, Lehrer, Sf, Magnusson, Pk, Martin, Ng, Mcgue, M, Pendleton, N, Penninx, Bw, Perola, M, Pirastu, Nicola, Pirastu, M, Polasek, O, Posthuma, D, Power, C, Province, Ma, Samani, Nj, Schlessinger, D, Schmidt, R, Sørensen, Ti, Spector, Td, Stefansson, K, Thorsteinsdottir, U, Thurik, Ar, Timpson, Nj, Tiemeier, H, Tung, Jy, Uitterlinden, Ag, Vitart, V, Vollenweider, P, Weir, Dr, Wright, Af, Conley, Dc, Krueger, Rf, Smith, Gd, Hofman, A, Laibson, Di, Medland, Se, Meyer, Mn, Johannesson, M, Visscher, Pm, Koellinger, Pd, Cesarini, D, and Benjamin, Dj

Subjects
Netherlands Twin Register (NTR), 0301 basic medicine, Male, Parents, education: longevity: prediction: polygenic score [genetics], Multifactorial Inheritance, polygenic, Lebenserwartung, Cohort Studies, 0302 clinical medicine, Databases, Genetic, Medicine, genetics, polygenic score, longevity, education, gene, Soziales und Gesundheit, media_common, Aged, 80 and over, education, Multidisciplinary, Longevity, Middle Aged, Biobank, humanities, 3. Good health, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], Cohort, Educational Status, Female, Cohort study, Estonia, education, longevity, polygenic, Offspring, media_common.quotation_subject, Kultursektor, Prognose, Lernen, Lower risk, Education, 03 medical and health sciences, longevity, SDG 3 - Good Health and Well-being, Commentaries, Polygenic score, Journal Article, Genetics, Humans, Non-Profit-Sektor, Genetic Association Studies, Aged, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], business.industry, ta1184, Genetic Variation, prediction, Educational attainment, United Kingdom, Gesundheitsstatistik, 030104 developmental biology, Genetic epidemiology, Scotland, Gesundheitszustand, Genetische Forschung, business, Prediction, Bildung, 030217 neurology & neurosurgery, Demography
Abstract

Educational attainment is associated with many health outcomes, including longevity. It is also known to be substantially heritable. Here, we used data from three large genetic epidemiology cohort studies (Generation Scotland, n = ∼17,000; UK Biobank, n = ∼115,000; and the Estonian Biobank, n = ∼6,000) to test whether education-linked genetic variants can predict lifespan length. We did so by using cohort members' polygenic profile score for education to predict their parents' longevity. Across the three cohorts, meta-analysis showed that a 1 SD higher polygenic education score was associated with ∼2.7% lower mortality risk for both mothers (total n deaths = 79,702) and ∼2.4% lower risk for fathers (total n deaths = 97,630). On average, the parents of offspring in the upper third of the polygenic score distribution lived 0.55 y longer compared with those of offspring in the lower third. Overall, these results indicate that the genetic contributions to educational attainment are useful in the prediction of human longevity. Marioni RE, Ritchie SJ, Joshi PK, Hagenaars SP, Okbay A, Fischer K, Adams MJ, Hill WD, Davies G, Social Science Genetic Association Consortium, Nagy R, Amador C, Läll K, Metspalu A, Liewald DC, Campbell A, Wilson JF, Hayward C, Esko T, Porteous DJ, Proceedings of the National Academy of Sciences of the United States of America, 2016, vol. 113, no. 47, pp. 13366-13371, 2016 Refereed/Peer-reviewed

Published
2016

23. Genome-wide association study identifies 74 loci associated with educational attainment

Author

K. Petrovic, Massimo Mangino, Daniele Cusi, Ozren Polasek, Rodney J. Scott, Yong Qian, Aysu Okbay, Jari Lahti, Bjarni Gunnarsson, George McMahon, Elizabeth G. Holliday, Thomas Meitinger, Frank J. A. van Rooij, Mika Kähönen, Martin Kroh, Ian J. Deary, Neil Pendleton, Pamela A. F. Madden, David J. Porteous, Lambertus A. Kiemeney, Sven Oskarsson, Edith Hofer, Robert F. Krueger, Olga Rostapshova, Georg Homuth, Paolo Gasparini, Aldo Rustichini, Sarah E. Medland, Christian Gieger, Veronique Vitart, Nicholas J. Timpson, George Dedoussis, Joseph K. Pickrell, Christopher Oldmeadow, Aldi T. Kraja, Johan G. Eriksson, Lydia Quaye, William G. Iacono, Danielle Posthuma, George Davey Smith, Karl-Oskar Lindgren, David C. Liewald, Pim van der Harst, Börge Schmidt, Christine Power, Francesco P. Cappuccio, Francesco Cucca, Simona Vaccargiu, Joyce Y. Tung, Aarno Palotie, Natalia Pervjakova, Jonas Bacelis, Jouke-Jan Hottenga, Helena Schmidt, Kari Stefansson, Tamara B. Harris, Momoko Horikoshi, Lude Franke, Wolfgang Hoffmann, Ingrid B. Borecki, William E R Ollier, Johannes Waage, Andreas J. Forstner, Caroline Hayward, Penelope A. Lind, Patricia A. Boyle, Kadri Kaasik, Jian Yang, Gerardus A. Meddens, Antti Latvala, John Attia, Pascal Timshel, Vilmundur Gudnason, Maël Lebreton, Valur Emilsson, James F. Wilson, Jonathan Marten, Ute Bültmann, Erika Salvi, Olli T. Raitakari, Peter M. Visscher, Niek Verweij, Elisabeth Steinhagen-Thiessen, Cristina Venturini, Lili Milani, Tessel E. Galesloot, Kevin Thom, Klaus Berger, Paul Lichtenstein, Tian Liu, Philipp Koellinger, Riccardo E. Marioni, Marjo-Riitta Järvelin, Clemens Baumbach, Unnur Thorsteinsdottir, Magnus Johannesson, Susan M. Ring, David A. Bennett, Anu Loukola, Hans-Jörgen Grabe, Jan A. Staessen, Igor Rudan, Ginevra Biino, Nicholas G. Martin, Jingyun Yang, Anna A. E. Vinkhuyzen, Katri Räikkönen, Zhihong Zhu, Gudmar Thorleifsson, Mary F. Feitosa, Ivana Kolcic, Alexander Teumer, Jaakko Kaprio, David Schlessinger, Katharina E. Schraut, Konstantin Strauch, Ilja Demuth, Albert V. Smith, Juergen Wellmann, Jennifer E. Huffman, Panos Deloukas, Mario Pirastu, Reedik Mägi, Maria Pina Concas, Jaime Derringer, Patrick J. F. Groenen, Henry Völzke, Wei Zhao, Abdel Abdellaoui, Andres Metspalu, Nicholas A. Furlotte, Christopher P. Nelson, Barbara Franke, Steven F. Lehrer, Patrick Turley, Tõnu Esko, Jun Ding, Pedro Marques-Vidal, S. Fleur W. Meddens, Zoltán Kutalik, Gonneke Willemsen, Andrew C. Heath, Michelle N. Meyer, James J. Lee, Roy Thurik, Antonietta Robino, Henning Tiemeier, Grant W. Montgomery, C. deLeeuw, Astanand Jugessur, Antti-Pekka Sarin, Veikko Salomaa, Dalton Conley, Tim D. Spector, Sebastian E. Baumeister, Gyda Bjornsdottir, Lavinia Paternoster, Tune H. Pers, Jacob Gratten, Martin D. Tobin, Daniel J. Benjamin, Douglas F. Levinson, Stavroula Kanoni, Elina Hyppönen, David R. Weir, Peter J. van der Most, Terho Lehtimäki, David A. Hinds, Pablo V. Gejman, Uwe Völker, Cornelia M. van Duijn, Karl-Heinz Jöckel, Bjarni V. Halldorsson, Markus Perola, Nicola Pirastu, Klaus Bønnelykke, Robert Karlsson, David Cesarini, Michael A. Province, Jianxin Shi, Najaf Amin, Dale R. Nyholt, Lenore J. Launer, Nilesh J. Samani, Sven J. van der Lee, Dorret I. Boomsma, Harry Campbell, Peter Vollenweider, Liisa Keltigangas-Jarvinen, David Laibson, Ronald de Vlaming, Lynne J. Hocking, Christopher F. Chabris, Blair H. Smith, Gail Davies, Niina Eklund, Ioanna P. Kalafati, Bo Jacobsson, Sheila Ulivi, Alan F. Wright, Sarah E. Harris, Mark Alan Fontana, Diego Vozzi, Tomi Mäki-Opas, Albert Hofman, Hans Bisgaard, Andrew Bakshi, Marika Kaakinen, Johannes H. Brandsma, Christa Meisinger, Ilaria Gandin, Tarunveer S. Ahluwalia, Jennifer A. Smith, Beate St Pourcain, Rico Rueedi, Lewin Eisele, Michael B. Miller, Brenda W.J.H. Penninx, Alan R. Sanders, Thorkild I. A. Sørensen, André G. Uitterlinden, Cornelius A. Rietveld, Peter Lichtner, Dragana Vuckovic, Giorgia Girotto, Behrooz Z. Alizadeh, Reinhold Schmidt, Raymond A. Poot, Judith M. Vonk, Antony Payton, Wouter J. Peyrot, Augustine Kong, Y. Milaneschi, Jessica D. Faul, Patrik K. E. Magnusson, Antonio Terracciano, David M. Evans, Sharon L.R. Kardia, Peter K. Joshi, Michael A. Horan, Matt McGue, Richa Gupta, Jonathan P. Beauchamp, Peter Eibich, Erin B. Ware, Lars Bertram, Philip L. De Jager, Nancy L. Pedersen, Ronny Myhre, Guo-Bo Chen, Harm-Jan Westra, Jan-Emmanuel De Neve, Evelin Mihailov, Leanne M. Hall, Seppo Koskinen, Rush University Medical Center [Chicago], Department of Epidemiology [Rotterdam], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Helmholtz-Zentrum München (HZM), University of Queensland [Brisbane], Erasmus University Rotterdam, Universidad de Navarra [Pamplona] (UNAV), National Institute for Health and Welfare [Helsinki], Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Consiglio Nazionale delle Ricerche (CNR), Montpellier Research in Management (MRM), Université Paul-Valéry - Montpellier 3 (UPVM)-Université de Perpignan Via Domitia (UPVD)-Groupe Sup de Co Montpellier (GSCM) - Montpellier Business School-Université de Montpellier (UM), University of Bristol [Bristol], Queensland Institute of Medical Research, Massachusetts General Hospital [Boston], Medical University Graz, Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), King‘s College London, Tampere University Hospital, University of Turku, AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Edinburgh, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Imperial College London, Reykjavík University, Donders Institute for Brain, Cognition and Behaviour, Radboud university [Nijmegen], Karolinska Institutet [Stockholm], Department of Health Sciences [Leicester], University of Leicester, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Department of Medical Epidemiology and Biostatistics (MEB), Dpt of Pharmacology and Personalised Medicine [Maastricht], Maastricht University [Maastricht], Florida State University [Tallahassee] (FSU), IT University of Copenhagen, University of Helsinki-University of Helsinki, Université Montpellier 1 (UM1)-Groupe Sup de Co Montpellier (GSCM) - Montpellier Business School-Université Paul-Valéry - Montpellier 3 (UPVM)-Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Perpignan Via Domitia (UPVD), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Université Sciences et Technologies - Bordeaux 1-Université Montesquieu - Bordeaux 4-Institut de Chimie du CNRS (INC), Faculteit Economie en Bedrijfskunde, Microeconomics (ASE, FEB), LifeLines Cohort Study, Alizadeh, BZ., de Boer, RA., Boezen, HM., Bruinenberg, M., Franke, L., van der Harst, P., Hillege, HL., van der Klauw, MM., Navis, G., Ormel, J., Postma, DS., Rosmalen, JG., Slaets, JP., Snieder, H., Stolk, RP., Wolffenbuttel, BH., Wijmenga, C., Applied Economics, Cell biology, Epidemiology, Erasmus MC other, Econometrics, Child and Adolescent Psychiatry / Psychology, Psychiatry, Internal Medicine, EMGO+ - Mental Health, Complex Trait Genetics, Biological Psychology, Functional Genomics, Economics, Amsterdam Neuroscience - Complex Trait Genetics, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Groningen Research Institute for Asthma and COPD (GRIAC), Public Health Research (PHR), Cardiovascular Centre (CVC), Life Course Epidemiology (LCE), Stem Cell Aging Leukemia and Lymphoma (SALL), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), Okbay, Aysu, Beauchamp, Jonathan P., Fontana, Mark Alan, Lee, James J., Pers, Tune H., Rietveld, Cornelius A., Turley, Patrick, Chen, Guo Bo, Emilsson, Valur, Meddens, S. Fleur W., Oskarsson, Sven, Pickrell, Joseph K., Thom, Kevin, Timshel, Pascal, De Vlaming, Ronald, Abdellaoui, Abdel, Ahluwalia, Tarunveer S., Bacelis, Jona, Baumbach, Clemen, Bjornsdottir, Gyda, Brandsma, Johannes H., Concas, MARIA PINA, Derringer, Jaime, Furlotte, Nicholas A., Galesloot, Tessel E., Girotto, Giorgia, Gupta, Richa, Hall, Leanne M., Harris, Sarah E., Hofer, Edith, Horikoshi, Momoko, Huffman, Jennifer E., Kaasik, Kadri, Kalafati, Ioanna P., Karlsson, Robert, Kong, Augustine, Lahti, Jari, Van Der Lee, Sven J., Deleeuw, Christiaan, Lind, Penelope A., Lindgren, Karl Oskar, Liu, Tian, Mangino, Massimo, Marten, Jonathan, Mihailov, Evelin, Miller, Michael B., Van Der Most, Peter J., Oldmeadow, Christopher, Payton, Antony, Pervjakova, Natalia, Peyrot, Wouter J., Qian, Yong, Raitakari, Olli, Rueedi, Rico, Salvi, Erika, Schmidt, Börge, Schraut, Katharina E., Shi, Jianxin, Smith, Albert V., Poot, Raymond A., St Pourcain, Beate, Teumer, Alexander, Thorleifsson, Gudmar, Verweij, Niek, Vuckovic, Dragana, Wellmann, Juergen, Westra, Harm Jan, Yang, Jingyun, Zhao, Wei, Zhu, Zhihong, Alizadeh, Behrooz Z., Amin, Najaf, Bakshi, Andrew, Baumeister, Sebastian E., Biino, Ginevra, Bønnelykke, Klau, Boyle, Patricia A., Campbell, Harry, Cappuccio, Francesco P., Davies, Gail, De Neve, Jan Emmanuel, Deloukas, Pano, Demuth, Ilja, Ding, Jun, Eibich, Peter, Eisele, Lewin, Eklund, Niina, Evans, David M., Faul, Jessica D., Feitosa, Mary F., Forstner, Andreas J., Gandin, Ilaria, Gunnarsson, Bjarni, Halldórsson, Bjarni V., Harris, Tamara B., Holliday, Elizabeth G., Heath, Andrew C., Hocking, Lynne J., Homuth, Georg, Horan, Michael A., Hottenga, Jouke Jan, De Jager, Philip L., Joshi, Peter K., Jugessur, Astanand, Kaakinen, Marika A., Kähönen, Mika, Kanoni, Stavroula, Keltigangas Järvinen, Liisa, Kiemeney, Lambertus A. L. M., Kolcic, Ivana, Koskinen, Seppo, Kraja, Aldi T., Kroh, Martin, Kutalik, Zoltan, Latvala, Antti, Launer, Lenore J., Lebreton, Maël P., Levinson, Douglas F., Lichtenstein, Paul, Lichtner, Peter, Liewald, David C. M., Loukola, Anu, Madden, Pamela A., Mägi, Reedik, Mäki Opas, Tomi, Marioni, Riccardo E., Marques Vidal, Pedro, Meddens, Gerardus A., Mcmahon, George, Meisinger, Christa, Meitinger, Thoma, Milaneschi, Yusplitri, Milani, Lili, Montgomery, Grant W., Myhre, Ronny, Nelson, Christopher P., Nyholt, Dale R., Ollier, William E. R., Palotie, Aarno, Paternoster, Lavinia, Pedersen, Nancy L., Petrovic, Katja E., Porteous, David J., Raïkkönen, Katri, Ring, Susan M., Robino, Antonietta, Rostapshova, Olga, Rudan, Igor, Rustichini, Aldo, Salomaa, Veikko, Sanders, Alan R., Sarin, Antti Pekka, Schmidt, Helena, Scott, Rodney J., Smith, Blair H., Smith, Jennifer A., Staessen, Jan A., Steinhagen Thiessen, Elisabeth, Strauch, Konstantin, Terracciano, Antonio, Tobin, Martin D., Ulivi, Sheila, Vaccargiu, Simona, Quaye, Lydia, Van Rooij, Frank J. A., Venturini, Cristina, Vinkhuyzen, Anna A. E., Völker, Uwe, Völzke, Henry, Vonk, Judith M., Vozzi, Diego, Waage, Johanne, Ware, Erin B., Willemsen, Gonneke, Attia, John R., Bennett, David A., Berger, Klau, Bertram, Lar, Bisgaard, Han, Boomsma, Dorret I., Borecki, Ingrid B., Bültmann, Ute, Chabris, Christopher F., Cucca, Francesco, Cusi, Daniele, Deary, Ian J., Dedoussis, George V., Van Duijn, Cornelia M., Eriksson, Johan G., Franke, Barbara, Franke, Lude, Gasparini, Paolo, Gejman, Pablo V., Gieger, Christian, Grabe, Hans Jörgen, Gratten, Jacob, Groenen, Patrick J. F., Gudnason, Vilmundur, Van Der Harst, Pim, Hayward, Caroline, Hinds, David A., Hoffmann, Wolfgang, Hyppönen, Elina, Iacono, William G., Jacobsson, Bo, Järvelin, Marjo Riitta, Jöckel, Karl Heinz, Kaprio, Jaakko, Kardia, Sharon L. R., Lehtimäki, Terho, Lehrer, Steven F., Magnusson, Patrik K. E., Martin, Nicholas G., Mcgue, Matt, Metspalu, Andre, Pendleton, Neil, Penninx, Brenda W. J. H., Perola, Marku, Pirastu, Nicola, Pirastu, Mario, Polasek, Ozren, Posthuma, Danielle, Power, Christine, Province, Michael A., Samani, Nilesh J., Schlessinger, David, Schmidt, Reinhold, Sørensen, Thorkild I. A., Spector, Tim D., Stefansson, Kari, Thorsteinsdottir, Unnur, Thurik, A. Roy, Timpson, Nicholas J., Tiemeier, Henning, Tung, Joyce Y., Uitterlinden, André G., Vitart, Veronique, Vollenweider, Peter, Weir, David R., Wilson, James F., Wright, Alan F., Conley, Dalton C., Krueger, Robert F., Davey Smith, George, Hofman, Albert, Laibson, David I., Medland, Sarah E., Meyer, Michelle N., Yang, Jian, Johannesson, Magnu, Visscher, Peter M., Esko, Toñu, Koellinger, Philipp D., Cesarini, David, Benjamin, Daniel J., EMGO - Mental health, IOO, Human genetics, Beauchamp, Jonathan P, Lee, James JJ, Hypponen, Elina, and Benjamin, Daniel J

Subjects
0301 basic medicine, Netherlands Twin Register (NTR), Candidate gene, Bipolar Disorder, Medizin, Genome-wide association study, Genome-wide association studies, 0302 clinical medicine, Cognition, Alzheimer Disease, Brain, Computational Biology, Fetus, Gene Expression Regulation, Gene-Environment Interaction, Great Britain, Humans, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Schizophrenia, Educational Status, Genome-Wide Association Study, Medicine (all), Multidisciplinary, Fetu, tau, Gene–environment interaction, Soziales und Gesundheit, Genetics, [QFIN]Quantitative Finance [q-fin], HERITABILITY, General Commentary, Alzheimer's disease, Biobank, Phenotype, Multidisciplinary Sciences, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], educational attainment, Behavioural genetics, Science & Technology - Other Topics, Bildungsniveau, TRAITS, Human, General Science & Technology, Kultursektor, SNP, ta3111, Polymorphism, Single Nucleotide, Learning and memory, Alzheimer Disease/genetics, Bipolar Disorder/genetics, Brain/metabolism, Fetus/metabolism, Gene Expression Regulation/genetics, Polymorphism, Single Nucleotide/genetics, Schizophrenia/genetics, 03 medical and health sciences, ACHIEVEMENT, MD Multidisciplinary, Non-Profit-Sektor, QH426, Science & Technology, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], tauopathies, Data Science, gene, education, school, Heritability, Educational Statu, Educational attainment, United Kingdom, 030104 developmental biology, IQ, Genetische Forschung, Psychiatric disorders, Bildung, 030217 neurology & neurosurgery, LifeLines Cohort Study, Neuroscience
Abstract

Contains fulltext : 167137.pdf (Publisher’s version ) (Closed access) Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.

Published
2016
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24. Targeted Next-Generation Sequencing for Molecular Diagnosis of Non-Syndromic Hearing Loss in Qatar

Author

Ajayeb Dakhilalla M H Al-Nabet, Barathy Logendra, Ramin Badii, Shruti Bhagat, Moza Khalifa Alkowari, Diego Vozzi, Khaled Abdulhadi, Anna Morgan, Giorgia Girotto, and Paolo Gasparini

Subjects
Sanger sequencing, education.field_of_study, dbSNP, business.industry, Population, Genomics, Computational biology, Bioinformatics, DNA sequencing, symbols.namesake, symbols, Medicine, 1000 Genomes Project, business, education, Exome sequencing, Personal genomics
Abstract

BackgroundSequencing technologies have grown exponentially in recent years resulting in next-generation sequencing (NGS) platforms which are more efficient in terms of biochemistry, time and cost. NGS is particularly applicable to highly heterogeneous diseases such as non-syndromic hearing loss (NSHL). Currently, more than 80 genes are clinically relevant and are known to cause hearing loss in humans (Vona B et al., 2015); however, there are about 129 disease associated loci (Vona B et al., 2014).AimsThe aim of this study is to introduce a molecular diagnostic test in Hamad Medical Corporation, Qatar, using a targeted custom made 80 gene panel on Ion Personal Genome Machine® (PGM™, Thermo Fisher Scientific, USA), in order to obtain rapid and accurate NGS results in compliance with guidelines of the College of American Pathologists (CAP) and the European Molecular Genetics Quality Network.MethodsWhole blood samples from 91 Qatari individuals (representing 31 unrelated families) that were received by the Molecular Genetics Laboratory for molecular diagnostic purposes since February 2009 were used in this study. DNA was extracted using the Promega Maxwell® 16 Blood DNA purification kit. Libraries were prepared using the Ion AmpliSeq™ Library kit with 200bp chemistry, amplified using emulsion PCR on the Ion OneTouch™ 2 system and enriched using the Ion One Touch™ ES system. Four barcoded libraries (i.e. 4 individuals) were sequenced in parallel on the Ion™ 318 v2 chip using the Ion PGM™. Base calling, signal processing and variant calling were performed using the Torrent Suite™ software. All variants were checked with the Ion Reporter™software and Intergrative Genomics Viewer (IGV, Broad institute) and in silico analysis was done using databases such as ClinVar, dbSNP, 1000 genomes browser, Deafness Variation Database, PolyPhen, SIFT, Human Splicing Finder and MutationTaster. All variants are being confirmed using Sanger sequencing which remains as the gold standard.ResultsWe have sequenced 91 affected and unaffected Qatari individuals from 31 unrelated families using the 80 gene panel on the Ion PGM™. On average, 4.1 million on target reads were generated per run with a mean depth of 270 and with mean coverage of 95% at 20X and 90% at 100X. On average about 325 variants were detected per individual. Causative variant(s) were identified based on factors such as pathogenicity or clinical relevance of the variant, minor allele frequency, coverage, quality and variant segregation within the family. The study has identified key players within the Qatari population such as TECTA, CDH23, OTOF, TMC1, TRIOBP and WFS1, with about 65% of the genes resulting in an autosomal recessive mode of inheritance and 35% being autosomal dominant. All missense mutations, including premature stop codon mutations, were covered at >100x whereas indels ranging from 2 to 78 bp were covered at >50x, in line with CAP guidelines. Furthermore, reproducibility of the results was checked by repeat sequencing of individuals at random resulting in up to 97% similarity between the runs. So far we have been able to detect causative mutation(s) in approx. 85% of the cases using the custom panel. For the remaining 15% of the families targeted resequencing and whole exome sequencing were performed in order to determine a genetic cause.ConclusionIdentification of disease causing variants for diagnosis of heterogenic disorders such as NSHL is challenging and laborious with traditional sequencing technologies. The advent of targeted NGS in molecular diagnostics has reformed the field, providing clinically significant information in a time and cost efficient manner. Our 80-gene custom panel for NSHL on the Ion PGM™ has proved to be a powerful diagnostic tool offering accurate results which is essential for genetic counselling of patients and their family members.

Published
2016

25. One-shot genetic analysis in monolithic Silicon/Pyrex microdevices

Author

D. Sonn, O. Rossotto, Diego Vozzi, R. Dallapiccola, Laura Pasquardini, Cristina Potrich, Cecilia Pederzolli, Ivan Ferrante, Lorenzo Lunelli, and L. Marocchi

Subjects
Silicon, Erythrocytes, Materials science, Passivation, DNA purification, Biomedical Engineering, chemistry.chemical_element, Nanotechnology, Polymerase Chain Reaction, chemistry.chemical_compound, LOC, Lab-On-A-Chip Devices, Humans, Molecular Biology, Chitosan, Microchannel, Propylamines, Genome, Human, Elution, Silicon microchip, DNA, Equipment Design, Microfluidic Analytical Techniques, Silanes, DNA extraction, genomic DNA, PCR, chemistry, Nanoparticles, Magnetic nanoparticles
Abstract

Modern Lab-on-a-chip (LOC) platforms for genomic applications integrate several biological tasks in a single device. Combination of these processes into a single device minimizes sample loss and contamination problems as well as reducing analysis time and costs. Here we present a study of a microchip platform aimed at analyzing issues arising from the combination of different functions, such as DNA purification from blood, target amplification by PCR and DNA detection in a single silicon-based device. DNA purification is realized through two different strategies: 1) amine groups coating microchannel surfaces and 2) magnetic nanoparticles coated by chitosan. In the first strategy silicon/Pyrex microdevices coated with 3-aminopropyltriethoxysilane (APTES) or 3-2-(2-aminoethylamino)-ethylamino]-propyltrimethoxysilane (AEEA) were examined and their efficiency in human genomic DNA adsorption/desorption was evaluated. APTES treatment was the most suitable for the purification of a reasonable amount of DNA in a state suitable for the following PCR step. The second strategy has instead the main advantage of avoiding an elution step, since the DNA adsorbed on the magnetic nanoparticles can be used as PCR template. On-chip PCR was performed in a custom thermocycler, while the detection of PCR products was carried out by fluorescence reading. A complete genetic analysis was demonstrated on the monolithic silicon/Pyrex microchip, starting from less than 1 [Formula: see text]L of human whole blood and arriving at SNPs identification. The successful integration of DNA purification, amplification and detection on a single microdevice was proven without the need for biological passivation steps and possibly simplifying the realization of genomic detection devices.

Published
2012

26. PSIP1/LEDGF: a new gene likely involved in sensorineural progressive hearing loss

Author

Diego Vozzi, Enrico Muzzi, Mariateresa Di Stazio, Deborah I. Scheffer, Anna Morgan, Stefano Pensiero, Anne Giersch, Elisa Rubinato, David P. Corey, Paolo Gasparini, Giorgia Girotto, Girotto, Giorgia, Scheffer, Déborah I., Morgan, Anna, Vozzi, Diego, Rubinato, Elisa, DI STAZIO, Mariateresa, Muzzi, Enrico, Pensiero, Stefano, Giersch, Anne B., Corey, David P., and Gasparini, Paolo

Subjects
Male, 0301 basic medicine, Candidate gene, RNA Stability, DNA Mutational Analysis, Deafness, medicine.disease_cause, Mice, Exome, Frameshift Mutation, Exome sequencing, Genetics, Mutation, Multidisciplinary, Pedigree, medicine.anatomical_structure, WES, Female, medicine.symptom, Adult, Adolescent, Hearing loss, Hearing Loss, Sensorineural, Molecular Sequence Data, Biology, Article, Frameshift mutation, Young Adult, 03 medical and health sciences, medicine, Animals, Humans, Family, Genetic Predisposition to Disease, Inner ear, Amino Acid Sequence, RNA, Messenger, Deafne, Gene, Adaptor Proteins, Signal Transducing, Base Sequence, Sequence Analysis, RNA, PSIP1/LEDGF, 030104 developmental biology, Gene Expression Regulation, Ear, Inner, sense organs, Transcription Factors
Abstract

Hereditary Hearing Loss (HHL) is an extremely heterogeneous disorder. Approximately 30 out of 80 known HHL genes are associated with autosomal dominant forms. Here, we identified PSIP1/LEDGF (isoform p75) as a novel strong candidate gene involved in dominant HHL. Using exome sequencing we found a frameshift deletion (c.1554_1555del leading to p.E518Dfs*2) in an Italian pedigree affected by sensorineural mild-to-moderate HHL but also showing a variable eye phenotype (i.e. uveitis, optic neuropathy). This deletion led to a premature stop codon (p.T519X) with truncation of the last 12 amino acids. PSIP1 was recently described as a transcriptional co-activator regulated by miR-135b in vestibular hair cells of the mouse inner ear as well as a possible protector against photoreceptor degeneration. Here, we demonstrate that it is ubiquitously expressed in the mouse inner ear. The PSIP1 mutation is associated with a peculiar audiometric slope toward the high frequencies. These findings indicate that PSIP1 likely plays an important role in HHL.

Published
2015

27. Altered germinal center reaction and abnormal B cell peripheral maturation in PI3KR1-mutated patients presenting with HIGM-like phenotype

Author

Silvia Giliani, Vassilios Lougaris, Anna Monica Bianco, Antonino Trizzino, Annalisa Marcuzzi, Fabio Facchetti, Daniele Moratto, Anders Fasth, Filippo Salvini, Erica Valencic, Manuela Baronio, Martina Girardelli, Alessandro Plebani, Elisa Piscianz, Gaetana Lanzi, Flavio Faletra, Alberto Tommasini, Diego Vozzi, Claudia Loganes, Lougaris, Vassilio, Faletra, Flavio, Lanzi, Gaetana, Vozzi, Diego, Marcuzzi, Annalisa, Valencic, Erica, Piscianz, Elisa, Bianco, ANNA MONICA ROSARIA, Girardelli, Martina, Baronio, Manuela, Loganes, Claudia, Fasth, Ander, Salvini, Filippo, Trizzino, Antonino, Moratto, Daniele, Facchetti, Fabio, Giliani, Silvia, Plebani, Alessandro, and Tommasini, Alberto

Subjects
Male, Hyper IgM syndrome, Hyper-IgM Immunodeficiency Syndrome, Immunology, Germinal Center (GC) reaction, Biology, medicine.disease_cause, NO, B cells, Hyper-IgM syndrome, PIK3R1, B-Lymphocytes, Child, Preschool, Female, Germinal Center, Humans, Infant, Mutation, Phenotype, Phosphatidylinositol 3-Kinases, RNA Splice Sites, Sequence Analysis, DNA, Immunology and Allergy, Child, Preschool, Sequence Analysis, DNA, medicine, B cell, B-Lymphocyte, Germinal center, medicine.disease, Peripheral, Class Ia Phosphatidylinositol 3-Kinase, medicine.anatomical_structure, RNA Splice Site, Phosphatidylinositol 3-Kinase, Human
Published
2015

28. 43rd European Mathematical Genetics Meeting (EMGM) 2015. April 16-17, 2015, Brest, France: Abstracts

Author

Priyanka Nandakumar, Giorgia Girotto, Steven C. Hunt, Paolo Gasparini, Aravinda Chakravarti, Weili Li, Nuo Cheng, Khanh-Dung H. Nguyen, Moza Khalifa Alkowari, Lisa J. Strug, Richard S. Houlston, Françoise Clerget-Darpoux, Khalid Abdulhadi, Deb K. Pal, Emmanuelle Génin, Ian Tomlinson, Druckerei Stückle, Victor G. Davila-Roman, Yun Ju Sung, Diego Vozzi, Dabeeru C. Rao, Ramin Badii, Massimo Mezzavilla, Sara E. Dobbins, Donna K. Arnett, Satz Mengensatzproduktion, and Jacob Basson

Subjects
History, Genetics, Physiology, Library science, Genetics (clinical)
Published
2015

29. Putative modifier genes in mevalonate kinase deficiency

Author

Paola Maura Tricarico, Sergio Crovella, Martina Girardelli, Elisa Piscianz, Alessandra Knowles, Anna Monica Bianco, Josef Vuch, Annalisa Marcuzzi, Alberto Tommasini, Diego Vozzi, Marcuzzi, Annalisa, Vozzi, Diego, Girardelli, Martina, Tricarico, PAOLA MAURA, Knowles, Alessandra, Crovella, Sergio, Vuch, Josef, Tommasini, Alberto, Piscianz, Elisa, and Bianco, ANNA MONICA ROSARIA

Subjects
0301 basic medicine, Male, Cancer Research, Gene, Biochemistry, Polymerase Chain Reaction, whole exome sequencing, chemistry.chemical_compound, 0302 clinical medicine, INDEL Mutation, Mevalonate kinase deficiency, Missense mutation, orphan disease, correlation genotype-phenotype, Exome sequencing, Regulator gene, Genetics, B-Lymphocytes, High-Throughput Nucleotide Sequencing, Exons, Phenotype, Oncology, Molecular Medicine, Female, Mevalonate pathway, Genotype, Mevalonic Acid, Mevalonic acid, Biology, NO, 03 medical and health sciences, Genetic, Correlation genotype-phenotype, Orphan disease, Whole exome sequencing, Molecular Biology, medicine, Humans, gene, correlation genotype-phenotype, orphan disease, mevalonate kinase deficiency, whole exome sequencing, gene, Uracil-DNA Glycosidase, Membrane Proteins, Sequence Analysis, DNA, medicine.disease, 030104 developmental biology, chemistry, Mevalonate Kinase Deficiency, 030217 neurology & neurosurgery
Abstract

Mevalonate kinase deficiency (MKD) is an autosomal recessive auto‑inflammatory disease, caused by impairment of the mevalonate pathway. Although the molecular mechanism remains to be elucidated, there is clinical evidence suggesting that other regulatory genes may be involved in determining the phenotype. The identification of novel target genes may explain non‑homogeneous genotype‑phenotype correlations, and provide evidence in support of the hypothesis that novel regulatory genes predispose or amplify deregulation of the mevalonate pathway in this orphan disease. In the present study, DNA samples were obtained from five patients with MKD, which were then analyzed using whole exome sequencing. A missense variation in the PEX11γ gene was observed in homozygosis in P2, possibly correlating with visual blurring. The UNG rare gene variant was detected in homozygosis in P5, without correlating with a specific clinical phenotype. A number of other variants were found in the five analyzed DNA samples from the MKD patients, however no correlation with the phenotype was established. The results of the presents study suggested that further analysis, using next generation sequencing approaches, is required on a larger sample size of patients with MKD, who share the same MVK mutations and exhibit ‘extreme’ clinical phenotypes. As MVK mutations may be associated with MKD, the identification of specific modifier genes may assist in providing an earlier diagnosis.

Published
2015

30. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

Author

Lynne J. Hocking, Caterina Barbieri, Jenny Chang-Claude, David Karasik, Dieter Flesch-Janys, James F. Wilson, Mark S. Goldberg, Henry Voelzke, Archie Campbell, Stig E. Bojesen, David R. Weir, Ailith Pirie, Megan L. Grove, Melissa Wellons, Georg Homuth, Corrado Masciullo, Jennifer A. Brody, Hermann Brenner, Paolo Gasparini, Andrew D. Johnson, Patrick Neven, Graham G. Giles, Peter Kraft, André G. Uitterlinden, Wei Zheng, Alkes L. Price, Anja Rudolph, Arto Mannermaa, Nicholas G. Martin, Christopher A. Haiman, Massimo Mangino, Melissa C. Southey, Daniela Ruggiero, Toshiko Tanaka, Kathryn L. Lunetta, Julie E. Buring, John R. B. Perry, Robert Winqvist, Laufey Tryggvadottir, Angela Cox, Serena Sanna, Nicola Pirastu, Anna Jakubowska, Paul D.P. Pharoah, David J. Porteous, Dragana Vuckovic, Andrea D. Coviello, Giorgia Girotto, Sara Lindstroem, Patrick Sulem, Astrid Petersmann, Xin Li, Maartje J. Hooning, Lili Milani, Sven Bergmann, Marek Zygmunt, Javier Benitez, Vilmundur Gudnason, Fernando Rivadeneira, Volker Arndt, Marina Ciullo, Caroline Hayward, Sheila Ulivi, Janet E. Olson, Hoda Anton-Culver, Maria Kabisch, Sara Margolin, Vessela N. Kristensen, Patrick F. McArdle, Tanguy Corre, Nora Franceschini, Veli-Matti Kosma, Hiltrud Brauch, Roger L. Milne, Eric Boerwinkle, Matthias W. Beckmann, Charles Kooperberg, Qin Wang, Jessica D. Faul, Stephen J. Chanock, Alexander Teumer, Mark O. Goodarzi, Unnur Thorsteinsdottir, R Maegi, Paul M. Ridker, Antonis C. Antoniou, Ozren Polasek, Daniel F. Gudbjartsson, Barbara McKnight, Melissa E. Garcia, Manjeet K. Bolla, Alanna C. Morrison, Paolo Radice, Xiuqing Guo, Lude L. Franke, Michela Traglia, Marjanka K. Schmidt, Heli Nevanlinna, Teresa Nutile, Cinzia Sala, Pascal Guénel, Jennifer E. Huffman, Stephen T. Turner, Anna Murray, Carl Blomqvist, Margaux F. Keller, Samuel E. Jones, Montserrat Garcia-Closas, Ivana Kolcic, Anne B. Newman, Jan Lubinski, Albert Hofman, Isabel dos-Santos-Silva, Hilary K. Finucane, Anne Lise Børresen-Dale, Alexander P. Reiner, Tim D. Spector, Gonneke Willemsen, John D. Eicher, Douglas F. Easton, Claudia Langenberg, Anthony J. Swerdlow, Natalia Bogdanova, Alison M. Dunning, Giorgio Pistis, Tõnu Esko, Behrooz Z. Alizadeh, Martina Mueller-Nurasyid, Eleonora Porcu, Laura M. Yerges-Armstrong, Leslie J. Raffel, Laura Crisponi, Gonçalo R. Abecasis, Jerome I. Rotter, Yii-Der Ida Chen, Antonietta Robino, Katri Pylkaes, Ken K. Ong, Thibaud Boutin, Elinor J. Sawyer, Daniel I. Chasman, Brian E. Henderson, Frank B. Hu, Leslie Bernstein, Drakoulis Yannoukakos, Tamara B. Harris, Dorret I. Boomsma, Katherine S. Ruth, Jie Yao, Keith Humphreys, Jennifer A. Smith, Elisabeth Altmaier, Ulrike Peters, Doris Stoeckl, Eva Albrecht, Tatijana Zemunik, Jenny A. Visser, Minouk J. Schoemaker, Diego Vozzi, Thilo Doerk, J. Ross Chapman, Irene L. Andrulis, Joanne M. Murabito, Alan F. Wright, Lisette Stolk, Jonathan Marten, Alice M. Arnold, Paolo Peterlongo, Harry Campbell, Natalia Pervjakova, Jingmei Li, Jennifer Kriebel, Alicia Beeghly-Fadiel, Immaculata De Vivo, Jouke-Jan Hottenga, Kari Stefansson, Cornelia M. van Duijn, Brendan Bulik-Sullivan, Evelin Mihailov, Chunyan He, Joe Dennis, Nicholas J. Wareham, Yongmei Liu, Sharon L.R. Kardia, Lynda M. Rose, Felix R. Day, Georgia Chenevix-Trench, Albert V. Smith, David J. Hunter, Sandosh Padmanabhan, Christian Gieger, Konstantin Strauch, Igor Rudan, Jacques Simard, Jian'an Luan, Robert A. Scott, Kyriaki Michailidou, Bruce M. Psaty, Per Hall, Suzette J. Bielinski, Rita K. Schmutzler, Julian Peto, Ellen W. Demerath, Ursula M. Schick, Rossella Sorice, Wei Zhao, Børge G. Nordestgaard, Andres Metspalu, Jonine D. Figueroa, Julia A. Knight, Barbara Burwinkel, Thomas Bruening, Judith Manz, Anna González-Neira, Ilaria Gandin, Ian Tomlinson, Thérèse Truong, Kent D. Taylor, Amanda E. Toland, Deborah J. Thompson, Alfons Meindl, Caroline M. Seynaeve, Benjamin M. Neale, Fergus J. Couch, Mike A. Nalls, Ute Hamann, Kamila Czene, John L. Hopper, Bruce H. R. Wolffenbuttel, Grant W. Montgomery, Hatef Darabi, Daniela Toniolo, Jinyan Huang, Peter Devilee, Cathy E. Elks, David Schlessinger, Luigi Ferrucci, Frank Schmidt, Peter A. Fasching, Diether Lambrechts, Najaf Amin, Day, Felix R, Ruth, Katherine S, Thompson, Deborah J, Lunetta, Kathryn L, Pervjakova, Natalia, Chasman, Daniel I, Stolk, Lisette, Finucane, Hilary K, Sulem, Patrick, Bulik Sullivan, Brendan, Esko, Tõnu, Johnson, Andrew D, Elks, Cathy E, Franceschini, Nora, He, Chunyan, Altmaier, Elisabeth, Brody, Jennifer A, Franke, Lude L, Huffman, Jennifer E, Keller, Margaux F, Mcardle, Patrick F, Nutile, Teresa, Porcu, Eleonora, Robino, Antonietta, Rose, Lynda M, Schick, Ursula M, Smith, Jennifer A, Teumer, Alexander, Traglia, Michela, Vuckovic, Dragana, Yao, Jie, Zhao, Wei, Albrecht, Eva, Amin, Najaf, Corre, Tanguy, Hottenga, Jouke Jan, Mangino, Massimo, Smith, Albert V, Tanaka, Toshiko, Abecasis, Gonçalo R, Andrulis, Irene L, Anton Culver, Hoda, Antoniou, Antonis C, Arndt, Volker, Arnold, Alice M, Barbieri, CATERINA MARIA, Beckmann, Matthias W, Beeghly Fadiel, Alicia, Benitez, Javier, Bernstein, Leslie, Bielinski, Suzette J, Blomqvist, Carl, Boerwinkle, Eric, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Borresen Dale, Anne Lise, Boutin, Thibaud S, Brauch, Hiltrud, Brenner, Hermann, Brüning, Thoma, Burwinkel, Barbara, Campbell, Archie, Campbell, Harry, Chanock, Stephen J, Chapman, J. Ro, Chen, Yii Der Ida, Chenevix Trench, Georgia, Couch, Fergus J, Coviello, Andrea D, Cox, Angela, Czene, Kamila, Darabi, Hatef, De Vivo, Immaculata, Demerath, Ellen W, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dos Santos Silva, Isabel, Dunning, Alison M, Eicher, John D, Fasching, Peter A, Faul, Jessica D, Figueroa, Jonine, Flesch Janys, Dieter, Gandin, Ilaria, Garcia, Melissa E, García Closas, Montserrat, Giles, Graham G, Girotto, Giorgia, Goldberg, Mark S, González Neira, Anna, Goodarzi, Mark O, Grove, Megan L, Gudbjartsson, Daniel F, Guénel, Pascal, Guo, Xiuqing, Haiman, Christopher A, Hall, Per, Hamann, Ute, Henderson, Brian E, Hocking, Lynne J, Hofman, Albert, Homuth, Georg, Hooning, Maartje J, Hopper, John L, Hu, Frank B, Huang, Jinyan, Humphreys, Keith, Hunter, David J, Jakubowska, Anna, Jones, Samuel E, Kabisch, Maria, Karasik, David, Knight, Julia A, Kolcic, Ivana, Kooperberg, Charle, Kosma, Veli Matti, Kriebel, Jennifer, Kristensen, Vessela, Lambrechts, Diether, Langenberg, Claudia, Li, Jingmei, Li, Xin, Lindström, Sara, Liu, Yongmei, Luan, Jian'An, Lubinski, Jan, Mägi, Reedik, Mannermaa, Arto, Manz, Judith, Margolin, Sara, Marten, Jonathan, Martin, Nicholas G, Masciullo, Corrado, Meindl, Alfon, Michailidou, Kyriaki, Mihailov, Evelin, Milani, Lili, Milne, Roger L, Müller Nurasyid, Martina, Nalls, Michael, Neale, Benjamin M, Nevanlinna, Heli, Neven, Patrick, Newman, Anne B, Nordestgaard, Børge G, Olson, Janet E, Padmanabhan, Sandosh, Peterlongo, Paolo, Peters, Ulrike, Petersmann, Astrid, Peto, Julian, Pharoah, Paul D. P, Pirastu, Nicola, Pirie, Ailith, Pistis, Giorgio, Polasek, Ozren, Porteous, David, Psaty, Bruce M, Pylkäs, Katri, Radice, Paolo, Raffel, Leslie J, Rivadeneira, Fernando, Rudan, Igor, Rudolph, Anja, Ruggiero, Daniela, Sala, Cinzia F, Sanna, Serena, Sawyer, Elinor J, Schlessinger, David, Schmidt, Marjanka K, Schmidt, Frank, Schmutzler, Rita K, Schoemaker, Minouk J, Scott, Robert A, Seynaeve, Caroline M, Simard, Jacque, Sorice, Rossella, Southey, Melissa C, Stöckl, Dori, Strauch, Konstantin, Swerdlow, Anthony, Taylor, Kent D, Thorsteinsdottir, Unnur, Toland, Amanda E, Tomlinson, Ian, Truong, Thérèse, Tryggvadottir, Laufey, Turner, Stephen T, Vozzi, Diego, Wang, Qin, Wellons, Melissa, Willemsen, Gonneke, Wilson, James F, Winqvist, Robert, Wolffenbuttel, Bruce B. H. R, Wright, Alan F, Yannoukakos, Drakouli, Zemunik, Tatijana, Zheng, Wei, Zygmunt, Marek, Bergmann, Sven, Boomsma, Dorret I, Buring, Julie E, Ferrucci, Luigi, Montgomery, Grant W, Gudnason, Vilmundur, Spector, Tim D, van Duijn, Cornelia M, Alizadeh, Behrooz Z, Ciullo, Marina, Crisponi, Laura, Easton, Douglas F, Gasparini, Paolo, Gieger, Christian, Harris, Tamara B, Hayward, Caroline, Kardia, Sharon L. R, Kraft, Peter, Mcknight, Barbara, Metspalu, Andre, Morrison, Alanna C, Reiner, Alex P, Ridker, Paul M, Rotter, Jerome I, Toniolo, Daniela, Uitterlinden, André G, Ulivi, Sheila, Völzke, Henry, Wareham, Nicholas J, Weir, David R, Yerges Armstrong, Laura M, Price, Alkes L, Stefansson, Kari, Visser, Jenny A, Ong, Ken K, Chang Claude, Jenny, Murabito, Joanne M, Perry, John R. B, Murray, Anna, Internal Medicine, Epidemiology, Medical Oncology, Clinical Genetics, Biological Psychology, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, EMGO+ - Lifestyle, Overweight and Diabetes, PRACTICAL Consortium, kConFab Investigators, AOCS Investigators, EPIC-InterAct Consortium, LifeLines Cohort Study, Generation, Scotland, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Lifestyle Medicine (LM), Life Course Epidemiology (LCE), Center for Liver, Digestive and Metabolic Diseases (CLDM), Stem Cell Aging Leukemia and Lymphoma (SALL), and Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET)

Subjects
Netherlands Twin Register (NTR), Aging, DNA Repair, LOCI, Genome-wide association study, BLOOD-PRESSURE, Disease, CHROMOSOMAL INSTABILITY, Bioinformatics, HOMOLOGOUS RECOMBINATION, PREMATURE OVARIAN FAILURE, Genotype, BRCA2 MUTATION CARRIERS, WIDE ASSOCIATION, Gene Regulatory Networks, NATURAL MENOPAUSE, Genetics, education.field_of_study, menopause, DDR, BODY-MASS INDEX, CELL-TYPES, BRCA1 Protein, Reproduction, BRCA1-mediated DNA repair, Age Factors, Obstetrics and Gynecology, General Medicine, Genomics, Middle Aged, 3. Good health, Menopause, Phenotype, Female, medicine.symptom, Signal Transduction, Delayed puberty, Adult, DNA repair, Population, Hypothalamus, Single-nucleotide polymorphism, Breast Neoplasms, Biology, Lower risk, DDR, Article, Breast cancer, SDG 3 - Good Health and Well-being, Mendelian randomization, medicine, Humans, Genetic Predisposition to Disease, Allele, education, Genetic association, Models, Genetic, business.industry, Genetic Variation, medicine.disease, Aging/genetics, BRCA1 Protein/genetics, Breast Neoplasms/genetics, Gene Regulatory Networks/genetics, Genetic Predisposition to Disease/genetics, Genome-Wide Association Study/methods, Genomics/methods, Hypothalamus/metabolism, Menopause/genetics, Reproduction/genetics, Signal Transduction/genetics, business, Genome-Wide Association Study
Abstract

Menopause timing has a major impact on infertility and risk of disease. Younger age at natural (nonsurgical) menopause (ANM) is associated with a higher risk of osteoporosis, cardiovascular disease, and type 2 diabetes and a lower risk of breast cancer. Late menopause is associated with a higher risk of breast cancer. It is well known that the age at which women go through menopause is partly determined by genes, but the underlying mechanisms are poorly understood. Genome-wide association studies have identified 18 common genetic variants associated with ANM. These variants explain less than 5% of the variation in ANM compared with the 21% explained by all common variants on genome-wide association study arrays. This genome-wide association study was the collaborative effort of researchers from 177 institutions worldwide. The study was designed to investigate genetic variants associated with timing of menopause among a population of approximately 70,000 women of European ancestry. A dual strategy was used to identify both common and, for the first time, low-frequency coding variants associated with ANM. The causal relationship between ANM and breast cancer was investigated using a Mendelian randomization approach. Combined analysis identified 1208 single-nucleotide polymorphisms (SNPs) of a total of approximately 2.6 million that reached the genome-wide significance threshold for association with ANM. Forty-four regions with common variants were identified; among these 44 loci were 2 rare low-frequency missense alleles of large effect. A majority of ANM SNPs were enriched in DNA damage response (DDR) genes, including the first common coding variant in BRCA1 associated with any complex trait. Mendelian randomization analyses supported a causal relationship between delayed ANM and breast cancer risk; there was approximately 6% increase in risk per year; P = 3 × 10-14); increased risk with delayed menopause appeared to be mediated primarily by prolonged sex hormone exposure in a woman’s lifetime, not DDR mechanisms. This is the first study to confirm the link between early and late menopause and breast cancer risk using genetic information. Age at natural menopause genetic variants influence breast cancer risk primarily through variation in menopause timing. Although carrying higher numbers of ANM-increasing variants and enrichment in DDR genes are associated with a modest increase in breast cancer risk, the major mechanism for increased risk appears to be prolonged estrogen and/or progesterone exposure due to delayed menopause.

Published
2015

31. Usher syndrome: An effective sequencing approach to establish a genetic and clinical diagnosis

Author

Pierangela Castorina, Stefania Lenarduzzi, Giorgia Girotto, Anna Morgan, Claudio Graziano, Cesare Rossi, Umberto Ambrosetti, Diego Vozzi, Angela D'Eustacchio, Elisa Rubinato, T.M. Osland, Marcello Morgutti, Lenarduzzi, Stefania, Vozzi, Diego, Morgan, Anna, Rubinato, Elisa, D'Eustacchio, A., Osland, TERESA MARIA, Rossi, C., Graziano, C., Castorina, P., Ambrosetti, U., Morgutti, Marcello, and Girotto, Giorgia

Subjects
Adult, Male, MYO7A, Usher syndrome, Genetic counseling, Cadherin Related Proteins, Genetic Counseling, Nerve Tissue Proteins, Biology, Myosins, Bioinformatics, Next generation sequencing, Retinitis pigmentosa, otorhinolaryngologic diseases, medicine, Humans, Allele, Alleles, Extracellular Matrix Proteins, Molecular epidemiology, Genetic heterogeneity, High-Throughput Nucleotide Sequencing, Middle Aged, medicine.disease, Cadherins, Sensory Systems, Usher Syndrome, Next generation sequencing, Myosin VIIa, Mutation, Female, Usher Syndrome, Usher Syndromes, PCDH15
Abstract

Usher syndrome is an autosomal recessive disorder characterized by retinitis pigmentosa, sensorineural hearing loss and, in some cases, vestibular dysfunction. The disorder is clinically and genetically heterogeneous and, to date, mutations in 11 genes have been described. This finding makes difficult to get a precise molecular diagnosis and offer patients accurate genetic counselling. To overcome this problem and to increase our knowledge of the molecular basis of Usher syndrome, we designed a targeted resequencing custom panel. In a first validation step a series of 16 Italian patients with known molecular diagnosis were analysed and 31 out of 32 alleles were detected (97% of accuracy). After this step, 31 patients without a molecular diagnosis were enrolled in the study. Three out of them with an uncertain Usher diagnosis were excluded. One causative allele was detected in 24 out 28 patients (86%) while the presence of both causative alleles characterized 19 patients out 28 (68%). Sixteen novel and 27 known alleles were found in the following genes: USH2A (50%), MYO7A (7%), CDH23 (11%), PCDH15 (7%) and USH1G (2%). Overall, on the 44 patients the protocol was able to characterize 74 alleles out of 88 (84%). These results suggest that our panel is an effective approach for the genetic diagnosis of Usher syndrome leading to: 1) an accurate molecular diagnosis, 2) better genetic counselling, 3) more precise molecular epidemiology data fundamental for future interventional plans.

Published
2015

32. Target sequencing approach intended to discover new mutations in non-syndromic intellectual disability

Author

Diego Vozzi, Paolo Bosco, Giovanni Battista Ferrero, Chiara Belcaro, Anna Morgan, Adamo Pio D'Adamo, Elisa Biamino, Orazio Palumbo, Erik Laurini, Flavio Faletra, Corrado Romano, Sabrina Pricl, Valentina Dal Col, Massimo Carella, Pietro Palumbo, Ilaria Gandin, Morgan, Anna, Gandin, Ilaria, Belcaro, Chiara, Palumbo, Pietro, Palumbo, Orazio, Biamino, Elisa, DAL COL, Valentina, Laurini, Erik, Pricl, Sabrina, Bosco, Paolo, Carella, Massimo, Ferrero, Giovanni Battista, Romano, Corrado, D'Adamo, ADAMO PIO, Faletra, Flavio, and Vozzi, Diego

Subjects
Male, Models, Molecular, X-linked Nuclear Protein, Protein Conformation, Health, Toxicology and Mutagenesis, DNA Mutational Analysis, Targeted sequencin, Biology, Molecular Dynamics Simulation, medicine.disease_cause, Non-syndromic intellectual disability, U5 Small Nuclear, Adenosine Triphosphate, Models, Intellectual Disability, Intellectual disability, Genetics, medicine, Humans, Toxicology and Mutagenesis, Molecular Biology, Gene, Ribonucleoprotein, U5 Small Nuclear, Mutation, Genetic heterogeneity, Genetic diagnosis, Targeted sequencing, DNA Helicases, DNA-Binding Proteins, Female, Nuclear Proteins, Transcription Factors, Medicine (all), Molecular, Ribonucleoprotein, medicine.disease, Phenotype, Health, Etiology, RNA Splicing Factors, Non syndromic
Abstract

The technological improvements over the last years made considerable progresses in the knowledge of the etiology of intellectual Disability (ID). However, at present very little is known about the genetic heterogeneity underlying the non-syndromic form of ID (NS-ID). To investigate the genetic basis of NS-ID we analyzed 43 trios and 22 isolated NS-ID patients using a targeted sequencing (TS) approach. 71 NS-ID genes have been selected and sequenced in all subjects. We found putative pathogenic mutations in 7 out of 65 patients. The pathogenic role of mutations was evaluated through sequence comparison and structural analysis was performed to predict the effect of alterations in a 3D computational model through molecular dynamics simulations. Additionally, a deep patient clinical re-evaluation has been performed after the molecular results. This approach allowed us to find novel pathogenic mutations with a detection rate close to 11% in our cohort of patients. This result supports the hypothesis that many NS-ID related genes still remain to be discovered and that NS-ID is a more complex phenotype compared to syndromic form, likely caused by a complex and broad interaction between genes alterations and environment factors.

Published
2015

33. Increased rate of deleterious variants in long runs of homozygosity of an inbred population from Qatar

Author

Massimo Mezzavilla, Moza Khalifa Alkowari, Diego Vozzi, Giorgia Girotto, Khalid Abdulhadi, Paolo Gasparini, Ramin Badii, Mezzavilla, Massimo, Vozzi, Diego, Badii, Ramin, Khalifa Alkowari, Moza, Abdulhadi, Khalid, Girotto, Giorgia, and Gasparini, Paolo

Subjects
Deleterious variant, Consanguinity, Biology, Runs of Homozygosity, Deleterious variants, Inbreeding, Qatar, Runs of homozygosity, Whole-exome sequencing, Polymorphism, Single Nucleotide, Cohort Studies, Genetic, Genetics, Humans, Polymorphism, Exome sequencing, Genetics (clinical), Mutation, Homozygote, Medicine (all), Single Nucleotide, Inbred population, Evolutionary biology, Cohort Studie, Human
Abstract

OBJECTIVE: The aim of this study is to evaluate the fraction of putatively deleterious variants within genomic runs of homozygosity (ROH) regions in an inbred and selected cohort of Qatari individuals. METHODS: High-density SNP array analysis was performed in 36 individuals, and for 14 of them whole-exome sequencing (WES) was also carried out. RESULTS: In all individuals, regions characterized by a high (hotspot) or low (coldspot) degree of homozygosity in all the analysed individuals were mapped, and the most frequent hotspot regions were selected. WES data were exploited to identify the single nucleotide variations (SNVs) harboured by genes located within both regions in each individual. Evolutionary conservation-based algorithms were employed to predict the potential deleteriousness of SNVs. The amount of in silico predicted deleterious SNVs was significantly different (p < 0.05) between homozygosity hotspot and coldspot regions. CONCLUSION: Genes located within ROH hotspot regions contain a significant burden of predicted putatively deleterious variants compared to genes located outside these regions, suggesting inbreeding as a possible mechanism allowing an enrichment of putatively deleterious variants at the homozygous state.

Published
2015

34. Excess of runs of homozygosity is associated with severe cognitive impairment in intellectual disability

Author

Corrado Romano, Adamo Pio D'Adamo, Giovanni Battista Ferrero, Flavio Faletra, Vanna Pecile, Chiara Belcaro, Orazio Palumbo, Pietro Palumbo, Ilaria Gandin, Elisa Biamino, Diego Vozzi, Massimo Carella, Francesca Faletra, Paolo Bosco, Gandin, Ilaria, Faletra, Flavio, Faletra, F, Carella, M, Pecile, Vanna, Ferrero, Gb, Biamino, E, Palumbo, P, Palumbo, O, Bosco, P, Romano, C, Belcaro, Chiara, Vozzi, Diego, and D'Adamo, ADAMO PIO

Subjects
Male, medicine.medical_specialty, Inbreeding Depression, intellectual disability, inbreeding, Genes, Recessive, Runs of Homozygosity, Consanguinity, Intellectual disability, Odds Ratio, medicine, Inbreeding depression, Humans, Cognitive impairment, Psychiatry, Genetic Association Studies, Genetics (clinical), runs of homozygosity, Intelligence quotient, business.industry, Homozygote, medicine.disease, Phenotype, Mutation, Cohort, Autism, Female, Cognition Disorders, business, Inbreeding
Abstract

Purpose:The harmful effects of inbreeding are well known by geneticists, and several studies have already reported cases of intellectual disability caused by recessive variants in consanguineous families. Nevertheless, the effects of inbreeding on the degree of intellectual disability are still poorly investigated. Here, we present a detailed analysis of the homozygosity regions in a cohort of 612 patients with intellectual disabilities of different degrees.Methods:We investigated (i) the runs of homozygosity distribution between syndromic and nonsyndromic ID (ii) the effect of runs of homozygosity on the ID degree, using the intelligence quotient score.Results:Our data revealed no significant differences in the first analysis; instead we detected significantly larger runs of homozygosity stretches in severe ID compared to nonsevere ID cases (P = 0.007), together with an increase of the percentage of genome covered by runs of homozygosity (P = 0.03).Conclusion:In accord with the recent findings regarding autism and other neurological disorders, this study reveals the important role of autosomal recessive variants in intellectual disability. The amount of homozygosity seems to modulate the degree of cognitive impairment despite the intellectual disability cause.

Published
2015

35. Rare coding variants and X-linked loci associated with age at menarche

Author

Kathryn L. Lunetta, Felix R. Day, Patrick Sulem, Katherine S. Ruth, Joyce Y. Tung, David A. Hinds, Tõnu Esko, Cathy E. Elks, Elisabeth Altmaier, Chunyan He, Jennifer E. Huffman, Evelin Mihailov, Eleonora Porcu, Antonietta Robino, Lynda M. Rose, Ursula M. Schick, Lisette Stolk, Alexander Teumer, Deborah J. Thompson, Michela Traglia, Carol A. Wang, Laura M. Yerges-Armstrong, Antonis C. Antoniou, Caterina Barbieri, Andrea D. Coviello, Francesco Cucca, Ellen W. Demerath, Alison M. Dunning, Ilaria Gandin, Megan L. Grove, Daniel F. Gudbjartsson, Lynne J. Hocking, Albert Hofman, Jinyan Huang, Rebecca D. Jackson, David Karasik, Jennifer Kriebel, Ethan M. Lange, Leslie A. Lange, Claudia Langenberg, Xin Li, Jian'an Luan, Reedik Mägi, Alanna C. Morrison, Sandosh Padmanabhan, Ailith Pirie, Ozren Polasek, David Porteous, Alex P. Reiner, Fernando Rivadeneira, Igor Rudan, Cinzia F. Sala, David Schlessinger, Robert A. Scott, Doris Stöckl, Jenny A. Visser, Uwe Völker, Diego Vozzi, James G. Wilson, Marek Zygmunt, Nita G. Forouhi, Nicola D. Kerrison, Stephen J. Sharp, Matt Sims, Inês Barroso, Panos Deloukas, Mark I. McCarthy, Larraitz Arriola, Beverley Balkau, Aurelio Barricarte, Heiner Boeing, Paul W. Franks, Carlos Gonzalez, Sara Grioni, Rudolf Kaaks, Timothy J. Key, Carmen Navarro, Peter M. Nilsson, Kim Overvad, Domenico Palli, Salvatore Panico, J Ramón Quirós, Olov Rolandsson, Carlotta Sacerdote, María‐José Sánchez, Nadia Slimani, Anne Tjonneland, Rosario Tumino, Daphne L. van der A, Yvonne T. van der Schouw, Elio Riboli, Blair H. Smith, Archie Campbell, Ian J. Deary, Andrew M. McIntosh, Eric Boerwinkle, Julie E. Buring, Laura Crisponi, Douglas F. Easton, Caroline Hayward, Frank B. Hu, Simin Liu, Andres Metspalu, Craig E. Pennell, Paul M. Ridker, Konstantin Strauch, Elizabeth A. Streeten, Daniela Toniolo, André G. Uitterlinden, Sheila Ulivi, Henry Völzke, Nicholas J. Wareham, Melissa Wellons, Nora Franceschini, Daniel I. Chasman, Unnur Thorsteinsdottir, Anna Murray, Kari Stefansson, Joanne M. Murabito, Ken K. Ong, John R. B. Perry

Published
2015
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36. Two‑gene mutation in a single patient: Biochemical and functional analysis for a correct interpretation of exome results

Author

Annalisa Marcuzzi, Alessandra Knowles, Martina Girardelli, Alberto Tommasini, Flavio Faletra, Giorgio Zauli, Diego Vozzi, Anna Monica Bianco, Bianco, ANNA MONICA ROSARIA, Faletra, Flavio, Vozzi, Diego, Girardelli, Martina, Knowles, A, Tommasini, Alberto, Zauli, Giorgio, and Marcuzzi, Annalisa

Subjects
Male, Cancer Research, Gene mutation, Genotype-phenotype, Mevalonate, Mevalonate kinase deficiency, RAB40AL, Rare disease, Biochemistry, Genetics, Molecular Biology, Molecular Medicine, Oncology, Bioinformatics, medicine.disease_cause, mevalonate, X Chromosome Inactivation, Genotype, Databases, Genetic, Missense mutation, Exome, Child, Exome sequencing, Mutation, High-Throughput Nucleotide Sequencing, Genetic Diseases, X-Linked, Phosphotransferases (Alcohol Group Acceptor), Phenotype, Receptors, Androgen, Female, Genetic Markers, Hearing Loss, Sensorineural, Mutation, Missense, rare disease, Mevalonic Acid, Mothers, Biology, NO, Mitochondrial Proteins, Intellectual Disability, Genetic variation, medicine, Humans, Abnormalities, Multiple, Genetic Association Studies, Genetic Variation, medicine.disease, genotype‑phenotype, ras Proteins, mevalonate, rare disease, RAB40AL, mevalonate kinase deficiency, genotype‑phenotype, Mevalonate Kinase Deficiency
Abstract

Next-generation sequencing (NGS) has generated a large amount of sequence data with the requirement of frequent critical revisions of reported mutations. This innovative tool has proved to be effective in detecting pathogenic mutations; however, it requires a certain degree of experience to identify incidental findings. In the present study, whole exome sequencing analysis was performed for the molecular diagnosis and correct genotype/phenotype correlation between parents and a patient presenting with an atypical phenotype. In addition, mevalonic acid quantification and frequency analysis of detected variants in public databases and X‑chromosome inactivation (XCI) studies on the patient's mother were performed. V377I as well as the S135L mutations were identified on the mevalonate kinase deficiency gene and the levels of mevalonic acid in the patient were 5,496 µg/ml. A D59G variation, reported in ESP6500 in two healthy individuals, was found on the Martin Probst syndrome gene (RAB40AL). Based on XCI studies on the patient's mother, it is likely that RAB40AL escapes XCI, while still remaining balanced. In conclusion, the results of the present study indicated that the Martin Probst syndrome is an X‑linked condition, which is probably not caused by RAB40AL mutations. Although NGS is a powerful tool to identify pathogenic mutations, the analysis of genetic data requires expert critical revision of all detected variants.

Published
2014

37. Contents Vol. 77, 2014

Author

Alison Shaw, Hasan Al-Dhekri, Taisa Manuela Bonfim Machado, I. Christopher Lloyd, Fernanda Bender, Nima Rezaei, Nadia Al-Hashmi, Alessandro Gialluisi, Lihadh Al-Gazali, Christine Petit, Hanan Hamamy, Mourad Sahbatou, Mohammad Jalal Abbasi-Shavazi, Insaf Rejeb, Kristen L. Sund, Marion D. Teare, Yosra Bouyacoub, Khalid Abdulhadi, Stavit A. Shalev, Trevor J. Pemberton, Nicholas J. Schork, Diego Vozzi, Mariem Ben Rekaya, Mohamed-Ridha Barbouche, Anne-Louise Leutenegger, Simona Ferrari, Graeme C.M. Black, Khalid Yunis, Noah A. Rosenberg, Nizar Ben Halim, Paolo Giorgi Rossi, Faten Ben Rhouma, Meimanat Hosseini-Chavoshi, Ramin Badii, Majdi Nagara, Steven Gazal, Habib Messai, Martina C. Cornel, Rym Kefi, Liliana Uribe-Bruce, Laura H. Goetz, Moza Khalifa Alkowari, Danjuma Quarless, Watfa Al-Mamari, Zafar Iqbal, Hussein A. Abbas, Emmanuelle Génin, Roberto Giugliani, Crystel Bonnet, Lilia Romdhane, Rachel L. Gillespie, M. Mazharul Islam, Olfa Messaoud, Ondrej Libiger, Tatiana Boa Sorte, Lidewij Henneman, Angelina Xavier Acosta, Said A. Al-Yahyaee, Sandra Leistner-Segal, Kiyoko Abe-Sandes, Giovanni Romeo, Druckerei Stückle, Hans van Bokhoven, Thais Bomfim, Catherine Rehder, Alan H. Bittles, Zied Riahi, Fabiana Moura Costa-Motta, Satz Mengensatzproduktion, Khalid Al-Thihli, Tommaso Pippucci, Andrea Finocchi, Waleed Al-Herz, Elizabeth C. Goyder, Danniel da Silva, Valentina Di Pierro, Marieke E. Teeuw, Leo P. ten Kate, Ken McElreavey, Hervé Perdry, Ibrahim M. Gosadi, Caterina Cancrini, Massimo Mezzavilla, Sonia Abdelhak, Alberto Magi, Joël Zlotogora, Paolo Gasparini, Dragana Vuckovic, Giorgia Girotto, Anu Bashamboo, Giulia Angelino, Roberta Zuntini, Fathiya Al-Murshedi, Sébastien Letort, Alan Bittles, and Peter C. Corry

Subjects
Genetics, Genetics (clinical)
Published
2014

38. Consanguinity and hereditary hearing loss in Qatar

Author

Paolo Gasparini, Moza Khalifa Alkowari, Diego Vozzi, Ramin Badii, Massimo Mezzavilla, Dragana Vuckovic, Khalid Abdulhadi, Giorgia Girotto, Girotto, Giorgia, Mezzavilla, Massimo, Khalid, Abdulhadi, Vuckovic, Dragana, Vozzi, Diego, Moza Khalifa, Alkowari, Gasparini, Paolo, and Ramin, Badii

Subjects
Hearing loss, Native population, Population, Inheritance Patterns, Disease, Consanguinity, Biology, Connexins, Hereditary hearing loss, Transcription Factor TFIIIB, Prevalence, Genetics, medicine, Humans, Hearing Loss, education, Qatar, Genetics (clinical), Persian, Principal Component Analysis, education.field_of_study, Genes, Genetic heterogeneity, Homozygote, humanities, language.human_language, Pedigree, Connexin 26, language, qatar, medicine.symptom, Inbreeding, Demography
Abstract

Qatar is a sovereign state located on the Eastern coast of the Arabian Peninsula in the Persian Gulf. Its native population consists of 3 major subgroups: people of Arabian origin or Bedouins, those from an Eastern or Persian ancestry and individuals with African admixture. Historically, all types of consanguineous marriages have been and still are common in the Qatari population, particularly among first and double-first cousins. Thus, there is a higher risk for most inherited diseases including hereditary hearing loss (HHL). In particular, a hearing loss prevalence of 5.2% has been reported in Qatar, with parental consanguinity being more common among affected individuals as compared with unaffected ones. Our recent molecular results confirm a high homogeneity and level of inbreeding in Qatari HHL patients. Among all HHL genes, GJB2, the major player worldwide, accounts for a minor proportion of cases and at least 3 additional genes have been found to be mutated in Qatari patients. Interestingly, one gene, BDP1, has been described to cause HHL only in this country. These results point towards an unexpected level of genetic heterogeneity despite the high level of inbreeding. This review provides an up-to-date picture of HHL in Qatar and of the impact of consanguinity on this disease.

Published
2014

39. New Hereditary Hearing Loss (hhl) Genes/mutations Identified By High Throughput Technologies In The Qatari Population

Author

Khalid Abdul Hadi, Giorgia Girotto, Paolo Gasparini, Dragana Vuckovic, Angela D'Eustacchio, Anna Morgan, Moza Khalifa Alkowari, Ramin Badii, Martina La Bianca, Diego Vozzi, and Elisa Rubinato

Subjects
Genetics, MYO15A, education.field_of_study, Genetic heterogeneity, Population, Genetic disorder, Consanguinity, Biology, medicine.disease, medicine, TECTA, education, Genotyping, Exome sequencing
Abstract

Objectives: Hereditary Hearing Loss (HHL) is a common genetic disorder accounting for at least 60% of prelingual deafness in children. The long tradition of consanguinity, which is widespread among populations of Arabian Peninsula, increases the prevalence of HHL. It is one of the most frequent causes for school failure in Qatar. GJB2 gene plays a worldwide major role in HHL recessive forms while in Qatar it has a minor role thus strongly suggesting the presence of additional causative genes. To overcome the remarkable genetic heterogeneity of HHL in Qatar population, an extremely powerful 2 steps "gene-identification strategy" was designed (Figure 1). STEP1 consists in a screening of 96 HHL genes by targeted re-sequencing (TS). Positive cases contribute to define an accurate molecular epidemiology picture while negative ones undergo STEP2, a combination of linkage studies and whole exome sequencing (WES) or directly to WES (depending on pedigree size). Methods: Ion Torrent (Life Technologies) (400X of mean target coverage and 581.000 Kb of targets size) was used for STEP1 and Illumina genotyping and Ion Proton (Life Technologies) (90X of mean coverage and 60Mb of target size) were used for STEP2. Sequencing variants were annotated/filtered according to standard pipelines. This strategy was applied to a first series of Qatari families. Results: STEP1 characterized 53% of Qatari families with HHL leading to the identification of 20 novel alleles in known HHL genes (i.e. GJB2, P2RX2, TECTA, TMPRSS3, LOXHD1, MYO15A, TMC1, TRIOBP, WFS1). STEP2 had already led to the discovery of 1 new gene (BDP1). The p*2625Gluext*11 mutation resulting in an elongation of 11 residues of the BDP1 protein was identified in a Qatari recessive family and its expression in the inner ear was confirmed by immunohistochemistry. Conclusion: This combined and powerful strategy proved to be very successful by explaining several HHL unsolved cases and by defining an accurate molecular epidemiology picture of Qatari genes/mutations. Moreover, this approach will be used for developing a "Qatari tailored" molecular diagnostic assay opening new important diagnostic perspectives for a such heterogeneous disorder as well as for defining targets for new possible therapeutic interventions

Published
2014

40. Next generation sequencing in nonsyndromic intellectual disability: From a negative molecular karyotype to a possible causative mutation detection

Author

Savina Dipresa, Danilo Licastro, Anna Morgan, Paolo Gasparini, Antonella Fabretto, Flavio Faletra, Adamo Pio D'Adamo, Vanna Pecile, Emmanouil Athanasakis, Xevi Biarnés, Diego Vozzi, Athanasakis, Emmanouil, Danilo, Licastro, Flavio, Faletra, Antonella, Fabretto, Savina, Dipresa, Vozzi, Diego, Morgan, Anna, D'Adamo, ADAMO PIO, Vanna, Pecile, Xevi, Biarné, and Gasparini, Paolo

Subjects
Male, Karyotype, Genome-wide association study, Genes, Recessive, Biology, DNA sequencing, Workflow, next generation sequencing, intellectual disability, Genes, X-Linked, Intellectual Disability, Intellectual disability, Genetics, medicine, Humans, Exome, Copy-number variation, Genetics (clinical), Exome sequencing, Computational Biology, High-Throughput Nucleotide Sequencing, medicine.disease, Molecular diagnostics, Mutation (genetic algorithm), Mutation, Female, Genome-Wide Association Study
Abstract

The identification of causes underlying intellectual disability (ID) is one of the most demanding challenges for clinical Geneticists and Researchers. Despite molecular diagnostics improvements, the vast majority of patients still remain without genetic diagnosis. Here, we report the results obtained using Whole Exome and Target Sequencing on nine patients affected by isolated ID without pathological copy number variations, which were accurately selected from an initial cohort of 236 patients. Three patterns of inheritance were used to search for: (1) de novo, (2) X-linked, and (3) autosomal recessive variants. In three of the nine proband-parent trios analyzed, we identified and validated two de novo and one X-linked potentially causative mutations located in three ID-related genes. We proposed three genes as ID candidate, carrying one de novo and three X-linked mutations. Overall, this systematic proband-parent trio approach using next generation sequencing could explain a consistent percentage of patients with isolated ID, thus increasing our knowledge on the molecular bases of this disease and opening new perspectives for a better diagnosis, counseling, and treatment.

Published
2014

41. Mevalonate kinase deficiency and IBD: shared genetic background

Author

Martina Girardelli, Sergio Crovella, Diego Vozzi, Annalisa Marcuzzi, Anna Monica Bianco, Giulio Kleiner, Bianco, A. M., Girardelli, Martina, Vozzi, Diego, Crovella, Sergio, Kleiner, G., and Marcuzzi, Annalisa

Subjects
Gene Mutation, medicine.medical_specialty, IBD, Intestinal Gene Regulation, Gene mutation, Genetic Polymorphisms, Inflammatory bowel disease, NO, Intestinal inflammation, mevalonate kinase deficiency, Molecular genetics, medicine, Genetic association, Inflammatory Bowel Disorders, Mevalonate kinase deficiency, molecular genetics, business.industry, Gastroenterology, PostScript, medicine.disease, Phenotype, digestive system diseases, Immunology, Etiology, business
Abstract

Dear editor, We read with interest the article entitled ‘Monogenic diseases associated with intestinal inflammation: implications for the understanding of inflammatory bowel disease’ written by Uhlig1 and published by Gut . The study, describing the very early onset of intestinal inflammation in several orphan monogenic diseases, aimed at determining the presence of a link between the IBD-like phenotype shown by these rare diseases and the intestinal inflammation seen in typical IBD. The IBD aetiology is multifactorial: at present, genome-wide association studies have identified 163 susceptibility loci associated with an increased risk of developing IBD.2 Beside these identified genetic loci that provide little contribution to explain IBD hereditability, the number of monogenic diseases presenting IBD-like symptoms is however continuously increasing. These monogenic diseases usually exhibit very early onset and very severe symptoms; in addition, they are often unresponsive to common drugs (anti-inflammatory and immunosuppressive treatments, such as anti-TNFα). In his article,1 Uhlig reports that …

Published
2014

42. Genetic landscape of populations along the Silk Road: admixture and migration patterns

Author

Vincenza Colonna, Nicola Pirastu, Pio D'Adamo, Massimo Mezzavilla, Giorgia Girotto, Paolo Gasparini, Diego Vozzi, Mezzavilla, Massimo, Vozzi, Diego, Pirastu, Nicola, Girotto, Giorgia, D'Adamo, ADAMO PIO, Gasparini, Paolo, and Colonna, Vincenza

Subjects
Gene Flow, Tajikistan, Future studies, Silk Road, Georgia, Azerbaijan, Human Migration, Central asia, Genomics, Context (language use), Admixture, Biology, Polymorphism, Single Nucleotide, White People, Gene flow, 03 medical and health sciences, Armenia, Central Asia, Effective population size, Kazakhstan, Migration patterns, Uzbekistan, Asian People, Genetics, Humans, Genetics(clinical), Genetics (clinical), 030304 developmental biology, 0303 health sciences, Principal Component Analysis, Middle East, Human migration, business.industry, 030305 genetics & heredity, Homozygote, Sequence Analysis, DNA, Geography, Commonwealth of Independent States, Phenotype, Silk Road, Admixture, Migration patterns, Central Asia, Effective population size, Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan, Evolutionary biology, Genetic structure, business, Research Article
Abstract

Background The ancient Silk Road has been a trading route between Europe and Central Asia from the 2nd century BCE to the 15th century CE. While most populations on this route have been characterized, the genetic background of others remains poorly understood, and little is known about past migration patterns. The scientific expedition “Marco Polo” has recently collected genetic and phenotypic data in six regions (Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan) along the Silk Road to study the genetics of a number of phenotypes. Results We characterized the genetic structure of these populations within a worldwide context. We observed a West-East subdivision albeit the existence of a genetic component shared within Central Asia and nearby populations from Europe and Near East. We observed a contribution of up to 50% from Europe and Asia to most of the populations that have been analyzed. The contribution from Asia dates back to ~25 generations and is limited to the Eastern Silk Road. Time and direction of this contribution are consistent with the Mongolian expansion era. Conclusions We clarified the genetic structure of six populations from Central Asia and suggested a complex pattern of gene flow among them. We provided a map of migration events in time and space and we quantified exchanges among populations. Altogether these novel findings will support the future studies aimed at understanding the genetics of the phenotypes that have been collected during the Marco Polo campaign, they will provide insights into the history of these populations, and they will be useful to reconstruct the developments and events that have shaped modern Eurasians genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0131-6) contains supplementary material, which is available to authorized users.

Published
2014

43. Hereditary hearing loss: a 96 gene targeted sequencing protocol reveals novel alleles in a series of Italian and Qatari patients

Author

Paolo Gasparini, Dragana Vuckovic, Giorgia Girotto, Elisa Rubinato, Anna Morgan, Khalid Abdulhadi, Diego Vozzi, Angela D'Eustacchio, Ramin Badii, Vozzi, Diego, Morgan, Anna, Vuckovic, Dragana, A., D'Eustacchio, K., Abdulhadi, E., Rubinato, R., Badii, Gasparini, Paolo, and Girotto, Giorgia

Subjects
Male, MYO15A, Hearing loss, Genetic counseling, Molecular Sequence Data, Biology, Deafness, Myosins, GPI-Linked Proteins, DNA sequencing, Untranslated Regions, otorhinolaryngologic diseases, Genetics, medicine, Humans, Amino Acid Sequence, Genetic Testing, TECTA, Deafne, Hearing Loss, Hearing Lo, Qatar, Alleles, Extracellular Matrix Proteins, Molecular epidemiology, Genetic heterogeneity, Serine Endopeptidases, Membrane Proteins, General Medicine, Ion semiconductor sequencing, Targeted sequencing, Sequence Analysis, DNA, Neoplasm Proteins, Pedigree, Italy, Mutation, Female, medicine.symptom, Carrier Proteins
Abstract

Deafness is a really common disorder in humans. It can begin at any age with any degree of severity. Hereditary hearing loss is characterized by a vast genetic heterogeneity with more than 140 loci described in humans but only 65 genes so far identified. Families affected by hearing impairment would have real advantages from an early molecular diagnosis that is of primary relevance in genetic counseling. In this perspective, here we report a family-based approach employing Ion Torrent DNA sequencing technology to analyze coding and UTR regions of 96 genes related to hearing function and loss in a first series of 12 families coming from Italy and Qatar. Using this approach we were able to find the causative gene in 4 out of these 12 families (33%). In particular 5 novel alleles were identified in the following genes LOXHD1, TMPRSS3, TECTA and MYO15A already associated with hearing impairment. Our study confirms the usefulness of a targeted sequencing approach despite larger numbers are required for further validation and for defining a molecular epidemiology picture of hearing loss in these two countries.

Published
2013

44. A novel P2RX2 mutation in an Italian family affected by autosomal dominant nonsyndromic hearing loss

Author

Anna Morgan, Diego Vozzi, Adamo Pio D'Adamo, Flavio Faletra, Giorgia Girotto, Paolo Gasparini, Flavio, Faletra, Girotto, Giorgia, D'Adamo, ADAMO PIO, Vozzi, Diego, Morgan, Anna, and Gasparini, Paolo

Subjects
Male, Genotype, Hearing loss, Hearing Loss, Sensorineural, Molecular Sequence Data, Mutation, Missense, Locus (genetics), Biology, Deafness, White People, Protein structure, Genetic linkage, Genetics, medicine, Missense mutation, Humans, Amino Acid Sequence, Gene, DFNA41, Genetic heterogeneity, General Medicine, Major gene, Pedigree, autosomal dominant non-syndromic hearing loss, Italy, Female, medicine.symptom, Receptors, Purinergic P2X2
Abstract

Hereditary hearing loss (HHL) is a common disorder accounting for at least 60% of prelingual deafness. It is characterized by a large genetic heterogeneity, and despite the presence of a major gene, still there is a need to search for new causative mutations/genes. Very recently, a mutation within ATP-gated P2X(2) receptor (ligand-gated ion channel, purinergic receptor 2) gene (P2RX2) at DNFA41 locus has been reported leading to a bilateral and symmetrical sensorineural non-syndromic autosomal dominant HHL in two Chinese families. We performed a linkage analysis in a large Italian family with a dominant pattern of inheritance showing a significant 3.31 LOD score in a 2 Mb region overlapping with the DNFA41 locus. Molecular analyses of P2RX2 identified a novel missense mutation (p.Gly353Arg) affecting a residue highly conserved across species. Visual inspection of the protein structure as obtained from comparative modeling suggests that substitution of the small glycine residue with a charged bulky residue such as an arginine that is close to the ‘neck’ of the region responsible for ion channel gating should have a high energetic cost and should lead to a severely destabilization of the fold. The identification of a second most likely causative mutation in P2RX2 gene further supports the possible role of this gene in causing autosomal dominant HHL.

Published
2013

45. Molecular diagnosis of usher syndrome: application of two different next generation sequencing-based procedures

Author

Emmanouil Athanasakis, Ivana Peluso, Angela D'Eustacchio, Vincenzo Nigro, Antonella Fabretto, Carmela Ziviello, Nienke Wieskamp, Danilo Licastro, Margherita Mutarelli, Francesca Simonelli, Paolo Gasparini, Rossella Rispoli, F. d’Amico, Kornelia Neveling, Diego Vozzi, Mariateresa Pizzo, Hans Scheffer, Sandro Banfi, Licastro, Danilo, Mutarelli, Margherita, Peluso, Ivana, Neveling, Kornelia, Wieskamp, Nienke, Rispoli, Rossella, Vozzi, Diego, Athanasakis, Emmanouil, D'Eustacchio, Angela, Pizzo, Mariateresa, D'Amico, Francesca, Ziviello, Carmela, Simonelli, Francesca, Fabretto, Antonella, Scheffer, Han, Gasparini, Paolo, Banfi, Sandro, Nigro, Vincenzo, Licastro, D, Mutarelli, M, Peluso, I, Neveling, K, Wieskamp, N, Rispoli, R, Vozzi, D, Athanasakis, E, D'Eustacchio, A, Pizzo, M, D'Amico, F, Ziviello, C, Fabretto, A, Scheffer, H, and Gasparini, P

Subjects
Genetics and Molecular Biology (all), Genetic Screens, Gene Identification and Analysis, lcsh:Medicine, Pilot Projects, Biochemistry, Genome Databases, Exome, Genome Sequencing, lcsh:Science, Child, Exome sequencing, Genetics, 0303 health sciences, Multidisciplinary, Massive parallel sequencing, Genome, Medicine (all), 030305 genetics & heredity, High-Throughput Nucleotide Sequencing, Genomics, 3. Good health, Molecular Diagnostic Techniques, Child, Preschool, Medicine, Usher Syndrome, Genome, Human, Humans, Sequence Analysis, DNA, Usher Syndromes, Agricultural and Biological Sciences (all), Biochemistry, Genetics and Molecular Biology (all), Sequence Analysis, Research Article, Human, Molecular Diagnostic Technique, Sequence Databases, Genetic Counseling, Biology, DNA sequencing, Genomic disorders and inherited multi-system disorders DCN MP - Plasticity and memory [IGMD 3], Genomic disorders and inherited multi-system disorders [IGMD 3], Molecular Genetics, 03 medical and health sciences, Pilot Project, Genetic Testing, Preschool, Genotyping, 030304 developmental biology, Clinical Genetics, lcsh:R, Personalized Medicine, Human Genetics, DNA, Molecular diagnostics, Otorhinolaryngology, Genetics of Disease, Mutation Databases, Human genome, lcsh:Q
Abstract

Contains fulltext : 108716.pdf (Publisher’s version ) (Open Access) Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS) technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25x, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified.

Published
2012

46. Organo-silane coated substrates for DNA purification

Author

M. Anderle, Lia Vanzetti, L. Marocchi, Cecilia Pederzolli, Cristina Potrich, Lorenzo Lunelli, Laura Pasquardini, Sonia Lucia Fiorilli, Diego Vozzi, Paolo Gasparini, Pasquardini, L., Lunelli, L., Potrich, C., Marocchi, L., Fiorilli, S., Vozzi, D., Vanzetti, L., Gasparini, P., Anderle, M., and Pederzolli, C.

Subjects
Organo-silane molecules, Chromatography, Materials science, Elution, Base pair, General Physics and Astronomy, Substrate (chemistry), Surfaces and Interfaces, General Chemistry, DNA separation by silica adsorption, Condensed Matter Physics, DNA extraction, Electrostatic interaction, Surfaces, Coatings and Films, Surfaces, Coatings and Films, chemistry.chemical_compound, genomic DNA, chemistry, Triethoxysilane, Organo-silane molecule, DNA
Abstract

The use of blood as DNA source to be employed in genetic analysis requires a purification process in order to remove proteins, lipids and any other contaminants, such as hemoglobin, which inhibit PCR. On the other hand, the increasing demand of miniaturized and automated biological tests able to reduce time and cost of analysis, requires the development and the characterization of materials aimed to perform the DNA purification processes in micro-devices. In this work we studied the interaction of DNA molecules with modified silicon based substrates, positively charged after deposition of a (3-aminopropyl)triethoxysilane (APTES) or 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (AEEA) interfacial layer. The evaluation of the DNA adsorption and elution capacity of different substrates (thermally grown silicon oxide, silicon oxide obtained by plasma enhanced chemical vapour deposition, and Pyrex ® ) was studied taking into account the nature of the substrate and the effect of DNA length (in the 208–50,000 base pairs range). Main findings are that DNA elution capacity depends both on the utilized substrate and on the choice of the silanizing agent. Higher DNA recovery was obtained from AEEA-modified substrates, but the eluted DNA had different electrophoretic properties from native DNA. DNA with the same electrophoretic behaviour as genomic DNA was instead recovered from APTES-treated surfaces. Furthermore, the length of DNA present in the starting material strongly modulates the elution efficiency, longer DNA being released in a lesser amount, suggesting that opportunely modified surfaces could be used as systems for differential DNA separation.

Published
2011

47. Effect of materials for micro-electro-mechanical systems on PCR yield

Author

Cristina Panciatichi, Laura Pasquardini, Lorenzo Lunelli, Cristina Potrich, Lia Vanzetti, M. Anderle, Cecilia Pederzolli, Diego Vozzi, and Stefania Forti

Subjects
Microelectromechanical systems, Silicon, Materials science, Passivation, Surface Properties, Photoelectron Spectroscopy, technology, industry, and agriculture, Biophysics, Analytical chemistry, chemistry.chemical_element, General Medicine, Chemical vapor deposition, DNA, Micro-Electrical-Mechanical Systems, Microscopy, Atomic Force, Silicon Dioxide, Polymerase Chain Reaction, chemistry, X-ray photoelectron spectroscopy, Plasma-enhanced chemical vapor deposition, Microscopy, Silicon oxide
Abstract

In this study we analyzed the surface properties of different silicon-based materials used for micro-electro-mechanical systems (MEMS) production, such as thermally grown silicon oxide, plasma-enhanced chemical vapor deposition (PECVD)-treated silicon oxide, reactive-ion etch (RIE)-treated silicon oxide, and Pyrex. Substrates were characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) to define the surface chemical and morphological properties, and by fluorescence microscopy to directly assess the absorption of the different polymerase chain reaction (PCR) components. By using microchips fabricated with the same materials we investigated their compatibility with PCR reactions, exploiting the use of different enzymes and reagents or proper surface treatments. We established the best conditions for DNA amplification in silicon/Pyrex microdevices depending on the type of device and fabrication method used and the quality of reagents, rather than on the passivation treatment or increment in standard Taq polymerase concentration.

Published
2009

48. Microarray and large-scale in silico-based identification of genes functionally related to Haptoglobin and/or Hemopexin

Author

Sharmila Fagoonee, Lorenzo Silengo, Emanuela Tolosano, Ferdinando Di Cunto, Paolo Gasparini, Diego Vozzi, Maurizio Pellegrino, Fiorella Altruda, Stefano Volinia, Fagoonee, S, DI CUNTO, F, Vozzi, Diego, Volinia, S, Pellegrino, M, Gasparini, Paolo, Silengo, L, Atruda, F, and Tolosano, E.

Subjects
hemopexin, Microarray, In silico, Computational biology, Mice, Complementary DNA, Genetics, polycyclic compounds, Animals, skin and connective tissue diseases, Molecular Biology, Gene, Oligonucleotide Array Sequence Analysis, Mice, Knockout, Haptoglobins, biology, Reverse Transcriptase Polymerase Chain Reaction, Microarray analysis techniques, Haptoglobin, Acute-phase protein, food and beverages, Hemopexin, Cell Biology, General Medicine, haptoglobin, Mice, Inbred C57BL, body regions, biology.protein, microarray
Abstract

Haptoglobin and Hemopexin are plasma acute phase proteins that bind with high-affinity hemoglobin and heme, respectively. They play a key role in the protection against oxidative stress and inflammation. To dissect in more detail the mechanism of action of Haptoglobin and Hemopexin, it is important to identify their downstream effectors as well as genes functionally related to them. To this end, we performed a cDNA microarray analysis to compare gene expression profiles of the liver of Haptoglobin and Hemopexin single and double null mice to that of wild-type controls. Then, to extract the best candidates considered to be functionally related to Haptoglobin and/or Hemopexin from microarray-derived gene lists, we used a bioinformatic approach consisting in the screening of published microarray data for genes showing coexpression with Haptoglobin or Hemopexin. This strategy allowed us to identify a group of genes coexpressed with Haptoglobin or Hemopexin and transcriptionally modulated by their lack. These genes present a high probability to be functionally related to Haptoglobin and Hemopexin. Based on literature data, we picked up from this group of genes the ras suppressor Rsu1, the member of the G-protein signal transduction family Gnai2, and the cytokine Mdk as the best candidates mediating the anti-inflammatory action of Haptoglobin and Hemopexin.

Published
2006

49. Correction: Corrigendum: Rare coding variants and X-linked loci associated with age at menarche

Author

Elizabeth A. Streeten, Joanne M. Murabito, Alison M. Dunning, Igor Rudan, Tõnu Esko, Lynne J. Hocking, Ailith Pirie, Douglas F. Easton, Laura Crisponi, Antonietta Robino, Ken K. Ong, David Karasik, Paul M. Ridker, Leslie A. Lange, Eleonora Porcu, Kathryn L. Lunetta, Ethan M. Lange, Lisette Stolk, Francesco Cucca, Anna Murray, Fernando Rivadeneira, Michela Traglia, Rebecca D. Jackson, Henry Völzke, John R. B. Perry, Cathy E. Elks, Ozren Polasek, Daniel F. Gudbjartsson, Jenny A. Visser, Albert Hofman, Claudia Langenberg, Andrea D. Coviello, Nora Franceschini, Diego Vozzi, Alexander P. Reiner, Sheila Ulivi, David Schlessinger, Jennifer E. Huffman, Laura M. Yerges-Armstrong, Elisabeth Altmaier, Daniela Toniolo, Jinyan Huang, Cinzia Sala, Patrick Sulem, Chunyan He, Frank B. Hu, Antonis C. Antoniou, Reedik Mägi, David A. Hinds, Jennifer Kriebel, Xin Li, Eric Boerwinkle, Marek Zygmunt, Caterina Barbieri, David J. Porteous, André G. Uitterlinden, Alanna C. Morrison, Joyce Y. Tung, Simin Liu, Carol A. Wang, Kari Stefansson, Megan L. Grove, Melissa Wellons, Doris Stöckl, Nicholas J. Wareham, Lynda M. Rose, Konstantin Strauch, Julie E. Buring, James G. Wilson, Caroline Hayward, Sandosh Padmanabhan, Evelin Mihailov, Alexander Teumer, Craig E. Pennell, Ursula M. Schick, Andres Metspalu, Deborah J. Thompson, Unnur Thorsteinsdottir, Katherine S. Ruth, Uwe Völker, Felix R. Day, Jian'an Luan, Robert A. Scott, Ellen W. Demerath, Ilaria Gandin, and Daniel I. Chasman

Subjects
Genetics, 03 medical and health sciences, 0302 clinical medicine, Multidisciplinary, 030220 oncology & carcinogenesis, 030232 urology & nephrology, Menarche, General Physics and Astronomy, General Chemistry, Biology, General Biochemistry, Genetics and Molecular Biology, Genealogy, Coding (social sciences)
Abstract

Nature Communications 6, Article number: 7756 10.1038/ncomms8756 (2015); Published August042015; Updated December172016 In the Results section and in the legend of Table 1 of this Article, the company deCODE genetics, Inc. is incorrectly referred to as ‘Diabetes Epidemiology: collaborative analysis of Diagnostic criteria in Europe'. In neither instance is deCODE an abbreviation.

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50. The p53 transcriptional pathway is preserved in ATMmutated and NOTCH1mutated chronic lymphocytic leukemias

Author

Elisa Piscianz, Chiara Agnoletto, Antonio Cuneo, Elisabetta Melloni, Simeone Dal Monego, Emmanouil Athanasakis, Rebecca Voltan, Paola Secchiero, Ludovica Segat, Diego Vozzi, Gian Matteo Rigolin, and Giorgio Zauli

Subjects
Male, Models, Molecular, p53, B-CLL, ATM, NOTCH1, Nutlin-3, Molecular Sequence Data, Ataxia Telangiectasia Mutated Proteins, Biology, DNA sequencing, NO, Transcription (biology), hemic and lymphatic diseases, Humans, Receptor, Notch1, Gene, neoplasms, Aged, Genetics, Aged, 80 and over, Base Sequence, Activator (genetics), DNA-binding domain, Genes, p53, Molecular biology, Leukemia, Lymphocytic, Chronic, B-Cell, In vitro, Oncology, Mutation, biology.protein, Mdm2, Female, Tumor Suppressor Protein p53, Signal Transduction, Research Paper
Abstract

// Emmanouil Athanasakis 1* , Elisabetta Melloni 2* , Gian Matteo Rigolin 3 , Chiara Agnoletto 2 , Rebecca Voltan 2 , Diego Vozzi 1 , Elisa Piscianz 1 , Ludovica Segat 1 , Simeone Dal Monego 4 , Antonio Cuneo 3 , Paola Secchiero 2 and Giorgio Zauli 1 1 Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, Trieste, Italy 2 Department of Morphology, Surgery, Experimental Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy 3 Department of Medical Sciences, University of Ferrara-Arcispedale S. Anna, Ferrara, Italy 4 Cluster in Biomedicine, CBM S.c.r.l., Bioinformatic Services, Area Science Park, Trieste, Italy * These authors contributed equally to this work Correspondence: Giorgio Zauli, email: // Keywords : B-CLL, p53, ATM, NOTCH1, Nutlin-3 Received : June 16, 2014 Accepted : July 11, 2014 Published : July 13, 2014 Abstract By using next generation sequencing, we have analyzed 108 B chronic lymphocytic leukemia (B-CLL) patients. Among genes involved in the TP53 pathway, we found frequent mutations in ATM (n=18), TP53 (n=10) and NOTCH1 (n=10) genes, rare mutations of NOTCH2 (n=2) and CDKN1A/p21 (n=1) and no mutations in BAX , MDM2 , TNFRSF10A and TNFRSF10B genes. The in vitro treatment of primary B-CLL cells with the activator of p53 Nutlin-3 induced the transcription of p53 target genes, without significant differences between the B-CLL without mutations and those harboring either ATM or NOTCH1 mutations. On the other hand, the subgroup of TP53 mutated B-CLL exhibited a significantly lower induction of the p53 target genes in response to Nutlin-3 as compared to the other B-CLL samples. However, among the TP53 mutated B-CLL, those showing mutations in the high hot spot region of the DNA binding domain [273-280 aa] maintained a significantly higher p53-dependent transcriptional activity as compared to the other TP53 mutated B-CLL samples. Since the ability to elicit a p53-dependent transcriptional activity in vitro has a positive prognostic significance, our data suggest that ATM mutated , NOTCH1 mutated and surprisingly, also a subset of TP53 mutated B-CLL patients might benefit from therapeutic combinations including small molecule activator of the p53 pathway.

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