,, Ministero dell' Istruzione, dell' Università e della Ricerca

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1 ,, Ministero dell' Istruzione, dell' Università e della Ricerca Dipartimento per l'università, l'alta Formazione Artistica, Musicale e Coreutica e per la Ricerca Direzione Generale per il Coordinamento e lo Sviluppo della Ricerca PROGRAMMI DI RICERCA SCIENTIFICA DI RILEVANTE INTERESSE NAZIONALE RICHIESTA DI COFINANZIAMENTO (D.M. 1152/ric del 27/12/2011) PROGETTO DI UNA UNITÀ DI RICERCA - MODELLO B Anno prot. 2010X3Y2Y2_ Area Scientifico-disciplinare 2 - Coordinatore Scientifico SIMONELLI FRANCESCA Professore Straordinario Seconda Università degli Studi di NAPOLI Facoltà di MEDICINA e CHIRURGIA Dipartimento di OFTALMOLOGIA 3 - Responsabile dell'unità di Ricerca VALENTE (Cognome) Professore Associato confermato (Qualifica) ENZA MARIA (Nome) 13/09/1972 (Data di nascita) VLNNMR72P53H501N (Codice fiscale) Università degli Studi di MESSINA (Università/Ente) Dipartimento di SCIENZE PEDIATRICHE MEDICHE E CHIRURGICHE (Dipartimento) (telefono) (fax) e.valente@css-mendel.it ( ) 4 - Curriculum scientifico Nata a Roma il 13/09/0972. Incarichi attuali: -Professore Associato Confermato di Genetica Medica, Università di Messina (da novembre 2006); - Coordinatore Unità di Neurogenetica Molecolare e Funzionale, Istituto CSS-Mendel, Roma (da gennaio 2001). Titoli di studio: - Laurea in Medicina e Chirurgia cum laude, Università Cattolica di Roma (luglio 1994); - Specializzazione in Neurologia cum laude, Università Cattolica di Roma (novembre 1999); - Dottorato di Ricerca internazionale (PhD) in Neurogenetica, University College of London (luglio 2003). Attività clinica: - Coordinatore Servizio di Neurogenetica, Dip. di Scienze Pediatriche Mediche e Chirurgiche, Università di Messina (da novembre 2006); - Responsabile Ambulatorio di Neurogenetica e di Neurologia, Istituto CSS-Mendel, Roma (da settembre 2011) Attività didattica: - Corsi di Genetica Medica e Patologia Generale, CdL in Farmacia, Biotecnologie ed Infermieristica Pediatrica, Università di Messina Attività di ricerca: - Studi di genetica clinica, molecolare e funzionale nell'ambito della neurogenetica, con particolare interesse alle patologie neurodegenerative, disturbi del movimento, atassie pediatriche e malformazioni congenite del cervelletto e del troncoencefalo. Premi: - Premio Novartis per la Neurologia (2001); - Premio l'oreal per le donne e la scienza (2006). Incarichi professionali e scientifici: - Vicepresidente dell'associazione Italiana Sindrome di Joubert e Atassie Congenite (AISJAC); - Membro del Comitato Scientifico dell'associazione Italiana Sindromi Neurodegenerativa da Accumulo di Ferro (AISNAF); - Invited reviewer per numerose riviste scientifiche internazionali e per la Michael J. Fox Foundation for Parkinson's Disease ; - Coautore dell'enciclopedia on-line Orphanet ; - Relatrice su invito a numerosi congressi nazionali ed internazionali, corsi di aggiornamento e lezioni in scuole di specializzazione di genetica medica e neurologia. Finanziamenti attivi:

2 - National Institute of Health (partner esterno, apr2004-mar2014); - European Community FP7-HEALTH-2009 (partner clinico, apr2010-mar2013); - Fondazione Telethon (PI, set2010-ago2012); - Ministero della Salute - malattie rare (PI, set2011-ago2014; co-pi, set2011-ago2014); - European Research Council Starting Grant (PI, set2011-ago2016) - Ministero della Salute - giovani ricercatori (PI, dic2011-nov2014; co-pi, lug2009-giu2012); - MIUR - FIRB accordi di programma (co-pi, dic2011-nov2015). Produzione scientifica: pubblicazioni scientifiche su riviste internazionali peer-reviewed (IF complessivo: 790.2, H-index: 32); - 8 capitoli di libri. Born in Rome on September 13th, Present positions: - Associate Professor of Medical Genetics, University of Messina; - Head, Molecular and Functional Neurogenetics Unit, CSS-Mendel Institute, IRCCS Casa Sollievo della Sofferenza, Rome. Education: - Degree in Medicine cum laude, Catholic University, Rome (July 1994); - Residency in Neurology cum laude, Catholic University, Rome (November 1999); - PhD in Neurogenetics, Institute of Neurology, London (May 2003). Clinical activity: - Head, Neurogenetic Section, Paediatric Genetic and Immunology Unit, Dept. of Medical and Surgical Paediatric Sciences, University of Messina; - Head, Neurogenetics and Neurology Clinics, CSS-Mendel Institute, Rome. Teaching activity: - Medical Genetics Courses for the Degrees of Medicine, Pharmacy, Chemistry and Biotechnology, University of Messina. Research activity: - Clinical, genetic and functional studies of several neurogenetic diseases, with particular focus to Parkinson's disease, dystonic syndromes, human ciliopathies and conditions associated to cerebellar and brainstem malformations. Honors: - Novartis Price for neurology (2001); - L'Oreal Prize for Women in Science (2006). Scientific and professional tasks: - Vicepresident, Italian Association of Joubert syndrome and congenital ataxias (AISJAC); - Member of the Scientific Committee, Italian Association of Neurodegenerative Syndromes with Iron Accumulation (AISNAF); - Invited reviewer for several international journals and international grant agencies; - Coauthor of Orphanet online enciclopaedia; - Invited speaker at national and international congresses; teaching courses and seminars to residents in medical genetics and neurology. Active funding sources: - National Institute of Health; - Italian Telethon Foundation; - Italian Ministry of Health; - Italian Ministry of University and Research; - European Research Council. Scientific publications: scientific publications on international peer-reviewed journals (total IF: 790.2, H-index: 32); - 8 book chapters. 5 - Pubblicazioni scientifiche più significative del Responsabile dell'unità di Ricerca 1. Lee JE, Silhavy JL, Zaki MS, Schroth J, Bielas SL, Marsh SE, Olvera J, Brancati F, Iannicelli M, Ikegami K, Schlossman AM, Merriman B, Attié-Bitach T, Logan CV, Glass IA, Cluckey A, Louie CM, Lee JH, Raynes HR, Rapin I, Setou M, Barbot C, Boltshauser E, Nelson SF, Hildebrandt F, Johnson CA, Doherty DA, VALENTE EM, Gleeson JG (2012). TSGA14 is mutated in Joubert syndrome ans is required for tubulin glutamylation at the cilium. NATURE GENETICS, vol. 44; p , ISSN: BRIGUGLIO M, PINELLI L, GIORDANO L, FERRARIS A, GERMANO E, MICHELETTI S, SEVERINO MS, BERNARDINI L, LODDO S, TORTORELLA G, ORMITTI F, GASPAROTTI R, CBCD-SG, ROSSI A, VALENTE EM (2011). Pontine Tegmental Cap Dysplasia: developmental and cognitive outcome in three adolescent patients. ORPHANET JOURNAL OF RARE DISEASES, vol. 6; p , ISSN: Chartier-Harlin MC, Dachsel JC, Vilariño-Güell C, Lincoln SJ, Leprêtre F, Hulihan MM, Kachergus J, Milnerwood AJ, Tapia L, Song MS, Le Rhun E, Mutez E, Larvor L, Duflot A, Vanbesien-Mailliot C, Kreisler A, Ross OA, Nishioka K, Soto-Ortolaza AI, Cobb SA, Melrose HL, Behrouz B, Keeling BH, Bacon JA, Hentati E, Williams L, Yanagiya A, Sonenberg N, Lockhart PJ, Zubair AC, Uitti RJ, Aasly JO, Krygowska-Wajs A, Opala G, Wszolek ZK, Frigerio R, Maraganore DM, Gosal D, Lynch T, Hutchinson M, Bentivoglio AR, VALENTE EM, Nichols WC, Pankratz N, Foroud T, Gibson RA, Hentati F, Dickson DW, Destée A, Farrer MJ. (2011). Translation initiator EIF4G1 mutations in familial Parkinson disease.. AMERICAN JOURNAL OF HUMAN GENETICS, vol. 89; p , ISSN: VALENTE EM, Brancati F, Boltshauser E, Dallapiccola B (2011). Clinical utility gene card for: Joubert syndrome. EUROPEAN JOURNAL OF HUMAN GENETICS, vol. 19(9); p. ---, ISSN: , doi: /ejhg Zanni G, Barresi S, Travaglini L, Bernardini L, Rizza T, Digilio MC, Mercuri E, Cianfarani S, Valeriani M, Ferraris A, Da Sacco L, Novelli A, VALENTE EM, Dallapiccola B, Bertini ES (2011). FGF17, a gene involved in cerebellar development, is downregulated in a patient with Dandy-Walker malformation carrying a de novo 8p deletion. NEUROGENETICS, vol. 12; p , ISSN: BRANCATI F, DALLAPICCOLA B, VALENTE EM (2010). Joubert Syndrome and related disorders. ORPHANET JOURNAL OF RARE DISEASES, vol. 5; p , ISSN: IANNICELLI M, BRANCATI F, MOUGOU-ZERELLI S, MAZZOTTA A, THOMAS S, ELKHARTOUFI N, TRAVAGLINI L, GOMES C, ARDISSINO GL, BERTINI E, BOLTSHAUSER E, CASTORINA P, D'ARRIGO S, FISCHETTO R, LEROY B, LOGET P, BONNIÈRE M, STARCK L, TANTAU J, GENTILIN B, MAJORE S, SWISTUN D, FLORI E, LALATTA F, PANTALEONI C, PENZIEN J, GRAMMATICO P, ALI PACHA L, TAZIR M, ZANKL A, LEVENTER R, GRATTAN-SMITH P, JANECKE A, D'HOOGHE M, SZNAJER Y, VAN COSTER R, DEMERLEIR L, DIAS K, MOCO C, MOREIRA A, AE KIM C, MAEGAWA G, LONCAREVIC D, MEJASKI-BOSNJAK V, PETKOVIC D, ABDEL-SALAM GM, ABDEL-ALEEM A, ZAKI MS, MARTI I, QUIJANO-ROY S, SIGAUDY S, DE LONLAY P, ROMANO S, VERLOES A, TOURAINE R, KOENIG M, LAGIER-TOURENNE C, MESSER J, COLLIGNON P, WOLF N, PHILIPPI H, LEMKE J, DACOU-VOUTETAKIS C, KITSIOU TZELI S, PONS R, SZTRIHA L, HALLDORSSON S, JOHANNSDOTTIR J, LUDVIGSSON P, PHADKE SR, UDANI V, STUART B, MAGEE A, LEV D, MICHELSON M, BEN-ZEEV B, DI GIACOMO M, GENTILE M, GUANTI G, D'ADDATO O, PAPADIA F, SPANO M, BERNARDI F, SERI M, BENEDICENTI F, STANZIAL F, BORGATTI R, ACCORSI P, BATTAGLIA S, FAZZI E, GIORDANO L, IZZI C, PINELLI L, BOCCONE L, GUANCIALI P, ROMOLI R, BIGONI S, FERLINI A, ANDREUCCI E, DONATI MA, GENUARDI M, CARIDI G, DIVIZIA MT, FARAVELLI F, GHIGGERI G, PESSAGNO, AMORINI M, BRIGUGLIO M, BRIUGLIA S, RIGOLI L, SALPIETRO C, TORTORELLA G, ADAMI A, MARRA G, RIVA D, SCELSA B, SPACCINI L, UZIEL G, COPPOLA G, DEL GIUDICE E, VITIELLO G, LAVERDA AM, LUDWIG K, PERMUNIAN A, SUPPIEJ A, MACALUSO C, SIGNORINI S, UGGETTI C, BATTINI R, DI GIACOMO M, PRIOLO M, CILIO MR, D'AMICO A, DI SABATO ML, EMMA F, LEUZZI V, PARISI P, STRINGINI G, ZANNI G, POLLAZZON M, RENIERI A, VASCOTTO M, SILENGO M, DE VESCOVI R, GRECO D, ROMANO C, CAZZAGON M, SIMONATI A, AL-TAWARI AA, BASTAKI L, MÉGARBANÉ A, MATULEVICIENE A, SABOLIC AVRAMOVSKA V, SAID E, DE JONG MM, PRESCOTT T, STROMME P, VON DER LIPPE C, KOUL R, RAJAB A, AZAM M, BARBOT C, JOCIC-JAKUBI B, GENER QUEROL B, MARTORELL SAMPOL L, RODRIGUEZ B, PASCUAL-CASTROVIEJO I, STROZZI S, FLUSS J, TEBER S, TOPCU M, ANLAR B, COMU S, KARACA E, KAYSERILI H, YÜKSEL A, AKGUL M, AKCAKUS M, AL GAZALI L, NICHOLL D, WOODS CG, BENNETT C, HURST J, SHERIDAN E, BARNICOAT A, CARR L, HEN... (2010). Novel TMEM67 mutations and genotype-phenotype

3 correlates in meckelin-related ciliopathies. HUMAN MUTATION, vol. 31(5); p. E1319-E1331, ISSN: , doi: /humu LOUIE CM, CARIDI G, LOPES VS, BRANCATI F, KISPERT A, LANCASTER MA, SCHLOSSMAN AM, OTTO EA, LEITGES M, GRÖNE HJ, LOPEZ I, GUDISEVA HV, O'TOOLE JF, VALLESPIN E, AYYAGARI R, AYUSO C, CREMERS FP, DEN HOLLANDER AI, KOENEKOOP RK, DALLAPICCOLA B, GHIGGERI GM, HILDEBRANDT F, VALENTE EM, WILLIAMS DS, GLEESON JG (2010). AHI1 is required for photoreceptor outer segment development and is a modifier for retinal degeneration in nephronophthisis. NATURE GENETICS, vol. 42; p , ISSN: V. STURM, H. LEIBA, M. N. MENKE, VALENTE EM, A. PORETTI, K. LANDAU, E. BOLTSHAUSER (2010). Ophthalmological findings in Joubert syndrome. EYE, vol. 24; p , ISSN: X, doi: /eye VALENTE EM, LOGAN CV, MOUGOU-ZERELLI S, LEE JH, SILHAVY JL, BRANCATI F, IANNICELLI M, TRAVAGLINI L, ROMANI S, ILLI B, ADAMS M, SZYMANSKA K, MAZZOTTA A, LEE JE, TOLENTINO JC, SWISTUN D, SALPIETRO CD, FEDE C, GABRIEL S, RUSS C, CIBULSKIS K, SOUGNEZ C, HILDEBRANDT F, OTTO EA, HELD S, DIPLAS BH, DAVIS EE, MIKULA M, STROM CM, BEN-ZEEV B, LEV D, SAGIE TL, MICHELSON M, YARON Y, KRAUSE A, BOLTSHAUSER E, ELKHARTOUFI N, ROUME J, SHALEV S, MUNNICH A, SAUNIER S, INGLEHEARN C, SAAD A, ALKINDY A, THOMAS S, VEKEMANS M, DALLAPICCOLA B, KATSANIS N, JOHNSON CA, ATTIÉ-BITACH T, GLEESON JG. (2010). Mutations in TMEM216 perturb ciliogenesis and cause Joubert, Meckel and related syndromes. NATURE GENETICS, vol. 42(7); p , ISSN: BIELAS S, SILHAVY JL, BRANCATI F, KISSELEVA MV, AL-GAZALI L, SZTRIHA L, BAYOUMI RA, ZAKI MS, ABDEL-ALEEM A, ROSTI O, KAYSERILI H, SWISTUN D, SCOTT LC, BERTINI E, BOLTSHAUSER E, FAZZI E, TRAVAGLINI L, FIELD SJ, GAYRAL S, JACOBY M, SCHURMANS S, DALLAPICCOLA B, MAJERUS PW, VALENTE EM, GLEESON JG (2009). Mutations in the inositol polyphosphate-5-phosphatase E gene link phosphatidyl inositol signaling to the ciliopathies. NATURE GENETICS, vol. 41; p , ISSN: BRANCATI F, IANNICELLI M, TRAVAGLINI L, MAZZOTTA A, BERTINI E, BOLTSHAUSER E, D'ARRIGO S, EMMA F, FAZZI E, GALLIZZI R, GENTILE M, LONCAREVIC D, MEJASKI-BOSNJAK V, PANTALEONI C, RIGOLI L, SALPIETRO CD, SIGNORINI S, STRINGINI GR, VERLOES A, ZABLOKA D, DALLAPICCOLA B, GLEESON JG, VALENTE EM, BRIUGLIA S, INTERNATIONAL JSRD STUDY GROUP. (2009). MKS3/TMEM67 Mutations Are a Major Cause of COACH Syndrome, a Joubert Syndrome Related Disorder with Liver Involvement. HUMAN MUTATION, vol. 30(2); p. E432-E442, ISSN: L. GIORDANO, A. VIGNOLI, L. PINELLI, F. BRANCATI, P. ACCORSI, F. FARAVELLI, R. GASPAROTTI, T. GRANATA, G. GIACCONE, F. INVERARDI, C. FRASSONI, B. DALLAPICCOLA, VALENTE EM, R. SPREAFICO (2009). Joubert syndrome with bilateral polymicrogyria: clinical and neuropathological findings in two brothers. AMERICAN JOURNAL OF MEDICAL GENETICS. PART A (ONLINE), vol. 149A; p , ISSN: , doi: /ajmg.a PORETTI A, DIETRICH ALBER F, BRANCATI F, DALLAPICCOLA B, VALENTE EM, BOLTSHAUSER E (2009). Normal cognitive functions in Joubert syndrome. NEUROPEDIATRICS, vol. 40; p , ISSN: X 15. S. MOUGOU-ZERELLI, S. THOMAS, E. SZENKER, S. AUDOLLENT, N. ELKHARTOUFI, C. BABARIT, S. ROMANO, R. SALOMON, J. AMIEL, C. ESCULPAVIT, M. GONZALES, E. ESCUDIER, B. LEHEUP, P. LOGET, S. ODENT, J. ROUME, M. GÉRARD, A. DELEZOIDE, S. KHUNG, S. PATRIER, M. CORDIER, R. BOUVIER, J. MARTINOVIC, M. GUBLER, N. BODDAERT, A. MUNNICH, F. ENCHA-RAZAVI, VALENTE EM, A. SAAD, S. SAUNIER, M. VEKEMANS, T. ATTIÉ-BITACH (2009). CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation. HUMAN MUTATION, vol. 30; p , ISSN: , doi: /humu TRAVAGLINI L, BRANCATI F, ATTIE-BITACH T, AUDOLLENT S, BERTINI E, KAPLAN J, PERRAULT I, IANNICELLI M, MANCUSO B, RIGOLI L, ROZET JM, SWISTUN D, TOLENTINO J, DALLAPICCOLA B, GLEESON JG, VALENTE EM, INTERNATIONAL JSRD STUDY GROUP, BRIUGLIA S, ZANKL A, LEVENTER R, GRATTAN-SMITH P, JANECKE A, D'HOOGHE M, SZNAJER Y, VAN COSTER R, DEMERLEIR L, DIAS K, MOCO C, MOREIRA A, KIM CA, MAEGAWA G, PETKOVIC D, ABDEL-SALAM GM, ABDEL-ALEEM A, ZAKI MS, MARTI I, QUIJANO-ROY S, SIGAUDY S, DE LONLAY P, ROMANO S, TOURAINE R, KOENIG M, LAGIER-TOURENNE C, MESSER J, COLLIGNON P, WOLF N, PHILIPPI H, KITSIOU TZELI S, HALLDORSSON S, JOHANNSDOTTIR J, LUDVIGSSON P, PHADKE SR, UDANI V, STUART B, MAGEE A, LEV D, MICHELSON M, BEN-ZEEV B, FISCHETTO R, BENEDICENTI F, STANZIAL F, BORGATTI R, ACCORSI P, BATTAGLIA S, FAZZI E, GIORDANO L, PINELLI L, BOCCONE L, BIGONI S, FERLINI A, DONATI MA, CARIDI G, DIVIZIA MT, FARAVELLI F, GHIGGERI G, PESSAGNO A, BRIGUGLIO M, BRIUGLIA S, SALPIETRO CD, TORTORELLA G, ADAMI A, CASTORINA P, LALATTA F, MARRA G, RIVA D, SCELSA B, SPACCINI L, UZIEL G, DEL GIUDICE E, LAVERDA AM, LUDWIG K, PERMUNIAN A, SUPPIEJ A, SIGNORINI S, UGGETTI C, BATTINI R, DI GIACOMO M, CILIO MR, DI SABATO ML, LEUZZI V, PARISI P, POLLAZZON M, SILENGO M, DE VESCOVI R, GRECO D, ROMANO C, CAZZAGON M, SIMONATI A, AL-TAWARI AA, BASTAKI L, MÉGARBANÉ A, SABOLIC AVRAMOVSKA V, DE JONG MM, STROMME P, KOUL R, RAJAB A, AZAM M, BARBOT C, MARTORELL SAMPOL L, RODRIGUEZ B, PASCUAL-CASTROVIEJO I, TEBER S, ANLAR B, COMU S, KARACA E, KAYSERILI H, YÜKSEL A, AKCAKUS M, AL GAZALI L, SZTRIHA L, NICHOLL D, WOODS CG, BENNETT C, HURST J, SHERIDAN E, BARNICOAT A, HENNEKAM R, LEES M, BLAIR E, BERNES S, SANCHEZ H, CLARK AE, DEMARCO E, DONAHUE C, SHERR E, HAHN J, SANGER TD, GALLAGER TE, DOBYNS WB, DAUGHERTY C, KRISHNAMOORTHY KS, SARCO D, WALSH CA, MCKANNA T, MILISA J, CHUNG WK, DE VIVO DC, RAYNES H, SCHUBERT R, SEWARD A, BROOKS DG, GOLDSTEIN A, CALDWELL J, FINSECKE E, MARIA BL, HOLDEN K, CRUSE RP, SWOBODA KJ, VISKOCHIL D. (2009). Expanding CEP290 mutational spectrum in ciliopathies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART A (ONLINE), vol. 149A(10); p , ISSN: BRANCATI F, IANNICELLI M, TRAVAGLINI L, MAZZOTTA A, BERTINI E, BOLTSHAUSER E, D'ARRIGO S, EMMA F, FAZZI E, GALLIZZI R, GENTILE M, LONCAREVIC D, MEJASKI-BOSNJAK V, PANTALEONI C, RIGOLI L, SALPIETRO CD, SIGNORINI S, STRINGINI GR, VERLOES A, ZABLOKA D, DALLAPICCOLA B, GLEESON JG, VALENTE EM, THE INTERNATIONAL JSRD STUDY GROUP (2008). MKS3/TMEM67 mutations are a major cause of COACH Syndrome, a Joubert syndrome related disorder with liver involvement. HUMAN MUTATION, vol. 4, ISSN: BRANCATI F, TRAVAGLINI L, ZABLOCKA D, BOLTSHAUSER E, ACCORSI P, MONTAGNA G, SILHAVY JL, BARRANO G, BERTINI E, EMMA F, RIGOLI L, INTERNATIONAL JSRD STUDY GROUP, DALLAPICCOLA B, GLEESON JG, VALENTE EM, LEVENTER R, GRATTAN-SMITH P, JANECKE A, D'HOOGHE M, VAN COSTER R, DIAS K, MOCO C, MOREIRA A, KIM CA, MAEGAWA G, ABDEL-SALAM GM, ABDEL-ALEEM A, ZAKI MS, MARTI I, QUIJANO-ROY S, DE LONLAY P, ROMANO S, VERLOES A, TOURAINE R, KOENIG M, LAGIER-TOURENNE C, MESSER J, PHILIPPI H, TZELI SK, HALLDORSSON S, JOHANNSDOTTIR J, LUDVIGSSON P, PHADKE SR, STUART B, MAGEE A, LEV D, MICHELSON M, BEN-ZEEV B, FISCHETTO R, GENTILE M, BATTAGLIA S, GIORDANO L, PINELLI L, BOCCONE L, RUGGIERI M, BIGONI S, FERLINI A, DONATI MA, PROCOPIO E, CARIDI G, FARAVELLI F, GHIGGERI G, BRIUGLIA S, SALPIETRO CD, TORTORELLA G., D'ARRIGO S, PANTALEONI C, RIVA D, UZIEL G, LAVERDA AM, PERMUNIAN A, BOVA S, BATTINI R, CILIO MR, DI SABATO M, LEUZZI V, PARISI P, SIMONATI A, AL-TAWARI AA, BASTAKI L, DE JONG MM, KOUL R, RAJAB A, AZAM M, BARBOT C, RODRIGUEZ B, PASCUAL-CASTROVIEJO I, KAYSERILI H, COMU S, AKCAKUS M, AL GAZALI L, SZTRIHA L, NICHOLL D, WOODS CG, BENNETT C, HURST J, HENNEKAM R, LEES M, BERNES S, SANCHEZ H, CLARK AE, DEMARCO E, DONAHUE C, SHERR E, HAHN J, SANGER TD, GALLAGER TE, DOBYNS WB, DAUGHERTY C, KRISHNAMOORTHY KS, SARCO D, WALSH CA, MCKANNA T, MILISA J, CHUNG WK, DE VIVO DC, RAYNES H, SCHUBERT R, SEWARD A, BROOKS DG, GOLDSTEIN A, CALDWELL J, FINSECKE E, MARIA BL, HOLDEN K, CRUSE RP, SWOBODA KJ, VISKOCHIL D (2008). RPGRIP1L mutations are mainly associated with the cerebello-renal phenotype of Joubert syndrome-related disorders. CLINICAL GENETICS, vol. 74; p , ISSN: CANTAGREL V, SILHAVY JL, BIELAS SL, SWISTUN D, MARSH SE, BERTRAND JY, AUDOLLENT S, ATTIÉ-BITACH T, HOLDEN KR, DOBYNS WB, TRAVER D, AL-GAZALI L, ALI BR, LINDNER TH, CASPARY T, OTTO EA, HILDEBRANDT F, GLASS IA, LOGAN CV, JOHNSON CA, BENNETT C, BRANCATI F, INTERNATIONAL JOUBERT SYNDROME RELATED DISORDERS STUDY GROUP, VALENTE EM, WOODS CG, GLEESON JG (2008). Mutations in the cilia gene ARL13B lead to the classical form of Joubert syndrome. AMERICAN JOURNAL OF HUMAN GENETICS, vol. 83; p , ISSN: , doi: doi: /j.ajhg VALENTE EM, BRANCATI F, DALLAPICCOLA B (2008). Genotypes and phenotypes of Joubert syndrome and related disorders. EUROPEAN JOURNAL OF MEDICAL GENETICS, vol. 51; p. 1-23, ISSN: VALENTE EM, FERRARIS A, DALLAPICCOLA B (2008). Genetic testing for paediatric neurological disorders. LANCET NEUROLOGY, vol. 7; p , ISSN: , doi: doi: /s (08) BRANCATI F, BARRANO G, SILHAVY JL, MARSH SE, TRAVAGLINI L, BIELAS SL, AMORINI M, ZABLOCKA D, KAYSERILI H, AL-GAZALI L, BERTINI E, BOLTSHAUSER E, DHOOGHE M, FAZZI E, FENERCI EY, HENNEKAM RCM, KISS A, LEES MM, MARCO E, PHADKE SR, RIGOLI L, ROMANO S, SALPIETRO SD, SHERR EH, SIGNORINI S, STROMME P, STUART B, SZTRIHA L, VISKOCHIL DH, YUKSEL A, DALLAPICCOLA B, THE INTERNATIONAL JSRD STUDY GROUP, VALENTE EM, GLEESON JG (2007). CEP290 Mutations Are Frequently Identified in the Oculo-Renal Form of Joubert Syndrome Related Disorders. AMERICAN JOURNAL OF HUMAN GENETICS, vol. 81; p , ISSN: SIMONELLI F, ZIVIELLO C, TESTA F, ROSSI S, FAZZI E, BIANCHI PE, FOSSARELLO M, SIGNORINI S, BERTONE C, GALANTUOMO S, BRANCATI F, VALENTE EM, CICCODICOLA A, RINALDI E, AURICCHIO A, BANFI S (2007). Clinical and molecular genetics of Leber's congenital amaurosis (LCA): a multi-center study of Italian patients. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, vol. 48; p , ISSN:

4 24. CARIDI G, DAGNINO M, ROSSI A, VALENTE EM, BERTINI E, FAZZI E, EMMA F, MURER L, VERRINA E, GHIGGERI GM (2006). Nephronophthisis type 1 deletion syndrome with neurological symptoms: Prevalence and significance of the association. KIDNEY INTERNATIONAL, vol. 70; p , ISSN: COX JJ, REIMANN F, NICHOLAS AK, THORNTON G, ROBERTS E, SPRINGELL K, KARBANI G, JAFRI H, MANNAN J, RAASHID Y, AL-GAZALI L, HAMAMY H, VALENTE EM, GORMAN S, WILLIAMS R, MCHALE DP, WOOD JN, GRIBBLE FM, WOODS CG (2006). An SCN9A channelopathy causes congenital inability to experience pain. NATURE, vol. 444; p , ISSN: VALENTE EM, BRANCATI F, SILHAVY JL, CASTORI M, MARSH SE, BARRANO G, BERTINI E, BOLTSHAUSER E, ZAKI MS, ABDEL-ALEEM A, ABDEL-SALAM GM, BELLACCHIO E, BATTINI R, CRUSE RP, DOBYNS WB, KRISHNAMOORTHY KS, LAGIER-TOURENNE C, MAGEE A, PASCUAL-CASTROVIEJO I, SALPIETRO DAMIANO C., SARCO D, DALLAPICCOLA B, GLEESON JG, INTERNATIONAL JSRD STUDY GROUP (2006). AHI1 gene mutations cause specific forms of Joubert syndrome-related disorders. ANNALS OF NEUROLOGY, vol. 59; p , ISSN: VALENTE EM, SILHAVY JL, BRANCATI F, BARRANO G, KRISHNASWAMI SR, CASTORI M, LANCASTER MA, BOLTSHAUSER E, BOCCONE L, AL-GAZALI L, FAZZI E, SIGNORINI S, LOUIE CM, BELLACCHIO E, BERTINI E, DALLAPICCOLA B, GLEESON JG (2006). Mutations in CEP290, which encodes a centrosomal protein, cause pleiotropic forms of Joubert syndrome. NATURE GENETICS, vol. 38; p , ISSN: CASTORI M, VALENTE EM, CLEMENTI M, TORMENE AP, BRANCATI F, CAPUTO V, DALLAPICCOLA B (2005). A novel locus for autosomal dominant cone and cone-rod dystrophies maps to the 6p gene cluster of retinal dystrophies. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, vol. 46; p , ISSN: CASTORI M, VALENTE EM, DONATI MA, SALVI S, FAZZI E, PROCOPIO E, GALLUCCIO T, EMMA F, DALLAPICCOLA B, BERTINI E (2005). NPHP1 gene deletion is a rare cause of Joubert syndrome related disorders. JOURNAL OF MEDICAL GENETICS, vol. 42; e9, ISSN: VALENTE EM, MARSH SE, CASTORI M, DIXON-SALAZAR T, BERTINI E, AL-GAZALI L, MESSER J, BARBOT C, WOODS CG, BOLTSHAUSER E, AL-TAWARI AA, SALPIETRO CD, KAYSERILI H, SZTRIHA L, GRIBAA M, KOENIG M, DALLAPICCOLA B, GLEESON JG (2005). Distinguishing the four genetic causes of Jouberts syndrome-related disorders. ANNALS OF NEUROLOGY, vol. 57; p , ISSN: Abstract dei compiti svolti dall'unità di Ricerca 7 - Settori di ricerca ERC (European Research Council) LS Life Sciences LS2 Genetics, Genomics, Bioinformatics and Systems Biology: genetics, population genetics, molecular genetics, genomics, transcriptomics, proteomics, metabolomics, bioinformatics, computational biology, biostatistics, biological modelling and simulation, systems biology, genetic epidemiology LS2_1 Genomics, comparative genomics, functional genomics LS2_10 Bioinformatics 8 - Collaborazioni con altri organismi di ricerca pubblici e privati, nazionali e internazionali, e indicazione degli eventuali collegamenti con gli obiettivi di Horizon Parole chiave CILIOPATIE SEQUENZIAMENTO DI NUOVA GENERAZIONE CORRELATI GENOTIPO-FENOTIPO CILIOPATHIES NEXT GENERATION SEQUENCING GENOTYPE-PHENOTYPE CORRELATES 10 - Stato dell'arte The generic term syndromic retinopathies defines a wide spectrum of retinal disorders manifesting in the frame of a complex phenotype due to pleiotropic multiorgan involvement. Systemic findings may variably include neurosensory hearing loss, developmental delay, central nervous system malformations, situs-inversus, infertility, disorders of limb and digit development, obesity, kidney cystic disease, liver fibrosis, and respiratory disease. The peculiar association of clinical signs and symptoms characterizes a large number of syndromes, many of which have a recognized mendelian basis. Among these, the most relevant are the so called ciliopathies, a fast-growing group of syndromic disorders caused by mutations in genes encoding proteins of the primary cilium. This long-forgotten organelle is a microtubule-based extension of cellular membranes found in nearly all cell types, including epithelium of renal tubules and bile ducts, retinal photoreceptors, and developing neurons (Goetz and Anderson, 2010, Novarino et al., 2011). Increasing evidence points to a fundamental role for primary cilia in regulating the functioning of many organs, as well as key pathways of embryonic development, such as Sonic Hedgehog (Shh) and Wnt. The Shh signaling plays a major role in events such as left-right axis asymmetry, limb development and neurogenesis and is tightly coupled with maintenance and function of primary cilia

5 (Roy, 2011, Ruat et al., 2011). Similarly, some ciliary proteins act as a molecular switch between canonical and non-canonical Wnt pathways (the latter also known as Planar Cell Polarity (PCP) pathway), thereby regulating cell adhesion and movements during gastrulation (Wallingford and Mitchell, 2011). Finally, the correct functioning of primary cilia at the embryonic node during gastrulation is necessary to establish the correct left-right asymmetry of the embryo. In the kidneys, cilial dysfunction has been identified as the principal culprit responsible for most types of cystic disease. Virtually all renal epithelial cells have one primary, non-motile cilium, that serves to sense environmental cues, such as tubular flow, and regulate a variety of intracellular signaling systems in order to maintain the growth-arrested phenotype of mature tubules (Hurd and Hildebrandt, 2011). Retinal vertebrate photoreceptors are polarized sensory neurons composed of an inner and an outer segment connected by a highly specialized primary cilium, the connecting cilium. Disruption of the function of ciliary proteins may result in a wide variety of phenotypes ranging from isolated retinal degeneration to more pleiotropic phenotypes (Adams et al., 2007, Mockel et al., 2011). For instance, the synthesis of materials required for the formation, maintenance, and function of the outer segment occurs in the inner segment. Consequently, intraflagellary transport responsible for moving cargo across the connecting cilium, is critical for the survival of photoreceptor cells, and underlies the pathogenesis of at least some forms of retinal degeneration. The requirement of delivering as many as 2000 photopigment molecules per minute to the mammalian outer segment might explain the sensitivity of photoreceptors to such defects. Besides the primary cilium, some proteins of the motile cilia may also be involved since retinitis pigmentosa can be a feature of Primary Ciliary Dyskinesia, with cilia exhibiting ultrastructural problems in the dynein arms and microtubule backbone. This association of defects characteristic of motile and sensory cilia are likely to be more common than expected, given the high overlap in protein content between the two types of cilia (Badano et al., 2006). The concept of "retinal ciliopathies" brings to attention the importance of further molecular analysis of this organelle as well as provides a potential common target for therapies for these disorders. Syndromic retinal ciliopathies include retinal degenerations associated with a large number of syndromes, such as Usher, Senior-Loken (SLS), Joubert and related disorders (JSRD), Bardet-Biedl (BBS), Meckel (MKS), Ellis-van Creveld (EVC), Jeune, Alstrom syndromes and so on (Adams et al., 2007). Most of these syndromes are genetically inherited with autosomal recessive transmission, and are characterized by extreme genetic heterogeneity, with dozens of causative genes identified to date. Intriguingly, there is marked phenotypic and genetic overlap among most ciliopathies, with intriguing allelic series and clinical correlations that have made these conditions a paradigmatic example of splitting and lumping in human genetics. A striking example is represented by the CEP290 gene, whose mutations cause not only the cerebello-oculo-renal subtype of JSRD, but also MKS, SLS and even isolated LCA, of which they represent one of the most frequent genetic determinants (den Hollander et al., 2006, Sayer et al., 2006, Valente et al., 2006, Helou et al., 2007). This extreme phenotypic variability associated with mutations in one and the same gene, often encompassing different syndromes of variable severity, remains a major open question. An intriguing explanation has implicated an oligogenic model of inheritance, with additional heterozygous mutations or variants at other ciliary genes epistatically interacting with the main recessive mutations to cause and/or modify the ciliopathy phenotype (Zaghloul and Katsanis, 2010). The oligogenic model has been initially demonstrated for BBS, a ciliopathy consisting of retinopathy, polydactyly, obesity, hypogenitalism and posterior fossa defects (Badano et al., 2006), and subsequently suggested also for NPH and JBTS (Hoefele et al., 2007, Tory et al., 2007, Davis et al., 2011). For instance, we and others have shown that the R830W variant in the AHI1 gene was associated with an increased risk to develop retinal or neurological involvement in a cohort of patients with NPH carrying the NPHP1 homozygous deletion (Tory et al., 2007, Louie et al., 2010). Similarly, the A229T variant in the RPGRIP1L gene was found to increase the risk to develop retinal degeneration in patients with ciliopathies caused by mutations in other genes (Khanna et al., 2009). These data suggest that discrete heterozygous nucleotide changes in ciliary genes may act as modifier factors of the ciliary phenotype. A systematic genetic screening of multiple ciliopathy genes is therefore a still unmet need to address this oligogenic model, and NGS technology represents a key tool to reach this challenging goal Riferimenti bibliografici - Adams NA, Awadein A, Toma HS. The retinal ciliopathies. Ophthalmic Genet. 2007;28(3): Badano JL, Leitch CC, Ansley SJ, May-Simera H, Lawson S, Lewis RA, et al. Dissection of epistasis in oligogenic Bardet-Biedl syndrome. Nature. 2006;439(7074): Badano JL, Mitsuma N, Beales PL, Katsanis N. The ciliopathies: an emerging class of human genetic disorders. Annu Rev Genomics Hum Genet. 2006;7: Bielas SL, Silhavy JL, Brancati F, Kisseleva MV, Al-Gazali L, Sztriha L, et al. Mutations in INPP5E, encoding inositol polyphosphate-5-phosphatase E, link phosphatidyl inositol signaling to the ciliopathies. Nat Genet. 2009;41(9): Brancati F, Barrano G, Silhavy JL, Marsh SE, Travaglini L, Bielas SL, et al. CEP290 mutations are frequently identified in the oculo-renal form of Joubert syndrome-related disorders. Am J Hum Genet. 2007;81(1): Brancati F, Iannicelli M, Travaglini L, Mazzotta A, Bertini E, Boltshauser E, et al. MKS3/TMEM67 mutations are a major cause of COACH Syndrome, a Joubert Syndrome related disorder with liver involvement. Hum Mutat. 2009;30(2):E Brancati F, Travaglini L, Zablocka D, Boltshauser E, Accorsi P, Montagna G, et al. RPGRIP1L mutations are mainly associated with the cerebello-renal phenotype of Joubert syndrome-related disorders. Clin Genet. 2008;74(2): Cantagrel V, Silhavy JL, Bielas SL, Swistun D, Marsh SE, Bertrand JY, et al. Mutations in the cilia gene ARL13B lead to the classical form of Joubert syndrome. Am J Hum Genet. 2008;83(2): Castori M, Valente EM, Donati MA, Salvi S, Fazzi E, Procopio E, et al. NPHP1 gene deletion is a rare cause of Joubert syndrome related disorders. J Med Genet. 2005;42(2):e9. - Davis EE, Zhang Q, Liu Q, Diplas BH, Davey LM, Hartley J, et al. TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum. Nat Genet. 2011;43(3): den Hollander AI, Koenekoop RK, Yzer S, Lopez I, Arends ML, Voesenek KE, et al. Mutations in the CEP290 (NPHP6) gene are a frequent cause of Leber congenital amaurosis. Am J Hum Genet. 2006;79(3): Goetz SC, Anderson KV. The primary cilium: a signalling centre during vertebrate development. Nat Rev Genet. 2010;11(5): Helou J, Otto EA, Attanasio M, Allen SJ, Parisi MA, Glass I, et al. Mutation analysis of NPHP6/CEP290 in patients with Joubert syndrome and Senior-Loken syndrome. J Med Genet. 2007;44(10): Hoefele J, Wolf MT, O'Toole JF, Otto EA, Schultheiss U, Deschenes G, et al. Evidence of oligogenic inheritance in nephronophthisis. J Am Soc Nephrol. 2007;18(10): Hurd TW, Hildebrandt F. Mechanisms of nephronophthisis and related ciliopathies. Nephron Exp Nephrol. 2011;118(1):e Iannicelli M, Brancati F, Mougou-Zerelli S, Mazzotta A, Thomas S, Elkhartoufi N, et al. Novel TMEM67 mutations and genotype-phenotype correlates in meckelin-related ciliopathies. Hum Mutat. 2010;31(5):E Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, et al. A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. Nat Genet. 2009;41(6): Lee JE, Silhavy JL, Zaki MS, Schroth J, Bielas SL, Marsh SE, et al. TSGA14 is mutated in Joubert syndrome ans is required for tubulin glutamylation at the cilium. Nat Genet. 2012;44(2): Lee JH, Silhavy JL, Lee JE, Al-Gazali L, Thomas S, Davis EE, et al. A single human ciliopathy locus highlights the evolutionary dynamics of non-duplicated but adjacent genes. Science (epub ahead of print). - Louie CM, Caridi G, Lopes VS, Brancati F, Kispert A, Lancaster MA, et al. AHI1 is required for photoreceptor outer segment development and is a modifier for retinal degeneration in nephronophthisis. Nat Genet. 2010;42(2): Menzaghi C, De Cosmo S, Copetti M, Salvemini L, De Bonis C, Mangiacotti D, et al. Relationship between ADIPOQ gene, circulating high molecular weight adiponectin and albuminuria in individuals with normal kidney function: evidence from a family-based study. Diabetologia. 2011;54(4): Mockel A, Perdomo Y, Stutzmann F, Letsch J, Marion V, Dollfus H. Retinal dystrophy in Bardet-Biedl syndrome and related syndromic ciliopathies. Prog Retin Eye Res. 2011;30(4): Mougou-Zerelli S, Thomas S, Szenker E, Audollent S, Elkhartoufi N, Babarit C, et al. CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation. Hum Mutat. 2009;30(11): Novarino G, Akizu N, Gleeson JG. Modeling human disease in humans: the ciliopathies. Cell. 2011;147(1): Riley RD, Abrams KR, Lambert PC, Sutton AJ, Thompson JR. An evaluation of bivariate random-effects meta-analysis for the joint synthesis of two correlated outcomes. Stat Med. 2007;26(1): Roy S. Cilia and Hedgehog: When and how was their marriage solemnized? Differentiation. 2012;83(2):S Ruat M, Roudaut H, Ferent J, Traiffort E. Hedgehog trafficking, cilia and brain functions. Differentiation. 2012;83(2):S Sayer JA, Otto EA, O'Toole JF, Nurnberg G, Kennedy MA, Becker C, et al. The centrosomal protein nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4. Nat Genet. 2006;38(6): Tory K, Lacoste T, Burglen L, Moriniere V, Boddaert N, Macher MA, et al. High NPHP1 and NPHP6 mutation rate in patients with Joubert syndrome and nephronophthisis: potential epistatic effect of NPHP6 and AHI1 mutations in patients with NPHP1 mutations. J Am Soc Nephrol. 2007;18(5): Valente EM, Brancati F, Dallapiccola B. Genotypes and phenotypes of Joubert syndrome and related disorders. Eur J Med Genet. 2008;51(1): Valente EM, Brancati F, Silhavy JL, Castori M, Marsh SE, Barrano G, et al. AHI1 gene mutations cause specific forms of Joubert syndrome-related disorders. Ann Neurol. 2006;59(3): Valente EM, Logan CV, Mougou-Zerelli S, Lee JH, Silhavy JL, Brancati F, et al. Mutations in TMEM216 perturb ciliogenesis and cause Joubert, Meckel and related syndromes. Nat Genet. 2010;42(7):

6 - Valente EM, Silhavy JL, Brancati F, Barrano G, Krishnaswami SR, Castori M, et al. Mutations in CEP290, which encodes a centrosomal protein, cause pleiotropic forms of Joubert syndrome. Nat Genet. 2006;38(6): Wallingford JB, Mitchell B. Strange as it may seem: the many links between Wnt signaling, planar cell polarity, and cilia. Genes Dev. 2011;25(3): Zaghloul NA, Katsanis N. Functional modules, mutational load and human genetic disease. Trends Genet. 2010;26(4): Descrizione dei compiti dell'unità di Ricerca Description of the Research Unit The coordinator of the Unit has a long standing experience in clinical, molecular genetic and functional research on syndromic retinopathies, in particular those falling within the expanding group of ciliopathies, including JSRD, MKS, SLS and other ciliopathies associated with Leber congenital amaurosis. Her main contributions to these fields have been the identification of six novel ciliopathy genes and the definition of the prevalence and phenotypic spectrum of several others (Castori et al., 2005, Valente et al., 2006, Valente et al., 2006, Brancati et al., 2007, Brancati et al., 2008, Cantagrel et al., 2008, Bielas et al., 2009, Brancati et al., 2009, Mougou-Zerelli et al., 2009, Iannicelli et al., 2010, Valente et al., 2010, Lee et al., 2012, Lee et al., 2012). In this field, the Unit coordinator has developed and still maintains several national and international collaborations, in particular with Prof. Joe Gleeson at UCSD, Prof. Eugen Boltshauser at the Childrens' Hospital in Zurich, Prof. Colin Johnson at Leeds University and Prof. Geff Woods at Cambridge University, who are world-leading experts in the field of ciliopathies. The Research Unit possesses all the necessary facilities for high throughput mutation screening of known genes in large cohorts; in particular, through the collaboration with the CSS-Mendel Institute, the Unit has gained access to a Solid 5500xL next generation sequencer with dedicated bioinformatics unit for data analysis. Protocols for whole exome sequencing and target resequencing of selected genes have been optimized over the past year. Preliminary results of the Unit Over the past ten years, the Unit Coordinator has established an Italian network composed of pediatricians, child neurologists, neuro-ophthalmologists, neuroradiologists and child nephrologists, who regularly refer patients with various types of ciliopathies (mainly JSRD but also MKS, NPHP, SLS and other ciliopathies). Moreover, together with Prof. Gleeson at UCSD, the Coordinator has founded the International JSRD Study Group, which gathers specialists referring ciliopathy patients from over 20 countries in the five continents. So far, >500 ciliopathy patients from about 400 families (of which 75 consanguineous) have been referred to the Unit. Blood or DNA samples have been obtained from the patients and in most cases from healthy relatives, with parental written informed consent. A standardized questionnaire has been established, to collect detailed clinical features in a consistent way (available online at Questionnaires are fed in a dedicated database, for statistical analysis and subgrouping of patients according to their clinical presentation. Additional patients will be recruited through the collaboration with the other research units participating to this project. A variable number of probands have already undergone mutation analysis of a subset of ciliary genes, based on conventional sequencing techniques or mutation screening approaches. However, this analysis remains largely incomplete, and the current prevalence and mutational load of ciliary genes in causing syndromic ciliopathies with and without retinal involvement still remains to be determined. Moreover, patients carriers of pathogenic mutations in a given gene have often been excluded from subsequent analysis of other genes, therefore precluding the possibility to detect genetic modifiers of the phenotype. Overall, homozygous or compound heterozygous mutations have been detected in 55 probands, while 19 patients were found to carry only one heterozygous mutation in a given gene. It is plausible that these heterozygous mutations may concur with additional mutations in another gene to determine or modify the phenotype, and indeed this was the case in three of our patients. These issues will be addressed in the present project by an innovative next-generation-based target resequencing approach which will simultaneously sequence all genes causative of known ciliopathies in our cohort. Specific aims Aims of this Unit, that will act in close collaboration with the Neurogenetics Unit of the CSS-Mendel Institute of Rome, will be the following: 1) to recruit and clinically characterize patients with retinal ciliopathies and other syndromic retinopathies, through the neurogenetics clinic of the Mendel Institute and well-established collaborations with several neuropediatric units which regularly refer patients for genetic testing from Italy and abroad. 2) to optimize an innovative next-generation-sequencing based protocol for target sequencing of a large number of genes implicated in the pathogenesis of syndromic retinopathies, to perform genetic testing in the available patients. In particular, the target resequencing protocol will be first applied to a sample of about 150 patients with variable phenotypes, and further genetic analysis will be addressed on the basis of the results of statistical analysis in this pilot cohort. 3) to perform statistical analysis aimed at correlating genetic with clinical and instrumental data generated during the course of the study. Experimental plan and methods Ascertainment of patients and clinical evaluation New patients with syndromic retinopathies will be continuously recruited throughout the project, through direct examination of referral from other specialists. A shared protocol for clinical assessment will include a thorough history and complete neurological and dysmorphology examination, a basic cognitive assessment, brain MRI whenever appropriate, detailed evaluation of ophthalmologic, renal and hepatic function and assessment of associated features and conditions such as congenital heart defects, skeletal abnormalities etc. In particular, ophthalmologic evaluation will include the evaluation of visual function (visual acuity, oculomotor abilities, color vision, visual field), fundus oculi, slit lamp examination and - whenever possible - visual evoked potentials and electroretinogram. Renal and hepatic evaluation will include blood test for renal and liver function, kidney and liver ultrasound and urinary concentration test after Desmopressin stimulation (DDAVP testing). Patients are followed-up every months on average. For newly referred patients, after obtaining parental written informed consent, 10ml blood will be obtained from probands and available relatives (6ml EDTA and 4ml PAX) for DNA and RNA extraction. A unique code will be assigned to each family and each individual within families. Genomic DNA and RNA will be extracted according to standard protocols. A selected subgroup of patients will also undergo a complete neuropsychological assessment to evaluate the degree of cognitive and behavioral disorders, that represent a major complication in the care of syndromic patients and are usually difficult to deal with. This study will allow evaluating possible correlations between specific behavioral and cognitive problems and distinct ciliary phenotypes (or genetic determinants), identifying prognostic indexes and adopting specific therapeutic strategies according to the type and degree of behavioral disorder. NGS-based target resequencing experiments A Life Technologies Solid 5500xL platform and its related equipment (Library Builder, EZ Bead Emulsifier, Amplifier and Enricher) will be adopted to perform next generation-based target resequencing of PD genes in the whole cohort. Target resequencing technique will be implemented using the TargetSeq Custom Enrichment System (Life Technologies), according to the specific manufacturer's protocols. Briefly, DNA libraries will be first fragmented to the requested size, then coupled with specific adaptors, enriched for the set of genes of interest, barcoded for pooling and then amplified by emulsion-pcr before sequencing. For target resequencing, we have selected a panel of PD-related genes to be simultaneously amplified and sequenced in the cohort of patients. For target resequencing, we have designed a panel of about 70 genes, to be simultaneously amplified and sequenced in the whole cohort of JSRD patients. These panels include all genes known to cause human ciliopathies (including JSRD, MKS, BBS, Usher, NPH, etc), as well as genes implicated in other syndromic retinopathies. Target resequencing has been designed to comprise all coding and non-coding exons including 50bp flanking sequences, and untranslated regions, spanning about 450 Kb of genomic DNA. Up to 48 samples can be multiplexed using specific barcodes, to be run in a single flowchip lane. This will allow to obtain an expected coverage up to 500x, while saving enrichment and sequencing costs. However, the target resequencing protocol will be initially tested and optimized to reach a minimal coverage of at least 20 reads per sequenced base. Patients already known to carry mutations in a given gene will be initially sequenced, both to assess the sensitivity of the technique and to search for additional genetic mutations/variants that could act as phenotypic modifiers. Bioinformatics analysis will ground on a quality consensus-based workflow. It will start mapping short-reads against a known reference genome by three different software tools (Lifescope, Shrimp and Bowtie) and will then select the best alignment according to the mapped/unmapped ratios and the mapping quality scores. To confer more confidence to the outcomes of the downstream analyses, both short-reads and alignments will undergo a deep quality evaluation of the base-per-position and mapping-per-read scores. Additionally, an exhaustive screening of the per-base/per-exone coverage will be given, so as to provide with a preliminary insight of the potential weaker genomics regions. Alignments will be scanned by three SNPs and short-indels callers (DiBayes, the GATK and Samtools). Detected polymorphisms and genotypes will be matched and scored according to the degree of consensus among the three tools, and polymorphisms will be annotated in three steps. Annovar and snpeff will be employed to capture the kind and chromosomal region of each mutation, while dbsnp (integrated with 1000 Genome dataset) will give information about MAF and clinical significance. Finally, the extent of dangerousness of each variant will be checked by a conservational and structurally conformational inspection by PolyPhen2, Sift and MutPred software. Relevant identified variants will be confirmed by conventional Sanger sequencing, as appropriate. The NGS-based targeted molecular screen proposed in this project is designed to rapidly and effectively test a large cohort of patients affected by various syndromic retinopathies for a large panel genes. This approach bears several advantages: i) the simultaneous analysis of many genes will allow to accurately determine the mutation frequency and phenotypic spectrum of all known genes, and at the same time to identify genetic modifiers as well as potential novel disease-genes. In

7 particular, the large scale detection of mutations or variants in distinct genes concurring to determine or modify the phenotype could help understand the extremely variable expression of many genes, improving genetic counseling that at present is hampered by the extreme clinical and genetic heterogeneity of these disorders and the lack of clear genotype-phenotype correlates; ii) the availability of a very large cohort of patients with various retinal ciliopathies will consent on one hand to rely on many patients with common phenotypes (i.e. JS plus retinopathy) that could result in increased power for statistical analysis, on the other hand to test also patients with rarer phenotypes; iii) the effort to obtain a full clinical and instrumental characterization for most patients (including a detailed evaluation of mild or preclinical signs of renal and/or retinal dysfunction) and the standardized collection of data will allow a high degree of accuracy in classifying patients in clinical subgroups, largely improving clinical correlates that are crucial for predicting the disease course; iv) the establishment of an optimized diagnostic protocol will make molecular testing, and consequent prenatal diagnosis, accessible to a large number of families. At present, the lack of molecular diagnosis represents a major drawback for many parents of a child with a syndromic ciliopathy, who are often unwilling to take the risk of having additional diseased children. Finally, the potential identification of novel genes will increase the availability of molecular diagnostic tools for patients testing negative for mutations in known genes, improving the chances of reaching a genetic diagnosis for a larger group of patients. Statistical analysis Statistical analysis will be performed as appropriate, through the collaboration with the Biostatistics Unit, Casa Sollievo della Sofferenza. The different clinical phenotypes, considered as outcomes, will be jointly modeled via a multivariate hierarchical generalized linear model (Riley et al., 2007, Menzaghi et al., 2011) to assess which mutations/rare variants or even polymorphisms in distinct genes may be associated with them. Such modeling accounts for possible correlated outcomes, i.e. two clinical phenotypes may systematically occur jointly in patients. Moreover the multivariate hierarchical modeling will allow us to identify the genetic modifiers which cause more than one phenotype, assess the homogeneity or heterogeneity of genetic modifiers-phenotype associations, and the degree of residual correlation between phenotypes. Statistical inference will be performed building ad-hoc contrast tests using the estimated covariance matrix of the regression coefficients and the between-phenotypes covariance matrix as well. P-values <0.05 will be considered significant. All analyses will be performed using SAS Software Release Descrizione delle attrezzature già disponibili ed utilizzabili per la ricerca proposta nº anno di acquisizione Descrizione Strumentazione per sequenziamento di nuova generazione Solid 5500xL Life Technologies, con relative apparecchiature per la preparazione dei campioni (Library builder, EZBeads ecc) Sequenziatore automatico capillare Applied Biosystems 3130XL nº anno di acquisizione Descrizione Solid 5500xL next generation sequencer (Life Technologies) with related equipment for sample preparation (Library builder, EZBeads etc) Capillary DNA sequencer Applied Biosystems 3130XL 14 - Elenco dei partecipanti all'unità di Ricerca 14.1 Personale dipendente dall'ateneo/ente cui afferisce l'unità di ricerca 14.1.a - Docenti / ricercatori / tecnologi nº Cognome Nome Qualifica costo annuo lordo (a) mesi/persona previsti (b) costo attribuito al progetto ((a/12)*b) 1. VALENTE Enza Maria Professore Associato confermato TOTALE b - Altro personale tecnico nº Cognome Nome Qualifica costo annuo lordo (a) mesi/persona previsti (b) costo attribuito al progetto ((a/12)*b) TOTALE Personale dipendente da altri Atenei/Enti 14.2.a - Docenti / ricercatori / tecnologi nº Cognome Nome Università/Ente Qualifica costo annuo lordo (a) mesi/persona previsti (b) costo attribuito al progetto ((a/12)*b) 1. MAZZA Tommaso Ospedale Casa Sollievo della Dirigente di ricerca a 0 3 0

8 Sofferenza (IRCCS) tempo det. TOTALE b - Altro personale tecnico nº Cognome Nome Università/Ente Qualifica costo annuo lordo (a) mesi/persona previsti (b) costo attribuito al progetto ((a/12)*b) TOTALE Personale non dipendente già presente presso l'ateneo/ente cui afferisce l'unità di Ricerca alla data di presentazione del progetto (da inserire a costo zero): Nessuno Personale dipendente e non dipendente da destinare a questo specifico Progetto: nº Tipologia di contratto costo annuo lordo (a) mesi/persona previsti (b) costo attribuito al progetto ((a/12)*b) Note 1. Assegnisti , Biologo post-doc dedicato full time al progetto TOTALE ,000 36, Personale di Enti/Istituzioni straniere nº Cognome Nome Qualifica (Università/Ente) Dipartimento/Istituto 15 - Mesi persona complessivi dedicati al Progetto Mesi/Persona 15.1 Personale dipendente dall'ateneo/ente cui afferisce l'unità di ricerca a) docenti / 6 ricercatori / tecnologi b) altro personale tecnico 15.2 Personale dipendente da altri Atenei/Enti a) docenti / ricercatori / tecnologi b) altro personale tecnico 15.3 Personale non dipendente già presente presso l'ateneo/ente cui afferisce l'unità di ricerca alla a) assegnisti 0 data di presentazione del progetto (da inserire a costo zero) b) dottorandi 0 c) professori a contratto d) co.co.co (solo per EPR) 15.4 Personale dipendente o non dipendente da destinare a questo specifico Progetto a) assegnisti 36 b) ricercatori a tempo determinato c) dottorandi 0 d) co.co.co. 0 TOTALE

9 16 - Costo complessivo dell'unità di Ricerca Voce di spesa A - Spese di personale (cofinanziamento ateneo/ente; punti 14.1 (A.1) (A.2); non superiore al 30% del costo del progetto) A - Spese di personale non dipendente da destinare a questo specifico progetto - punto 14.4 (A.4) B - Spese generali (quota forfettaria pari al 60% del costo totale del personale, spesa A) C - Attrezzature, strumentazioni e prodotti software D - Servizi di consulenza e simili E - Altri costi di esercizio Spesa in Euro Descrizione dettagliata (in italiano) Stipendio del coordinatore di Unità di Ricerca Salario per un biologo post-doc a tempo pieno con esperienza in sequenziamento di nuova generazione Descrizione dettagliata (in inglese) Salary of the Research Unit coordinator Full-time salary for a post doc biologist with experience in next-generation-sequencing Spese generali (quota forfettaria pari al 60% del costo totale del personale, spesa A) Costi di consulenza per sequenziamento di nuova generazione, analisi bioinformatica e biostatistica Consumabili per esperimenti di sequenziamento di nuova generazione Consultancy fees for NGS, bioinformatics and biostatistics analysis Consumables for next-generation-sequencing experiments Costo Complessivo dell'unità di Ricerca Finanziamento MIUR Costo a carico Ateneo / Ente N.B. - I costi relativi al personale dipendente già operante presso gli atenei e gli enti di ricerca alla data di scadenza del presente bando non possono superare il 30% del costo del progetto. I dati contenuti nella domanda di finanziamento sono trattati esclusivamente per lo svolgimento delle funzioni istituzionali del MIUR. Incaricato del trattamento è il CINECA- Dipartimento Servizi per il MIUR. La consultazione è altresì riservata agli atenei e agli enti di ricerca (ciascuno per le parti di propria competenza), al MIUR - D.G. per il Coordinamento e lo Sviluppo della Ricerca - Ufficio V, al CNGR e ai CdS. Il MIUR potrà anche procedere alla diffusione dei principali dati economici e scientifici relativi ai progetti finanziati. Firma Data (dal sistema alla chiusura della domanda)

10 Curricula scientifici dei componenti il gruppo di ricerca 1. MAZZA Tommaso Curriculum: Nato a Catanzaro l'8 giugno 1979, ha studiato ingegneria informatica presso l'università della Calabria. Ha conseguito il dottorato di ricerca in ingegneria informatica e biomedica presso l'università Magna Græcia' di Catanzaro. Nel 2004 ha lavorato nell'ambito del progetto Cofin 2003 Tumori ereditari della mammella: studi genetici ed analisi del proteoma. Nel 2005, si è occupato della progettazione di un'interfaccia software per la conversione di spettri di massa grezzi (MALDI-TOF e LC) in formato mzdata. Nel marzo 2006, ha visitato il centro di ricerca The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), dove ha collaborato per la definizione ed implementazione di Cyto-Sim, un simulatore stocastico di processi chimici. In particolare, ha lavorato alla realizzazione di una routine software per l'unmarshalling di files SBML in files di input per il simulatore. Nell'estate del 2006, Tommaso ha visitato il centro di ricerca Microsoft Research Cambridge dove ha investigato la possibilità di parallelizzare e distribuire gli algoritmi di simulazione stocastica. Nel 2007, è entrato a far parte della Bioinformatics Italian Society (B.IT.S.). Da gennaio 2008, Tommaso è ricercatore a contratto presso COSBI, dove si occupa di simulazione stocastica parallela di sistemi biologici, databases biologici, progettazione di soluzioni software ad alte prestazioni per la biologia dei sistemi. Da Ottobre 2010 a luglio 2011, Tommaso lavora nel laboratorio di genetica traslazionale presso il Centro di Biologia Integrativa (CIBIO), dove ha la responsabilità di progettare il database AURA: the Atlas of UTR Regulatory Activity. Da Luglio 2011 ad oggi, Tommaso occupa la posizione di Vice-Chair per l'europa dell'ieee Technical Committee for Simulation (TC-SIM). E' ricercatore presso l'irccs Casa Sollievo della Sofferenza (FG) e CSS-Mendel (Rome), presso l'unità di bioinformatica. Pubblicazioni: E. Dassi, A. Malossini, A. Re, MAZZA T., T. Tebaldi, L. Caputi, A. Quattrone (2012). AURA: Atlas of UTR Regulatory Actiity. BIOINFORMATICS, vol. 28; p , ISSN: E. Chiefari, S. Tanyolaç, F. Paonessa, C. R. Pullinger, C. Capula, S. Iiritano, MAZZA T., M. Forlin, A. Fusco, V. Durlach, A. Durlach, M. J. Malloy, J. P. Kane, S. W. Heiner, M. Filocamo, D. P. Foti, I. D. Goldfine, A. Brunetti (2011). Functional Variants of the HMGA1 Gene and Type 2 Diabetes Mellitus. JAMA, vol. 305; p , ISSN: Cavaliere M, MAZZA T. (2010). Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins. ELECTRONIC NOTES IN THEORETICAL COMPUTER SCIENCE; p , ISSN: MAZZA T. (2010). Editorial: Accelerating systems biology. BRIEFINGS IN BIOINFORMATICS, vol. 11; p , ISSN: MAZZA T., G. Iaccarino, C. Priami (2010). Snazer: the simulations and networks analyzer. BMC SYSTEMS BIOLOGY, vol. vol. 4; p. 2-17, ISSN: , doi: / MAZZA T., Romanel A, Jordán F (2010). Estimating the divisibility of complex biological networks by sparseness indices. BRIEFINGS IN BIOINFORMATICS, vol. 11; p , ISSN: P. Ballarini, R.Guido, MAZZA T., D. Prandi (2009). Taming the complexity of biological pathways through parallel computing. BRIEFINGS IN BIOINFORMATICS, ISSN: Cannataro M, Guzzi PH, MAZZA T., Tradigo G, Veltri P (2007). Using Ontologies for Preprocessing and Mining Spectra Data on the Grid. FUTURE GENERATION COMPUTER SYSTEMS, vol. 2; p , ISSN: X Sedwards S, MAZZA T. (2007). Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane- Enclosed Biochemical Processes. BIOINFORMATICS, vol. 23; p , ISSN: Cannataro M, Guzzi PH, MAZZA T., Tradigo G, Veltri P (2006). Managing Ontologies for Grid Computing. MULTIAGENT AND GRID SYSTEMS, vol. 2; p , ISSN: MAZZA Tommaso Curriculum: Tommaso Mazza was born in Catanzaro, Italy, on 8 June He studied Computer Science Engineering at the University of Calabria and received a PhD in Computer Science and Biomedical Engineering in November 2007 from the Magna Græcia University of Catanzaro. In 2004, he worked on the Cofin 2003 Project titled Hereditary tumors: genetic studies and proteomic analysis. In 2005, he worked on the design of a common interface to translate mass spectrometry raw data (MALDI-TOF and LC) into mzdata. In March 2006, he visited COSBI, where he dynamically collaborated in the design and implementation of Cyto-Sim, a stochastic simulator of biochemical processes. Moreover, he worked on the definition of a common interface for unmarshalling SBML models into the Cyto-Sim syntax and vice-versa. In summer 2006, Tommaso visited Microsoft Research Cambridge where he investigated the possibility of parallelizing and distributing simulation algorithms. In 2007, he joined the Bioinformatics Italian Society (B.IT.S.). Tommaso joined COSBI in January 2008 where he dealt with parallel stochastic simulation of biological systems, biological data storing and handling, design of high performance software solutions for systems biology. Since October 2010 till July 2011, Tommaso worked in the Laboratory of Translational Genomics at CIBIO where he was involved in the job of structuring AURA: the Atlas of UTR Regulatory Activity. Since July 2011, Tommaso holds the position of Vice-Chair for Europe of the IEEE Technical Committee for Simulation (TC-SIM) and of researcher at Casa Sollievo della Sofferenza (FG) and CSS-Mendel (Rome), Italy, where he leads the Bioinformatics unit. Pubblicazioni: E. Dassi, A. Malossini, A. Re, MAZZA T., T. Tebaldi, L. Caputi, A. Quattrone (2012). AURA: Atlas of UTR Regulatory Actiity. BIOINFORMATICS, vol. 28; p , ISSN: E. Chiefari, S. Tanyolaç, F. Paonessa, C. R. Pullinger, C. Capula, S. Iiritano, MAZZA T., M. Forlin, A. Fusco, V. Durlach, A. Durlach, M. J. Malloy, J. P. Kane, S. W. Heiner, M. Filocamo, D. P. Foti, I. D. Goldfine, A. Brunetti (2011). Functional Variants of the HMGA1 Gene and Type 2 Diabetes Mellitus. JAMA, vol. 305; p , ISSN: Cavaliere M, MAZZA T. (2010). Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins. ELECTRONIC NOTES IN THEORETICAL COMPUTER SCIENCE; p , ISSN: MAZZA T. (2010). Editorial: Accelerating systems biology. BRIEFINGS IN BIOINFORMATICS, vol. 11; p , ISSN: MAZZA T., G. Iaccarino, C. Priami (2010). Snazer: the simulations and networks analyzer. BMC SYSTEMS BIOLOGY, vol. vol. 4; p. 2-17, ISSN: , doi: / MAZZA T., Romanel A, Jordán F (2010). Estimating the divisibility of complex biological networks by sparseness indices. BRIEFINGS IN BIOINFORMATICS, vol. 11; p , ISSN: P. Ballarini, R.Guido, MAZZA T., D. Prandi (2009). Taming the complexity of biological pathways through parallel computing. BRIEFINGS IN BIOINFORMATICS, ISSN: Cannataro M, Guzzi PH, MAZZA T., Tradigo G, Veltri P (2007). Using Ontologies for Preprocessing and Mining Spectra Data on the Grid. FUTURE GENERATION COMPUTER SYSTEMS, vol. 2; p , ISSN: X Sedwards S, MAZZA T. (2007). Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane- Enclosed Biochemical Processes. BIOINFORMATICS, vol. 23; p , ISSN: Cannataro M, Guzzi PH, MAZZA T., Tradigo G, Veltri P (2006). Managing Ontologies for Grid Computing. MULTIAGENT AND GRID SYSTEMS, vol. 2; p , ISSN: