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Pagliara D, Ciolfi A, Pedace L, Haghshenas S, Ferilli M, Levy MA, Miele E, Nardini C, Cappelletti C, Relator R, Pitisci A, De Vito R, Pizzi S, Kerkhof J, McConkey H, Nazio F, Kant SG, Di Donato M, Agolini E, Matraxia M, Pasini B, Pelle A, Galluccio T, Novelli A, Barakat TS, Andreani M, Rossi F, Mecucci C, Savoia A, Sadikovic B, Locatelli F, Tartaglia M. Identification of a robust DNA methylation signature for Fanconi anemia. Am J Hum Genet 2023; 110:1938-1949. [PMID: 37865086 PMCID: PMC10645556 DOI: 10.1016/j.ajhg.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/23/2023] Open
Abstract
Fanconi anemia (FA) is a clinically variable and genetically heterogeneous cancer-predisposing disorder representing the most common bone marrow failure syndrome. It is caused by inactivating predominantly biallelic mutations involving >20 genes encoding proteins with roles in the FA/BRCA DNA repair pathway. Molecular diagnosis of FA is challenging due to the wide spectrum of the contributing gene mutations and structural rearrangements. The assessment of chromosomal fragility after exposure to DNA cross-linking agents is generally required to definitively confirm diagnosis. We assessed peripheral blood genome-wide DNA methylation (DNAm) profiles in 25 subjects with molecularly confirmed clinical diagnosis of FA (FANCA complementation group) using Illumina's Infinium EPIC array. We identified 82 differentially methylated CpG sites that allow to distinguish subjects with FA from healthy individuals and subjects with other genetic disorders, defining an FA-specific DNAm signature. The episignature was validated using a second cohort of subjects with FA involving different complementation groups, documenting broader genetic sensitivity and demonstrating its specificity using the EpiSign Knowledge Database. The episignature properly classified DNA samples obtained from bone marrow aspirates, demonstrating robustness. Using the selected probes, we trained a machine-learning model able to classify EPIC DNAm profiles in molecularly unsolved cases. Finally, we show that the generated episignature includes CpG sites that do not undergo functional selective pressure, allowing diagnosis of FA in individuals with reverted phenotype due to gene conversion. These findings provide a tool to accelerate diagnostic testing in FA and broaden the clinical utility of DNAm profiling in the diagnostic setting.
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Affiliation(s)
- Daria Pagliara
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Lucia Pedace
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Marco Ferilli
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Evelina Miele
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Claudia Nardini
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Camilla Cappelletti
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Angela Pitisci
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Rita De Vito
- Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Francesca Nazio
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Sarina G Kant
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 Rotterdam, the Netherlands
| | - Maddalena Di Donato
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Marta Matraxia
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Barbara Pasini
- AOU Città della salute e della scienza di Torino, Molinette's Hospital, 10126 Torino, Italy
| | - Alessandra Pelle
- AOU Città della salute e della scienza di Torino, Molinette's Hospital, 10126 Torino, Italy
| | - Tiziana Galluccio
- Laboratory of Transplant Immunogenetics, Department of Hematology/Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC University Medical Center, 3015 Rotterdam, the Netherlands
| | - Marco Andreani
- Laboratory of Transplant Immunogenetics, Department of Hematology/Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Francesca Rossi
- Department of Woman, Child and of General and Specialist Surgery, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Cristina Mecucci
- Institute of Hematology and Center for Hemato-Oncology Research, University and Hospital of Perugia, 06123 Perugia, Italy
| | - Anna Savoia
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Franco Locatelli
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy; Department of Pediatrics, Catholic University of the Sacred Hearth, 00168 Rome, Italy.
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
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Persico I, Fiscarelli I, Pelle A, Faleschini M, Pasini B, Savoia A, Bottega R. Phenotype reversion as "natural gene therapy" in Fanconi anemia by a gene conversion event. Front Genet 2023; 14:1240758. [PMID: 37790699 PMCID: PMC10544911 DOI: 10.3389/fgene.2023.1240758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
Somatic mosaicism appears as a recurrent phenomenon among patients suffering from Fanconi anemia (FA), but its direct prognostic significance mostly remains an open question. The clinical picture of FA mosaic subjects could indeed vary from just mild features to severe hematologic failure. Here, we illustrate the case of a proband whose FA familiarity, modest signs (absence of hematological anomalies and fertility issues), and chromosome fragility test transition to negative overtime were suggestive of somatic mosaicism. In line with this hypothesis, genetic testing on patient's peripheral blood and buccal swab reported the presence of the only FANCA paternal variant (FANCA:c.2638C>T, p. Arg880*) and of both parental alleles (the additional FANCA:c.3164G>A, p. Arg1055Gln), respectively. Moreover, the SNP analysis performed on the same biological specimens allowed us to attribute the proband's mosaicism status to a possible gene conversion mechanism. Our case clearly depicts the positive association between somatic mosaicism and the proband's favorable clinical course due to the occurrence of the reversion event at the hematopoietic stem cell level. Since this condition concerns only a limited subgroup of FA individuals, the accurate evaluation of the origin and extent of clonality would be key to steer clinicians toward the most appropriate therapeutic decision for their FA mosaic patients.
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Affiliation(s)
- Ilaria Persico
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Ilaria Fiscarelli
- Dipartimento di Scienze Mediche, Università degli Studi di Torino, Torino, Italy
- SC Genetica Medica U, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Alessandra Pelle
- SC Genetica Medica U, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Barbara Pasini
- Dipartimento di Scienze Mediche, Università degli Studi di Torino, Torino, Italy
- SC Genetica Medica U, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Anna Savoia
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
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3
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Mellone S, Puricelli C, Vurchio D, Ronzani S, Favini S, Maruzzi A, Peruzzi C, Papa A, Spano A, Sirchia F, Mandrile G, Pelle A, Rasmini P, Vercellino F, Zonta A, Rabbone I, Dianzani U, Viri M, Giordano M. The Usefulness of a Targeted Next Generation Sequencing Gene Panel in Providing Molecular Diagnosis to Patients With a Broad Spectrum of Neurodevelopmental Disorders. Front Genet 2022; 13:875182. [PMID: 36035117 PMCID: PMC9403311 DOI: 10.3389/fgene.2022.875182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Neurodevelopmental disorders comprise a clinically and genetically heterogeneous group of conditions that affect 2%–5% of children and represents a public health challenge due to complexity of the etiology. Only few patients with unexplained syndromic and non-syndromic NDDs receive a diagnosis through first-tier genetic tests as array-CGH and the search for FMR1 CGG expansion. The aim of this study was to evaluate the clinical performance of a targeted next-generation sequencing (NGS) gene panel as a second-tier test in a group of undiagnosed patients with NDDs.Method: A 221-gene next-generation sequencing custom panel was designed and used to analyze a cohort of 338 patients with a broad spectrum of NDDs (202 males and 136 females) including Intellectual Disability (ID), Autism Spectrum Disorders (ASD), Epilepsy, language and motor disorders.Results: A molecular diagnosis was established in 71 patients (21%) and a de novo origin was present in 38 (64.4%) of the available trios. The diagnostic yield was significantly higher in females than in males (29.4% vs. 15.3%; p = 0.0019) in particular in ASD (36.8% vs. 7.6%; p = 0.0026) and Epilepsy (38.9% vs. 14.4% p = 0.001). The most involved genes were SLC2A1, SCN1A, ANKRD11, ATP1A2, CACNA1A, FOXP1, and GNAS altered in more than two patients and accounting for the 19.7% of the diagnosis.Conclusion: Our findings showed that this NGS panel represents a powerful and affordable clinical tool, significantly increasing the diagnostic yield in patients with different form of NDDs in a cost- and time-effective manner without the need of large investments in data storage and bioinformatic analysis.
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Affiliation(s)
- Simona Mellone
- Laboratory of Genetics, Clinical Biochemistry, University Hospital Maggiore della Carità, Novara, Italy
| | - Chiara Puricelli
- Laboratory of Genetics, Clinical Biochemistry, University Hospital Maggiore della Carità, Novara, Italy
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Denise Vurchio
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Sara Ronzani
- Laboratory of Genetics, Clinical Biochemistry, University Hospital Maggiore della Carità, Novara, Italy
| | - Simone Favini
- Laboratory of Genetics, Clinical Biochemistry, University Hospital Maggiore della Carità, Novara, Italy
| | - Arianna Maruzzi
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Cinzia Peruzzi
- Child Neuropsychiatry Unit, Ospedale San Gerardo Monza-Università degli Studi di Milano Bicocca, Monza, Italy
| | - Amanda Papa
- Department of Child Neuropsychiatry, Hospital Maggiore della Carità, Novara, Italy
| | - Alice Spano
- Laboratory of Genetics, Clinical Biochemistry, University Hospital Maggiore della Carità, Novara, Italy
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Alessandra Pelle
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | - Fabiana Vercellino
- Child Neuropsychiatry Unit, SS. Antonio e Biagio e Cesare Arrigo Hospital, Alessandria, Italy
| | - Andrea Zonta
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Ivana Rabbone
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
- Division of Pediatrics, University Hospital Maggiore della Carità, Novara, Italy
| | - Umberto Dianzani
- Laboratory of Genetics, Clinical Biochemistry, University Hospital Maggiore della Carità, Novara, Italy
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Maurizio Viri
- Department of Child Neuropsychiatry, Hospital Maggiore della Carità, Novara, Italy
| | - Mara Giordano
- Laboratory of Genetics, Clinical Biochemistry, University Hospital Maggiore della Carità, Novara, Italy
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
- *Correspondence: Mara Giordano,
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Mandrile G, Pelle A, Sciannameo V, Benetti E, D'Alessandro MM, Emma F, Montini G, Peruzzi L, Petrarulo M, Romagnoli R, Vitale C, Cellini B, Giachino D. Primary hyperoxaluria in Italy: the past 30 years and the near future of a (not so) rare disease. J Nephrol 2022; 35:841-850. [PMID: 35218550 PMCID: PMC8995259 DOI: 10.1007/s40620-022-01258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/12/2022] [Indexed: 11/29/2022]
Abstract
Background Primary hyperoxalurias (PHs) are rare autosomal recessive diseases of the glyoxylate metabolism; PH1 is caused by mutations in the AGXT gene, PH2 in GRHPR and PH3 in HOGA1. Methods Here we report the first large multi-center cohort of Italian PH patients collected over 30 years (1992–2020 median follow-up time 8.5 years). Complete genotype was available for 94/95 PH1 patients and for all PH2 (n = 3) and PH3 (n = 5) patients. Symptoms at onset were mainly nephrolithiasis (46.3%) and nephrocalcinosis (33.7%). Median age at onset of symptoms and diagnosis were 4.0 years and 9.9 years, respectively. Results Fifty-four patients (56.8%) were diagnosed after chronic kidney disease. Sixty-three patients (66.3%) developed end stage kidney disease (median age 14.0 years). Twenty-one patients had a kidney-only transplant and, among them, seven had a second kidney transplant combined with liver transplant. A combined kidney–liver transplant was carried out in 29 patients and a sequential kidney–liver transplant was performed in two. In five cases a preemptive liver transplant was performed. Those receiving a liver-only transplant tended to have lower kidney function at last follow-up. Conclusion Our study of PHs in Italy underlines a considerable diagnostic delay, which has only slightly decreased in recent years. Therefore, we suggest a more extensive use of both metabolic screening among patients with recurrent kidney stones and genotyping, including unambiguous assignment of minor/major allele status in order to promptly begin appropriate treatment. This will be fundamental in order to have access to the new therapies, which are mainly focused on substrate reduction for the oxalate-producing enzymes using RNA-interference. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s40620-022-01258-4.
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Affiliation(s)
- Giorgia Mandrile
- Genetic Unit and Thalassemia Center, San Luigi Gonzaga University Hospital, Regione Gonzole 10, 10043, Orbassano, TO, Italy.
| | - Alessandra Pelle
- Medical Genetics Unit, AOU Città della Salute e della Scienza, Turin, Italy
| | - Veronica Sciannameo
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Elisa Benetti
- Pediatric Nephrology, Dialysis and Transplant Unit, Department of Women's and Children's Health, Padua University Hospital, Padua, Italy
| | - Maria Michela D'Alessandro
- Pediatric Nephrology Unit, Ospedale dei Bambini, A.R.N.A.S. Civico-G. Di Cristina, Benfratelli Palermo, PA, Italy
| | - Francesco Emma
- Division of Nephrology, Department of Pediatric Subspecialties, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milano, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Licia Peruzzi
- Pediatric Nephrology Unit, "Regina Margherita Department of Children's Diseases", Città della Salute e della Scienza di Torino, Turin, Italy
| | - Michele Petrarulo
- Kidney Stone Laboratory-Chemical-Clinical Laboratory Unit, Azienda Ospedaliera Ordine Mauriziano di Torino, Turin, Italy
| | - Renato Romagnoli
- Liver Transplant Unit, General Surgery 2U, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, University of Turin, Turin, Italy
| | - Corrado Vitale
- Nephrology and Dialysis Unit, Azienda Ospedaliera Ordine Mauriziano di Torino, Turin, Italy
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Daniela Giachino
- Medical Genetic Unit, San Luigi Gonzaga University Hospital, Orbassano, TO, Italy.,Medical Genetics, Department Clinical and Biological Sciences, University of Torino, Turin, Italy
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5
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Pelle A, Pezzoli L, Apuril E, Iascone M, Selicorni A. A novel HIST1HE pathogenic variant in a girl with macrocephaly and intellectual disability: a new case and review of literature. Clin Dysmorphol 2021; 30:39-43. [PMID: 33086257 DOI: 10.1097/mcd.0000000000000352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pathogenic variants of HIST1H1Egene have recently been associated with a condition known as Rahman syndrome, characterized by overgrowth, intellectual disability and nonspecific dysmorphic features (high hairline, full cheeks, wide nasal bridge). Wide clinical variability is reported, especially regarding the level of neurodevelopment delay and intellectual disability. We report a 10-year-old girl with macrocephaly and global developmental delay, in whom a novel heterozygous variant in the HIST1H1Egene [c.392_395dup (p.Gly133fs)] was discovered, but involving the same C-terminal domain-protein domain reported previously. Comparing the clinical data of our patient with those previously described, a 'core phenotype' with macrocephaly, psychomotor delay/intellectual disability and mild facial dysmorphisms seems evident.
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Affiliation(s)
- Alessandra Pelle
- Department of clinical and biological sciences, University of Torino, AOU San Luigi Gonzaga, Orbassano, Torino
- Pediatric Unit, A.S.S.T. Lariana Sant'Anna Hospital, San Fermo della Battaglia, Como
| | - Laura Pezzoli
- Laboratorio di genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Erika Apuril
- Pediatric Unit, A.S.S.T. Lariana Sant'Anna Hospital, San Fermo della Battaglia, Como
| | - Maria Iascone
- Laboratorio di genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Angelo Selicorni
- Pediatric Unit, A.S.S.T. Lariana Sant'Anna Hospital, San Fermo della Battaglia, Como
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Vaisitti T, Sorbini M, Callegari M, Kalantari S, Bracciamà V, Arruga F, Vanzino SB, Rendine S, Togliatto G, Giachino D, Pelle A, Cocchi E, Benvenuta C, Baldovino S, Rollino C, Fenoglio R, Sciascia S, Tamagnone M, Vitale C, Calabrese G, Biancone L, Bussolino S, Savoldi S, Borzumati M, Cantaluppi V, Chiappero F, Ungari S, Peruzzi L, Roccatello D, Amoroso A, Deaglio S. Clinical exome sequencing is a powerful tool in the diagnostic flow of monogenic kidney diseases: an Italian experience. J Nephrol 2020; 34:1767-1781. [PMID: 33226606 PMCID: PMC8494711 DOI: 10.1007/s40620-020-00898-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/02/2020] [Indexed: 11/30/2022]
Abstract
Background A considerable minority of patients on waiting lists for kidney transplantation either have no diagnosis (and fall into the subset of undiagnosed cases) because kidney biopsy was not performed or histological findings were non-specific, or do not fall into any well-defined clinical category. Some of these patients might be affected by a previously unrecognised monogenic disease. Methods Through a multidisciplinary cooperative effort, we built an analytical pipeline to identify patients with chronic kidney disease (CKD) with a clinical suspicion of a monogenic condition or without a well-defined diagnosis. Following the stringent phenotypical and clinical characterization required by the flowchart, candidates meeting these criteria were further investigated by clinical exome sequencing followed by in silico analysis of 225 kidney-disease-related genes. Results By using an ad hoc web-based platform, we enrolled 160 patients from 13 different Nephrology and Genetics Units located across the Piedmont region over 15 months. A preliminary “remote” evaluation based on well-defined inclusion criteria allowed us to define eligibility for NGS analysis. Among the 138 recruited patients, 52 (37.7%) were children and 86 (62.3%) were adults. Up to 48% of them had a positive family history for kidney disease. Overall, applying this workflow led to the identification of genetic variants potentially explaining the phenotype in 78 (56.5%) cases. Conclusions These results underline the importance of clinical exome sequencing as a versatile and highly useful, non-invasive tool for genetic diagnosis of kidney diseases. Identifying patients who can benefit from targeted therapies, and improving the management of organ transplantation are further expected applications. Electronic supplementary material The online version of this article (10.1007/s40620-020-00898-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tiziana Vaisitti
- Department of Medical Sciences, University of Turin, via Santena 19, 10126, Turin, Italy
| | - Monica Sorbini
- Department of Medical Sciences, University of Turin, via Santena 19, 10126, Turin, Italy
| | - Martina Callegari
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Silvia Kalantari
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Valeria Bracciamà
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Francesca Arruga
- Department of Medical Sciences, University of Turin, via Santena 19, 10126, Turin, Italy
| | - Silvia Bruna Vanzino
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Sabina Rendine
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Gabriele Togliatto
- Department of Medical Sciences, University of Turin, via Santena 19, 10126, Turin, Italy
| | - Daniela Giachino
- Service of Genetic Counseling, San Luigi Gonzaga University Hospital, Orbassano, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Alessandra Pelle
- Service of Genetic Counseling, San Luigi Gonzaga University Hospital, Orbassano, Turin, Italy
| | - Enrico Cocchi
- Pediatric Nephrology Dialysis and Transplantation Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Chiara Benvenuta
- Pediatric Nephrology Dialysis and Transplantation Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Simone Baldovino
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.,Nephrology and Dialysis Unit (ERKnet Member)-CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Bosco Hospital, Turin, Italy
| | - Cristiana Rollino
- Nephrology and Dialysis Unit (ERKnet Member)-CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Bosco Hospital, Turin, Italy
| | - Roberta Fenoglio
- Nephrology and Dialysis Unit (ERKnet Member)-CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Bosco Hospital, Turin, Italy
| | - Savino Sciascia
- Nephrology and Dialysis Unit (ERKnet Member)-CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Bosco Hospital, Turin, Italy
| | | | - Corrado Vitale
- Nephrology and Dialysis Unit, Ordine Mauriziano di Torino, Turin, Italy
| | | | - Luigi Biancone
- Department of Medical Sciences, University of Turin, via Santena 19, 10126, Turin, Italy.,Renal Transplantation Unit 'A. Vercellone,' Division of Nephrology Dialysis and Transplantation, Città della Salute e della Scienza University Hospital, Turin, Italy
| | | | | | - Maurizio Borzumati
- Nephrology and Dialysis Unit of Verbania ASL VCO, Verbano Cusio Ossola, Verbania, Italy
| | - Vincenzo Cantaluppi
- Nephrology and Kidney Transplantation Unit, Maggiore Della Carità University Hospital, Novara, Italy
| | | | - Silvana Ungari
- Struttura Semplice Genetics and Molecular Biology, ASL CN1, Cuneo, Italy
| | - Licia Peruzzi
- Pediatric Nephrology Dialysis and Transplantation Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Dario Roccatello
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.,Nephrology and Dialysis Unit (ERKnet Member)-CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Bosco Hospital, Turin, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, via Santena 19, 10126, Turin, Italy. .,Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy.
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, via Santena 19, 10126, Turin, Italy.,Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza University Hospital, Turin, Italy
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7
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Dindo M, Mandrile G, Conter C, Montone R, Giachino D, Pelle A, Costantini C, Cellini B. The ILE56 mutation on different genetic backgrounds of alanine:glyoxylate aminotransferase: Clinical features and biochemical characterization. Mol Genet Metab 2020; 131:171-180. [PMID: 32792227 DOI: 10.1016/j.ymgme.2020.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 01/20/2023]
Abstract
Primary Hyperoxaluria type I (PH1) is a rare disease caused by mutations in the AGXT gene encoding alanine:glyoxylate aminotransferase (AGT), a liver enzyme involved in the detoxification of glyoxylate, the failure of which results in accumulation of oxalate and kidney stones formation. The role of protein misfolding in the AGT deficit caused by most PH1-causing mutations is increasingly being recognized. In addition, the genetic background in which a mutation occurs is emerging as a critical risk factor for disease onset and/or severity. Based on these premises, in this study we have analyzed the clinical, biochemical and cellular effects of the p.Ile56Asn mutation, recently described in a PH1 patient, as a function of the residue at position 11, a hot-spot for both polymorphic (p.Pro11Leu) and pathogenic (p.Pro11Arg) mutations. We have found that the p.Ile56Asn mutation induces a structural defect mostly related to the apo-form of AGT. The effects are more pronounced when the substitution of Ile56 is combined with the p.Pro11Leu and, at higher degree, the p.Pro11Arg mutation. As compared with the non-pathogenic forms, AGT variants display reduced expression and activity in mammalian cells. Vitamin B6, a currently approved treatment for PH1, can overcome the effects of the p.Ile56Asn mutation only when it is associated with Pro at position 11. Our results provide a first proof that the genetic background influences the effects of PH1-causing mutations and the responsiveness to treatment and suggest that molecular and cellular studies can integrate clinical data to identify the best therapeutic strategy for PH1 patients.
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Affiliation(s)
- Mirco Dindo
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy; Genetica e Thalassemia Unit, San Luigi University Hospital, Orbassano (TO), Italy
| | - Carolina Conter
- Department of Neurological, Biomedical, and Movement Sciences, University of Verona, Verona, Italy
| | - Rosa Montone
- Department of Neurological, Biomedical, and Movement Sciences, University of Verona, Verona, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy
| | - Alessandra Pelle
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy
| | - Claudio Costantini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy.
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8
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Vaisitti T, Sorbini M, Callegari M, Kalantari S, Bracciamà V, Arruga F, Vanzino SB, Pelle A, Giachino D, Cocchi E, Baldovino S, Rollino C, Fenoglio R, Tamagnone M, Gherzi M, Soragna G, Vitale C, Berta V, Calabrese G, Leonardi G, Biancone L, Strampelli E, Maroni S, Santi S, Funaro L, Borzumati M, Bertinetto P, Viglino G, Gianoglio B, Peruzzi L, Roccatello D, Amoroso A, Deaglio S. P0051NOVEL AND KNOWN MUTATIONS IDENTIFIED BY CLINICAL EXOME SEQUENCING FOR THE DIAGNOSIS OF POLYCYSTIC KIDNEY DISEASE. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa142.p0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background and Aims
Autosomal dominant PKD determines formation of multiple cysts predominantly in the kidneys and usually becomes symptomatic during adulthood and can lead to renal failure. In contrast, in autosomal recessive PKD cysts occur in both the kidneys and the liver and usually presents an earlier onset. Obtaining genetic diagnosis is important to confirm clinical diagnosis and is required before treating with vasopressin 2 receptor blockers, which are the only drugs known to slow down the disease. Furthermore, in the case of kidney transplant from a living family member it is essential to exclude the presence of the mutation in the donor. We used clinical exome sequencing to provide genetic diagnosis to a cohort of patients with a clinical suspicion of PKD.
Method
175 patients were referred to the Immunogenetics and Transplant Biology Service of the Turin University Hospital through a network of nephrology centers operating in the Piedmont region. Some patients were referred following genetic counseling. All patients signed an informed consent and the referring physicians provided relevant clinical data. DNA from eligible patients was extracted, checked for integrity, quantified and used for library preparation. A clinical exome sequencing (CES) kit by Illumina was used, allowing the analysis of 6,700 clinically relevant genes.
Results
Out of the 175 recruited patients eligible for CES, 38 (21.7%) had a clinical suspicion or diagnosis of PKD, with 50% of them presenting family history. The majority of the cohort was represented by male subjects (60.5%) and included both children (34.2%) and adults. The analytical approach was based on initial analysis of genes responsible for PKD (PKD1, PKD2 and PKHD1). If no mutation could be identified, analysis was then extended to a panel of 99 genes responsible for ciliopathies. This approach led to the identification of causative variants in 33/38 (86.8%) of the PKD cohort, while no variant could be identified in 5/38 patients. In 5/33 (15.2%) patients, mutations were inconclusive as found in heterozygosity in genes known to have an autosomal recessive mode of inheritance, while 27/33 (81.8%) were in line with the initial clinical suspicion/diagnosis. Of these, the majority was represented by missense mutations (12), followed by frameshift and nonsense mutations (6 each) and 3 splicing variants. As expected, the majority of mutations were found in PKD1 17/27 (63%), PKD2 3/27 (11.1%) and PKHD1 2/27 (7.4%). In these two latter patients, variants were found as compound heterozygosity. We also found mutations in other genes known to cause cysts, including TSC2 and CPT2. Of note, in 7 patients carrying PKD1 mutations, we found a second variant in PKD1 or PKHD1. Interestingly, when looking at patients characterized by kidney failure but lacking a clinical suspicion at recruitment or diagnosed with other phenotypes (66/175), we found variants in PKD1 and in PKD2 in 11 patients (9 and 2, respectively).
Of all identified variants in PKD1, PKD2 and PKHD1 genes, 17.6% were annotated as pathogenic (C5), 41.2% were likely pathogenic (C4) and 41.2% were variants of unknown significance (C3). 19 variants in these genes were not previously reported. All the variants found in genes responsible for PKD were validated and confirmed by Sanger sequencing. Family segregation studies are ongoing.
Finally, it is worth mentioning that in a portion of cases (5/38) with clinical and phenotypic features of PKD, supported also by a positive family history, we could not detect mutations in causative genes. These results may be explained by the presence of intronic variants, in line with data reported in literature.
Conclusion
These results demonstrate that CES may be applied to PKD patients to identify causative variants during their routine diagnostic flow. Furthermore, CES may be a useful tool to detect mutations in PKD-related genes in patients with undiagnosed diseases, considering its rapidly decreasing costs.
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Affiliation(s)
- Tiziana Vaisitti
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Monica Sorbini
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Martina Callegari
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Silvia Kalantari
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Valeria Bracciamà
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Francesca Arruga
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Silvia Bruna Vanzino
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | | | - Daniela Giachino
- AOU San Luigi Gonzaga, Orbassano, Turin & Department of Clinical and Biological Sciences, University of Turin, Torino, Italy
| | - Enrico Cocchi
- Nephrology Dialysis and Transplantation, Regina Margherita Children's Hospital, Turin, Torino, Italy
| | - Simone Baldovino
- Department of Clinical and Biological Sciences, University of Turin & SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin, Torino, Italy
| | - Cristiana Rollino
- SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin
| | - Roberta Fenoglio
- SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin
| | | | | | - Giorgio Soragna
- Nephrology and Dialysis Unit Mauriziano Hospital, Turin, Torino, Italy
| | - Corrado Vitale
- Nephrology and Dialysis Unit Mauriziano Hospital, Turin, Torino, Italy
| | - Valentina Berta
- Nephrology and Dialysis Unit of Casale Monferrato, Alessandria, Alessandria, Italy
| | - Giovanni Calabrese
- Nephrology and Dialysis Unit of Casale Monferrato, Alessandria, Alessandria, Italy
| | - Gianluca Leonardi
- Nephrology and Dialysis Unit, Città della Salute e della Scienza, Turin, Torino, Italy
| | - Luigi Biancone
- Nephrology and Dialysis Unit, Città della Salute e della Scienza, Turin, Torino, Italy
| | | | - Serena Maroni
- Nephrology and Dialysis Unit ASL TO4, Turin, Torino, Italy
| | - Sonia Santi
- Nephrology and Dialysis Unit of Chivasso ASL TO4, Turin, Torino, Italy
| | - Loredana Funaro
- Nephrology and Dialysis Unit of Verbania ASL VCO, Verbano Cusio Ossola, Verbania, Italy
| | - Maurizio Borzumati
- Nephrology and Dialysis Unit of Verbania ASL VCO, Verbano Cusio Ossola, Verbania, Italy
| | | | - Giusto Viglino
- Nephrology and Dialysis Unit of Alba ASL CN2, Alba, Alba, Italy
| | - Bruno Gianoglio
- Nephrology Dialysis and Transplantation, Regina Margherita Children's Hospital, Turin, Torino, Italy
| | - Licia Peruzzi
- Nephrology Dialysis and Transplantation, Regina Margherita Children's Hospital, Turin, Torino, Italy
| | - Dario Roccatello
- Department of Clinical and Biological Sciences, University of Turin & SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin, Torino, Italy
| | - Antonio Amoroso
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Silvia Deaglio
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
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9
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Vaisitti T, Sorbini M, Callegari M, Kalantari S, Bracciamà V, Arruga F, Vanzino SB, Pelle A, Giachino D, Cocchi E, Baldovino S, Rollino C, Fenoglio R, Peruzzi L, Roccatello D, Amoroso A, Deaglio S. P0056USE OF CLINICAL EXOME SEQUENCING IN THE DIAGNOSTIC FLOW OF MONOGENIC KIDNEY DISEASES: THE PIEDMONT EXPERIENCE. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa142.p0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background and Aims
next-generation sequencing (NGS) technologies are becoming a powerful diagnostic tool in precision medicine. Specifically, exome sequencing can help in the diagnosis of selected diseases, in their medical management and therapeutic choices. Inherited kidney diseases (IKD) are among the major causes for kidney failure, both in children and adults, resulting in increased mortality, high health care costs and need for organ transplantation. In addition, it is worth mentioning that a significant proportion of patients in the kidney transplant lacks a clear diagnosis. This subset of diseases may thus benefit from the application of NGS technology, as the simultaneous investigation of hundreds of genes can lead to the identification of causative variants in a vast population of patients.
The aim of this study is to validate the use of a clinical exome sequencing approach in the diagnostic flow for kidney diseases leading to organ failure to i) confirm the clinical diagnosis, ii) find the genetic cause of previously unrecognized diseases and iii) improve the outcome of organ transplantation by excluding live-donors carrying the same mutational burden.
Method
160 patients were recruited, directly or following a genetic counseling, exploiting a network of 21 nephrology centers spread across the Piedmont region, coordinated by the “Centro Regionale Trapianti (CRT)” of Torino. Patients were then evaluated for NGS eligibility. DNA extracted from blood samples was checked for integrity, quantified and used for library preparation. A clinical exome sequencing (CES) kit by Illumina was used, allowing for targeted capture, enrichment and sequencing of 6700 clinically relevant genes. Reads were aligned to hg37 reference genome using the Isaac enrichment tool and variants filtered using an ad-hoc set up pipeline of analysis.
Results
clinical exome sequencing was performed on a diagnostic cohort of 138 patients, both children (37.7%) and adults (62.3%), with a prevalence of male subjects (56.5%). The majority of the cohort (51.5%) presented a positive family history for kidney disease, while 22 patients were excluded from the study as organ failure was most likely the result of secondary events. The cohort was highly heterogeneous with 21% of patients presenting with ciliopathies, 18.1% with glomerular disease, 7.2% with tubular disease while the remaining cohort presented other diseases or was undiagnosed (44.3%). An ad hoc analytical pipeline was designed, based on selected genotype-phenotype correlation database, filter-in metrics, inheritance model and annotation of variants based on public databases and in-silico prediction tools. By adopting well defined criteria of recruitment and analysis, causative genes were identified in 61.6% of cases and in the 57.3% of cases results were in line with the original diagnostic hypothesis. Moreover, 50.8% of cases with organ failure for unknown reasons were solved with the identification of causative genes. Out of the 133 total variants found in the cohort, 63 were classified as pathogenic or likely pathogenic. The remaining 70 identified variants were annotated as variant of unknown significance and will be further investigated.
Conclusion
Taken together, these results show that CES is a powerful non-invasive tool for the genetic diagnosis of IKD. Identification of disease causative variants may represent a critical step for the diagnosis, clinical management of the patients, and potentially for optimal live-donor selection.
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Affiliation(s)
- Tiziana Vaisitti
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Monica Sorbini
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Martina Callegari
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Silvia Kalantari
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Valeria Bracciamà
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Francesca Arruga
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Silvia Bruna Vanzino
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | | | - Daniela Giachino
- AOU San Luigi Gonzaga, Orbassano, Turin & Department of Clinical and Biological Sciences, University of Turin, Torino, Italy
| | - Enrico Cocchi
- Nephrology Dialysis and Transplantation, Regina Margherita Children's Hospital, Turin, Torino, Italy
| | - Simone Baldovino
- Department of Clinical and Biological Sciences, University of Turin & SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin, Torino, Italy
| | - Cristiana Rollino
- SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin
| | - Roberta Fenoglio
- SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin
| | - Licia Peruzzi
- Nephrology Dialysis and Transplantation, Regina Margherita Children's Hospital, Turin, Torino, Italy
| | - Dario Roccatello
- Department of Clinical and Biological Sciences, University of Turin & SCU Nephrology and Dialysis (ERKnet member) - CMID, Center of Research of Immunopathology and Rare Diseases, San Giovanni Hospital, Turin, Torino, Italy
| | - Antonio Amoroso
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
| | - Silvia Deaglio
- Transplant Regional Center-Piedmont region, Immunogenetics and Transplant Biology, AOU Città della Salute e della Scienza & Department of Medical Sciences, University of Turin, Torino, Italy
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10
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Krishnamurthy S, Kartha GB, Venkateswaran VS, Prasannakumar M, Mahadevan S, Gowda M, Pelle A, Giachino D. Primary Hyperoxaluria Type 1 with Homozygosity for a Double-mutated AGXT Allele in a 2-year-old Child. Indian J Nephrol 2017; 27:402-405. [PMID: 28904440 PMCID: PMC5590421 DOI: 10.4103/ijn.ijn_261_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary hyperoxaluria (PH) Type 1 is a rare, genetic disorder caused by deficiency of the liver enzyme alanine-glyoxylate aminotransferase, which is encoded by AGXT gene. We report a 2-year-old South Indian Tamil child with nephrocalcinosis due to PH Type 1, in whom a homozygous genotype for two missense mutations in the AGXT gene was found: first, a C to G transversion (c. 32C>G) in exon 1 resulting in the amino acid substitution p.Pro11Arg; second, a T to A transversion (c. 167T>A) in exon 2 resulting in p.Ile56Asn. A therapy based on potassium citrate and pyridoxine was started. This is the first report of molecular testing-proven childhood onset-PH Type 1 from South India and is notable for the co-occurrence of two missense mutations in one AGXT allele, which might lead to different and more severe phenotype than each mutation alone. To the best of our knowledge, AGXT allele carrying two already known mutations has not been previously reported.
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Affiliation(s)
- S Krishnamurthy
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - G B Kartha
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - V S Venkateswaran
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - M Prasannakumar
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - S Mahadevan
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - M Gowda
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - A Pelle
- Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Orbassano, Torino, Italy
| | - D Giachino
- Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Orbassano, Torino, Italy
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11
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Di Gregorio E, Riberi E, Belligni EF, Biamino E, Spielmann M, Ala U, Calcia A, Bagnasco I, Carli D, Gai G, Giordano M, Guala A, Keller R, Mandrile G, Arduino C, Maffè A, Naretto VG, Sirchia F, Sorasio L, Ungari S, Zonta A, Zacchetti G, Talarico F, Pappi P, Cavalieri S, Giorgio E, Mancini C, Ferrero M, Brussino A, Savin E, Gandione M, Pelle A, Giachino DF, De Marchi M, Restagno G, Provero P, Cirillo Silengo M, Grosso E, Buxbaum JD, Pasini B, De Rubeis S, Brusco A, Ferrero GB. Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes. Clin Genet 2017; 92:415-422. [PMID: 28295210 DOI: 10.1111/cge.13009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). AIMS Identification of genomic disorders in DD/ID. MATERIALS AND METHODS We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. RESULTS We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape. DISCUSSION AND CONCLUSION We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects.
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Affiliation(s)
- E Di Gregorio
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - E Riberi
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E F Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Biamino
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - M Spielmann
- Research Group Mundlos, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - U Ala
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - A Calcia
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - I Bagnasco
- Neuropsichiatria Infantile, Martini Hospital, ASL TO1, Turin, Italy
| | - D Carli
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - G Gai
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Giordano
- Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - A Guala
- SOC Pediatria, Castelli Hospital, Verbania, Italy
| | - R Keller
- Mental Health Department, ASL TO2, Adult Autism Center, Turin, Italy
| | - G Mandrile
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - C Arduino
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - A Maffè
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - V G Naretto
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - F Sirchia
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - L Sorasio
- Pediatrics, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S Ungari
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - A Zonta
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G Zacchetti
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - F Talarico
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Pappi
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - S Cavalieri
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Giorgio
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - C Mancini
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - M Ferrero
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - A Brussino
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Savin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Gandione
- Department of Neuropsychiatry, University of Torino, Turin, Italy
| | - A Pelle
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - D F Giachino
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - M De Marchi
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - G Restagno
- Laboratory of Molecular Genetics, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Provero
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - M Cirillo Silengo
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Grosso
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - J D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - B Pasini
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - A Brusco
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G B Ferrero
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
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Abstract
To study the effects of a therapeutical dose of corticosteroid alone or associated with beta-2 agonist on performance and substrate response during intense submaximal exercise, seven healthy moderately trained male volunteers participated in the double-blind randomized cross-over study. An intense endurance exercise test to exhaustion was performed after ingestion of placebo (Pla), 20 mg prednisolone (Pred), and 20 mg prednisolone plus 4 mg salbutamol (Pred-Sal). Blood samples were collected at rest, after 5, 10 min of exercise, at exhaustion, and after 5 (r5), 10 (r10), and 20 (r20) min of passive recovery for ACTH, growth hormone, insulin, blood glucose, and lactate measurements. There were no significant differences in exercise time to exhaustion between the three treatments (Pla: 21.5 +/- 2.9; Pred: 22.0 +/- 2.5; Pred-Sal: 24.2 +/- 2.8 min). ACTH was significantly lowered after Pred and Pred-Sal vs. Pla from the start of exercise to the end of the experiment (p < 0.05). Pred and Pred-Sal increased resting and recovery (r10 and r20) significantly but not exercise blood glucose values. There were no significant differences in growth hormone concentrations between the three treatments whereas insulin was significantly higher at rest, during exercise, and at r20 after Pred-Sal administration vs. Pred and Pla (p < 0.05). Pred and Pred-Sal showed no significant effect on blood lactate compared with Pla treatment. These preliminary results do not support the hypothesis that acute oral therapeutic corticosteroid intake alone or associated with beta-2 mimetic improves performance during intense submaximal exercise, but further studies are necessary with tests of longer duration.
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Affiliation(s)
- A Arlettaz
- Atosep Laboratory, Faculty of Sports Sciences, University of Orleans, Vendôme street BP 6237, 45062 Orléans, France
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14
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Abstract
Insulin pump therapy can be successfully initiated in an ambulatory setting if the patient's motivation is high, the health care team is available 24 hours a day, and a comprehensive educational program is implemented. Details of patient selection and teaching sessions are discussed.
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15
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Robins B, Bucholtz HK, Pelle A, D'Agostino M. Continuous subcutaneous insulin infusion via portable pumps in ambulatory diabetics. J Med Soc N J 1982; 79:490-3. [PMID: 6956738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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Businco L, Bruzzese E, Scozzarro A, Servino G, Salsiccia S, Niro A, Ricciotti F, Altieri A, Corgiolu M, Di Nardo A, Leoni A, Mancini L, Oddo C, Pelle A, Pitzalis A, Pitzalis F, Bancheri C, Ragno V, Mesiano G, Vitali L. Skin eosinophilia from influenza viruses. An experimental histological study. Allergol Immunopathol (Madr) 1980; 8:429-38. [PMID: 7468394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The authors would first like to stress the increasing frequency of bronchial asthma during or after influenza. To find an explanation for this occurrence they observed tissue reactions following an injection of viral material. In their experiments, they injected into the skin of guinea pigs, strains of the Hong Kong, Texas and USSR influenza viruses using current vaccines, sacrificing groups of animals 2, 6, 24, 48 hours and 7 days after the injection. The histological study revealed the following picture of reaction to influenza viruses. Two hours after the injection: marked and diffuse infiltration of eosinophils in the connective tissue of the skin. After 6 hours: the infiltration shows a predominance of neutrophils. After 24 hours: the neutrophil infiltration is predominant and diffuse. There is evidence of considerable degranulation of eosinophils. The cutaneous histiocytes undergo fibrocytic and marcophagic proliferation. After 28 hours, the same picture. After 7 days there is sever degeneration with a peripheral fibroblastic reaction. The most important finding of this experiment is the early marked infiltration of eosinophils which follows the injection of the influenza viruses. The eosinophil infiltration appears to be related to the release of histamine caused by influenza viruses. The histological examination did not reveal the presence of immune allergic-type cells at any time. Therefore, the onset of asthmatic attacks would appear to be more related to the histamine-releasing action of the influenza viruses rather than to their sensitizing activity. Naturally, the latter may occur in human pathologies.
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17
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Costin ID, Petrica L, Garoiu M, Onică P, Pelle A, Dinu N. Correlation between origin and biochemical behaviour of salmonella gallinarum and salmonella pullorum cultures. Zentralbl Bakteriol Orig 1964; 194:342-50. [PMID: 5832431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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