1
|
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] [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.
Collapse
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.
| |
Collapse
|
3
|
Soulier J, Leblanc T, Larghero J, Dastot H, Shimamura A, Guardiola P, Esperou H, Ferry C, Jubert C, Feugeas JP, Henri A, Toubert A, Socié G, Baruchel A, Sigaux F, D'Andrea AD, Gluckman E. Detection of somatic mosaicism and classification of Fanconi anemia patients by analysis of the FA/BRCA pathway. Blood 2004; 105:1329-36. [PMID: 15383454 DOI: 10.1182/blood-2004-05-1852] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fanconi anemia (FA) is characterized by congenital abnormalities, bone marrow failure, chromosome fragility, and cancer susceptibility. Eight FA-associated genes have been identified so far, the products of which function in the FA/BRCA pathway. A key event in the pathway is the monoubiquitination of the FANCD2 protein, which depends on a multiprotein FA core complex. In a number of patients, spontaneous genetic reversion can correct FA mutations, leading to somatic mosaicism. We analyzed the FA/BRCA pathway in 53 FA patients by FANCD2 immunoblots and chromosome breakage tests. Strikingly, FANCD2 monoubiquitination was detected in peripheral blood lymphocytes (PBLs) in 8 (15%) patients. FA reversion was further shown in these patients by comparison of primary fibro-blasts and PBLs. Reversion was associated with higher blood counts and clinical stability or improvement. Once constitutional FANCD2 patterns were determined, patients could be classified based on the level of FA/BRCA pathway disruption, as "FA core" (upstream inactivation; n = 47, 89%), FA-D2 (n = 4, 8%), and an unidentified downstream group (n = 2, 4%). FA-D2 and unidentified group patients were therefore relatively common, and they had more severe congenital phenotypes. These results show that specific analysis of the FA/BRCA pathway, combined with clinical and chromosome breakage data, allows a comprehensive characterization of FA patients.
Collapse
Affiliation(s)
- Jean Soulier
- Genome Rearrangements and Cancer Laboratory, U462 INSERM, Laboratoire Central d'Hématologie and Institut Universitaire d'Hématologie, Hopital Saint-Louis, 1 Ave Claude Vellefaux, 75010 Paris, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Gross M, Hanenberg H, Lobitz S, Friedl R, Herterich S, Dietrich R, Gruhn B, Schindler D, Hoehn H. Reverse mosaicism in Fanconi anemia: natural gene therapy via molecular self-correction. Cytogenet Genome Res 2003; 98:126-35. [PMID: 12697994 DOI: 10.1159/000069805] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2002] [Accepted: 12/10/2002] [Indexed: 11/19/2022] Open
Abstract
Fanconi anemia (FA) is a genetically and phenotypically heterogenous autosomal recessive disease associated with chromosomal instability and hypersensitivity to DNA crosslinkers. Prognosis is poor due to progressive bone marrow failure and increased risk of neoplasia, but revertant mosaicism may improve survival. Mechanisms of reversion include back mutation, intragenic crossover, gene conversion and compensating deletions/insertions. We describe the types of reversions found in five mosaic FA patients who are compound heterozygotes for single base mutations in FANCA or FANCC. Intragenic crossover could be shown as the mechanism of self-correction in the FANCC patient. Restoration to wildtype via back mutation or gene conversion of either the paternal or maternal allele was observed in the FANCA patients. The sequence environments of these mutations/reversions were indicative of high mutability, and selective advantage of bone marrow precursor cells carrying a completely restored FANCA allele might explain the surprisingly uniform pattern of these reversions. We also describe a first example of in vitro phenotypic reversion via the emergence of a compensating missense mutation 15 amino acids downstream of the constitutional mutation, which explains the reversion to MMC resistance of the respective lymphoblastoid cell line. With one exception, our mosaic patients showed improvement of their hematological status during a three- to six-year observation period, indicating a proliferative advantage of the reverted cell lineages. In patients with Fanconi anemia, genetic instability due to defective caretaker genes sharply increases the risk of neoplasia, but at the same time increases the chance for revertant mosaicism leading to improved bone marrow function.
Collapse
Affiliation(s)
- M Gross
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Deviren A, Yalman N, Hacihanefioglu S. Differential diagnosis of Fanconi anemia by nitrogen mustard and diepoxybutane. Ann Hematol 2003; 82:223-7. [PMID: 12707724 DOI: 10.1007/s00277-003-0614-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2002] [Accepted: 01/04/2003] [Indexed: 10/25/2022]
Abstract
Fanconi anemia (FA) is an autosomal recessive inherited disorder which is associated with a variety of congenital anomalies. These include morphometric abnormalities involving mainly the head and face, skeletal malformations particularly of the radial ray, growth retardation, abnormal skin pigmentation, deafness, and renal, ocular, genital, and cardiac defects. The cardinal clinical feature is a severe progressive pancytopenia. The overall aim of our study was to compare two different alkylating agents that would permit rapid and unequivocal detection of FA. A total of 271 patients underwent nitrogen mustard (NTM) and diepoxybutane (DEB) tests in our laboratory; baseline chromosomal breakage was studied for all of them. After the results of the chromosomal breakage studies, 72 patients were diagnosed as affected and 136 patients as unaffected by FA. We also studied 63 family members of FA patients. According to our study, NTM seems more specific to identify chromosomal breakages in FA parents than DEB.
Collapse
Affiliation(s)
- A Deviren
- Istanbul University, Cerrahpasa Medical Faculty, Genetics Department, Baharlibahce Sokak Kibris Apt No:17 Daire:14, 34740 Bakirkoy-Istanbul, Turkey.
| | | | | |
Collapse
|