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Lombardo A, Sinibaldi L, Genovese S, Catino G, Mei V, Pompili D, Sallicandro E, Falasca R, Liambo MT, Faggiano MV, Roberti MC, Di Donato M, Vitelli A, Russo S, Giannini R, Micalizzi A, Pietrafusa N, Digilio MC, Novelli A, Fusco L, Alesi V. A Case of CDKL5 Deficiency Due to an X Chromosome Pericentric Inversion: Delineation of Structural Rearrangements as an Overlooked Recurrent Pathological Mechanism. Int J Mol Sci 2024; 25:6912. [PMID: 39000022 PMCID: PMC11241409 DOI: 10.3390/ijms25136912] [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: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/14/2024] Open
Abstract
CDKL5 deficiency disorder (CDD) is an X-linked dominant epileptic encephalopathy, characterized by early-onset and drug-resistant seizures, psychomotor delay, and slight facial features. Genomic variants inactivating CDKL5 or impairing its protein product kinase activity have been reported, making next-generation sequencing (NGS) and chromosomal microarray analysis (CMA) the standard diagnostic tests. We report a suspicious case of CDD in a female child who tested negative upon NGS and CMA and harbored an X chromosome de novo pericentric inversion. The use of recently developed genomic techniques (optical genome mapping and whole-genome sequencing) allowed us to finely characterize the breakpoints, with one of them interrupting CDKL5 at intron 1. This is the fifth case of CDD reported in the scientific literature harboring a structural rearrangement on the X chromosome, providing evidence for the hypothesis that this type of anomaly can represent a recurrent pathogenic mechanism, whose frequency is likely underestimated, with it being overlooked by standard techniques. The identification of the molecular etiology of the disorder is extremely important in evaluating the pathological outcome and to better investigate the mechanisms associated with drug resistance, paving the way for the development of specific therapies. Karyotype and genomic techniques should be considered in all cases presenting with CDD without molecular confirmation.
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Affiliation(s)
- Antonietta Lombardo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Lorenzo Sinibaldi
- Medical Genetics Unit, IRCCS Bambino Gesù Children Hospital, 00165 Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Valerio Mei
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Daniele Pompili
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Ester Sallicandro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Roberto Falasca
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maria Teresa Liambo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maria Vittoria Faggiano
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maria Cristina Roberti
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maddalena Di Donato
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Anna Vitelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Serena Russo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Rosalinda Giannini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Alessia Micalizzi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Medical Genetics Unit, San Pietro Fatebenefratelli Hospital, 00189 Rome, Italy
| | - Nicola Pietrafusa
- Neurology, Epilepsy and Movement Disorders Unit, Bambino Gesù, IRCCS Children’s Hospital, 00165 Rome, Italy
| | | | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Lucia Fusco
- Neurology, Epilepsy and Movement Disorders Unit, Bambino Gesù, IRCCS Children’s Hospital, 00165 Rome, Italy
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
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Jourdy Y, Chatron N, Frétigny M, Zawadzki C, Lienhart A, Stieltjes N, Rohrlich PS, Thauvin-Robinet C, Volot F, Hamida YF, Hariti G, Leuci A, Dargaud Y, Sanlaville D, Vinciguerra C. Whole F8 gene sequencing identified pathogenic structural variants in the remaining unsolved patients with severe hemophilia A. J Thromb Haemost 2024; 22:1616-1626. [PMID: 38484912 DOI: 10.1016/j.jtha.2024.03.002] [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: 12/18/2023] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND No F8 genetic abnormality is detected in approximately 1% to 2% of patients with severe hemophilia A (HA) using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal. OBJECTIVES The study aimed to identify the causal variation in families with a history of severe HA for whom genetic investigations failed. METHODS We performed whole F8 gene sequencing in 8 propositi. Genomic rearrangements were confirmed by Sanger sequencing of breakpoint junctions and/or quantitative polymerase chain reaction. RESULTS A structural variant disrupting F8 was found in each propositus, so that all the 815 families with a history of severe HA registered in our laboratory received a conclusive genetic diagnosis. These structural variants consisted of 3 balanced inversions, 3 large insertions of gained regions, and 1 retrotransposition of a mobile element. The 3 inversions were 105 Mb, 1.97 Mb, and 0.362 Mb in size. Among the insertions of gained regions, one corresponded to the insertion of a 34 kb gained region from chromosome 6q27 in F8 intron 6, another was the insertion of a 447 kb duplicated region from chromosome 9p22.1 in F8 intron 14, and the last one was the insertion of an Xq28 349 kb gained in F8 intron 5. CONCLUSION All the genetically unsolved cases of severe HA in this cohort were due to structural variants disrupting F8. This study highlights the effectiveness of whole F8 sequencing to improve the molecular diagnosis of HA when the conventional approach fails.
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Affiliation(s)
- Yohann Jourdy
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France.
| | - Nicolas Chatron
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France; Université Claude Bernard Lyon 1 - CNRS UMR 5261 -INSERM U1315, Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Lyon, France
| | - Mathilde Frétigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
| | - Christophe Zawadzki
- Pôle de Biologie Pathologie Génétique, Institut d'Hématologie - Transfusion, CHU Lille, Lille, France
| | - Anne Lienhart
- Hospices Civils de Lyon, Lyon Hemophilia Center and Clinical Haemostasis Unit, Bron, France
| | | | | | - Christel Thauvin-Robinet
- Centre de Génétique, Centre de Référence, Déficiences Intellectuelles de Causes Rares, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | | | | | - Ghania Hariti
- Laboratoire de recherche en hémostase, Université d'Alger 1, Alger, Algérie
| | - Alexandre Leuci
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
| | - Yesim Dargaud
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France; Hospices Civils de Lyon, Lyon Hemophilia Center and Clinical Haemostasis Unit, Bron, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France; Université Claude Bernard Lyon 1 - CNRS UMR 5261 -INSERM U1315, Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Lyon, France
| | - Christine Vinciguerra
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
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Chatron N, Schluth-Bolard C, Frétigny M, Labalme A, Vilchez G, Castet SM, Négrier C, Sanlaville D, Vinciguerra C, Jourdy Y. Severe hemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing. J Thromb Haemost 2019; 17:1097-1103. [PMID: 31021037 DOI: 10.1111/jth.14460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/18/2019] [Indexed: 01/23/2023]
Abstract
Essentials No F8 genetic abnormality is detected in about 2% of severe hemophilia A patients. Detection of F8 structural variants remains a challenge. We identified a new F8 rearrangement in a severe hemophilia A patient using nanopore sequencing. We highlight the value of single-molecule long-read sequencing technologies in a genomics laboratory. BACKGROUND No F8 genetic abnormality is detected in about 2% of severe hemophilia A patients using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal. OBJECTIVE To characterize, in a genetically unresolved severe hemophilia A patient, a new Xq28 rearrangement disrupting F8 using comprehensive molecular techniques including nanopore sequencing. RESULTS Long-range polymerase chain reaction (PCR) performed throughout F8 identified a nonamplifiable region in intron 25 indicating the presence of a genomic rearrangement. F8 messanger ribonucleic acid (mRNA) analysis including 3'rapid amplification of complementary deoxyribonucleic acid (cDNA) ends and nanopore sequencing found the presence of a F8 fusion transcript in which F8 exon 26 was replaced by a 742-bp pseudoexon corresponding to a noncoding region located at the beginning of the long arm of chromosome X (Xq12; chrX: 66 310 352-66 311 093, GRCh37/hg19). Cytogenetic microarray analysis found the presence of a Xq11.1q12 gain of 3.8 Mb. The PCR amplification of junction fragments and fluorescent in situ hybridization (FISH) analysis found that the Xq11q12 duplicated region was inserted in the F8 intron 25 genomic region. CONCLUSION We characterized a novel genomic rearrangement in which a 3.8-Mb Xq11.1q12 gain inserted in the F8 intron 25 led to an aberrant fusion transcript in a patient with severe hemophilia A (HA), using comprehensive molecular techniques. This study highlights the value of single-molecule long-read sequencing technologies for molecular diagnosis of HA especially when conventional genetic approaches have failed.
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Affiliation(s)
- Nicolas Chatron
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard, Lyon, France
| | - Caroline Schluth-Bolard
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard, Lyon, France
| | | | - Audrey Labalme
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Gaëlle Vilchez
- Groupe Hospitalier Est, Cellule bioinformatique de la plateforme de séquençage NGS du CHU de Lyon, Bron, France
| | - Sabine-Marie Castet
- Centre de ressources et compétences-maladies hémorragiques constitutionnelles, Hôpital Universitaire de Bordeaux, Bordeaux, France
| | - Claude Négrier
- Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- EA 4609 Hémostase et cancer, Université Claude Bernard, Lyon, France
| | - Damien Sanlaville
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard, Lyon, France
| | - Christine Vinciguerra
- Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- EA 4609 Hémostase et cancer, Université Claude Bernard, Lyon, France
| | - Yohann Jourdy
- Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- EA 4609 Hémostase et cancer, Université Claude Bernard, Lyon, France
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