1
|
Liao JZ, Chung HL, Shih C, Wong KKL, Dutta D, Nil Z, Burns CG, Kanca O, Park YJ, Zuo Z, Marcogliese PC, Sew K, Bellen HJ, Verheyen EM. Cdk8/CDK19 promotes mitochondrial fission through Drp1 phosphorylation and can phenotypically suppress pink1 deficiency in Drosophila. Nat Commun 2024; 15:3326. [PMID: 38637532 PMCID: PMC11026413 DOI: 10.1038/s41467-024-47623-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Cdk8 in Drosophila is the orthologue of vertebrate CDK8 and CDK19. These proteins have been shown to modulate transcriptional control by RNA polymerase II. We found that neuronal loss of Cdk8 severely reduces fly lifespan and causes bang sensitivity. Remarkably, these defects can be rescued by expression of human CDK19, found in the cytoplasm of neurons, suggesting a non-nuclear function of CDK19/Cdk8. Here we show that Cdk8 plays a critical role in the cytoplasm, with its loss causing elongated mitochondria in both muscles and neurons. We find that endogenous GFP-tagged Cdk8 can be found in both the cytoplasm and nucleus. We show that Cdk8 promotes the phosphorylation of Drp1 at S616, a protein required for mitochondrial fission. Interestingly, Pink1, a mitochondrial kinase implicated in Parkinson's disease, also phosphorylates Drp1 at the same residue. Indeed, overexpression of Cdk8 significantly suppresses the phenotypes observed in flies with low levels of Pink1, including elevated levels of ROS, mitochondrial dysmorphology, and behavioral defects. In summary, we propose that Pink1 and Cdk8 perform similar functions to promote Drp1-mediated fission.
Collapse
Affiliation(s)
- Jenny Zhe Liao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A1S6, BC, Canada
- Center for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, V5A1S6, BC, Canada
| | - Hyung-Lok Chung
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, USA
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Claire Shih
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A1S6, BC, Canada
- Center for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, V5A1S6, BC, Canada
| | - Kenneth Kin Lam Wong
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A1S6, BC, Canada
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zelha Nil
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Catherine Grace Burns
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ye-Jin Park
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paul C Marcogliese
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, R3E0J9, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, R3E3P4, MB, Canada
| | - Katherine Sew
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A1S6, BC, Canada
- Center for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, V5A1S6, BC, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Esther M Verheyen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A1S6, BC, Canada.
- Center for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, V5A1S6, BC, Canada.
| |
Collapse
|
2
|
Giatti S, Cioffi L, Diviccaro S, Piazza R, Melcangi RC. Analysis of the finasteride treatment and its withdrawal in the rat hypothalamus and hippocampus at whole-transcriptome level. J Endocrinol Invest 2024:10.1007/s40618-024-02345-y. [PMID: 38493246 DOI: 10.1007/s40618-024-02345-y] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/18/2024] [Indexed: 03/18/2024]
Abstract
PURPOSE As reported in patients treated for androgenetic alopecia with finasteride (i.e., a blocker of the enzyme 5 alpha-reductase) and in an animal model, side effects affecting sexual, psychiatric, neurological, and physical domains, may occur during the treatment and persist with drug suspension. The etiopathogenesis of these side effects has been poorly explored. Therefore, we performed a genome-wide analysis of finasteride effects in the brain of adult male rat. METHODS Animals were treated (i.e., for 20 days) with finasteride (1mg/rat/day). 24 h after the last treatment and 1 month after drug suspension, RNA sequencing analysis was performed in hypothalamus and hippocampus. Data were analyzed by differential expression analysis and Gene-Set Enrichment Analyses (GSEA). RESULTS Data obtained after finasteride treatment showed that 186 genes (i.e., 171 up- and 15 downregulated) and 19 (i.e., 17 up- and 2 downregulated) were differentially expressed in the hypothalamus and hippocampus, respectively. Differential expression analysis at the drug withdrawal failed to identify dysregulated genes. Several gene-sets were enriched in these brain areas at both time points. CONCLUSION Some of the genes reported to be differentially expressed (i.e., TTR, DIO2, CLDN1, CLDN2, SLC4A5, KCNE2, CROT, HCRT, MARCKSL1, VGF, IRF2BPL) and GSEA, suggest a potential link with specific side effects previously observed in patients and in the animal model, such as depression, anxiety, disturbance in memory and attention, and sleep disturbance. These data may provide an important background for future experiments aimed at confirming the pathological role of these genes.
Collapse
Affiliation(s)
- S Giatti
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - L Cioffi
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - S Diviccaro
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - R Piazza
- Dipartimento di Medicina e Chirurgia, Università di Milano-Bicocca, Milan, Italy
| | - R C Melcangi
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy.
| |
Collapse
|
3
|
Heide S, Davoine CS, Cunha P, Scherer-Gagou C, Keren B, Stevanin G, Charles P, Heron D, Brice A, Durr A. IRF2BPL Causes Mild Intellectual Disability Followed by Late-Onset Ataxia. Neurol Genet 2023; 9:e200096. [PMID: 38235039 PMCID: PMC10586800 DOI: 10.1212/nxg.0000000000200096] [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: 02/01/2023] [Accepted: 08/04/2023] [Indexed: 01/19/2024]
Abstract
Background and Objectives Neurodevelopmental and neurodegenerative disorders have long been considered as different clinical and molecular entities, and only a few genes are known to be involved in both processes. The IRF2BPL (interferon regulatory factor 2 binding protein like) gene was implicated in a severe pediatric phenotype characterized by developmental and epileptic encephalopathy and early regression. In parallel, inherited IRF2BPL variants have been reported in cohorts of patients with late-onset progressive dystonic and ataxic syndrome with few information about the neurodevelopment of these patients. This study aimed to describe both neurodevelopmental and neurodegenerative aspects of the phenotype in adults with IRF2BPL pathogenic variant. Methods We report here the clinical and molecular data of 18 individuals carrying truncating IRF2BPL variants (identified by either exome or genome sequencing), including a large pedigree of 16 patients presenting with a neurodevelopmental disorder (NDD) associated with late-onset cerebellar ataxia and atrophy. Results Genome sequencing identified the p.(Gln117*) variant in a large family first assessed for familial ataxia, with multiple individuals presenting with NDD. The p.(Ser313*) variant was identified by exome sequencing in a second family with a young adult patient with NDD without ataxia which was inherited from her asymptomatic mother, suggesting incomplete penetrance of IRF2BPL-linked disorders. Discussion This study illustrates the importance of neurologic evaluation of adult patients initially diagnosed with NDD to detect a late-onset neurodegenerative condition. Two different disorders may be clinically diagnosed in the same family, when not considering that NDD and late cerebellar changes may be part of the same molecular spectrum such as for IRF2BPL.
Collapse
Affiliation(s)
- Solveig Heide
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Claire-Sophie Davoine
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Paulina Cunha
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Clarisse Scherer-Gagou
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Boris Keren
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Giovanni Stevanin
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Perrine Charles
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Delphine Heron
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Alexis Brice
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| | - Alexandra Durr
- From the Genetic Department (S.H., B.K., P. Charles, D.H., A.D.), Assistance Publique-Hôpitaux de Paris (AP-HP) Pitié-Salpêtrière; Reference Center for Rare Diseases « Intellectual disabilites of rare causes » « Déficiences Intellectuelles de Causes Rares » (S.H., P. Charles, D.H.), Pitié-Salpêtrière Hospital; Sorbonne Université (C.-S.D., P. Cunha, G.S., A.B., A.D.), Paris Brain Institute (ICM Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP); Department of Neurology (C.S.-G.), University Hospital d'Angers; and INCIA (G.S.), EPHE, Université de Bordeaux, France
| |
Collapse
|
4
|
Schlüter A, Vélez-Santamaría V, Verdura E, Rodríguez-Palmero A, Ruiz M, Fourcade S, Planas-Serra L, Launay N, Guilera C, Martínez JJ, Homedes-Pedret C, Albertí-Aguiló MA, Zulaika M, Martí I, Troncoso M, Tomás-Vila M, Bullich G, García-Pérez MA, Sobrido-Gómez MJ, López-Laso E, Fons C, Del Toro M, Macaya A, Beltran S, Gutiérrez-Solana LG, Pérez-Jurado LA, Aguilera-Albesa S, de Munain AL, Casasnovas C, Pujol A. ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization. Genome Med 2023; 15:68. [PMID: 37679823 PMCID: PMC10486091 DOI: 10.1186/s13073-023-01214-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have become indispensable tools to solve rare Mendelian genetic conditions. Nevertheless, there is still an urgent need for sensitive, fast algorithms to maximise WES/WGS diagnostic yield in rare disease patients. Most tools devoted to this aim take advantage of patient phenotype information for prioritization of genomic data, although are often limited by incomplete gene-phenotype knowledge stored in biomedical databases and a lack of proper benchmarking on real-world patient cohorts. METHODS We developed ClinPrior, a novel method for the analysis of WES/WGS data that ranks candidate causal variants based on the patient's standardized phenotypic features (in Human Phenotype Ontology (HPO) terms). The algorithm propagates the data through an interactome network-based prioritization approach. This algorithm was thoroughly benchmarked using a synthetic patient cohort and was subsequently tested on a heterogeneous prospective, real-world series of 135 families affected by hereditary spastic paraplegia (HSP) and/or cerebellar ataxia (CA). RESULTS ClinPrior successfully identified causative variants achieving a final positive diagnostic yield of 70% in our real-world cohort. This includes 10 novel candidate genes not previously associated with disease, 7 of which were functionally validated within this project. We used the knowledge generated by ClinPrior to create a specific interactome for HSP/CA disorders thus enabling future diagnoses as well as the discovery of novel disease genes. CONCLUSIONS ClinPrior is an algorithm that uses standardized phenotype information and interactome data to improve clinical genomic diagnosis. It helps in identifying atypical cases and efficiently predicts novel disease-causing genes. This leads to increasing diagnostic yield, shortening of the diagnostic Odysseys and advancing our understanding of human illnesses.
Collapse
Affiliation(s)
- Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Valentina Vélez-Santamaría
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
| | - Edgard Verdura
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Unit, Pediatrics Department, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Nathalie Launay
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Cristina Guilera
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Juan José Martínez
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Christian Homedes-Pedret
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
- Neurology Department, Hospital Universitari General de Catalunya, Barcelona, Spain
| | - M Antonia Albertí-Aguiló
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
| | - Miren Zulaika
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
| | - Itxaso Martí
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Donostia University Hospital, University of the Basque Country (UPV-EHU), San Sebastian, Spain
| | - Mónica Troncoso
- Pediatric Neurology Department, Central Campus, Hospital Clínico San Borja Arriarán, Universidad de Chile, Santiago, Chile
| | - Miguel Tomás-Vila
- Neuropediatrics Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Gemma Bullich
- Centro Nacional Análisis Genómico (CNAG) - Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - M Asunción García-Pérez
- Pediatric Neurology Unit, Pediatrics Department, Hospital Universitario Fundación Alcorcón, Madrid, Spain
| | - María-Jesús Sobrido-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Coruña Institute of Biomedical Research (INIBIC), A Coruña, Spain
- Hospital Clínico Universitario, A Coruña, Spain
| | - Eduardo López-Laso
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Unit, Pediatrics Department, Reina Sofía University Hospital, Córdoba, Spain
- Maimonides Institute For Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
| | - Carme Fons
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Sant Joan de Déu University Hospital, Member of the ERN EpiCARE, Barcelona, Spain
- Sant Joan de Déu Research Institute, (IRSJD), Barcelona, Spain
| | - Mireia Del Toro
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alfons Macaya
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Beltran
- Centro Nacional Análisis Genómico (CNAG) - Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Facultat de Biologia, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, 08028, Spain
| | - Luis G Gutiérrez-Solana
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Children's University Hospital Niño Jesús, Madrid, Spain
| | - Luis A Pérez-Jurado
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Genetics Service, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sergio Aguilera-Albesa
- Pediatric Neurology Unit, Pediatrics Department, Navarra Health Service, Pamplona, Spain
- Navarrabiomed, Biomedical Research Center, Pamplona, Spain
| | - Adolfo López de Munain
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
- Neurology Department, Donostia University Hospital, San Sebastian, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain.
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain.
| |
Collapse
|
5
|
Khan WJ, Maqsood H, Younus S. Novel IRF2BPL gene mutation manifesting as a broad spectrum of neurological disorders: a case report. BMJ Neurol Open 2023; 5:e000459. [PMID: 37649702 PMCID: PMC10462932 DOI: 10.1136/bmjno-2023-000459] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/01/2023] Open
Abstract
Background IRF2BPL (interferon regulatory factor 2-binding protein-like) gene is an intronless gene present ubiquitously in the human body, including the brain. Pathogenic variants lead to neurodegeneration and present with phenotypic features of a neurological disorder, including dyslexia, dyscalculia, epilepsy, dystonia, neurodevelopmental regression, loss of motor skills and cerebellar ataxia. Case We present a case of a 9-year-old boy who was brought to the emergency department with generalised tonic-clonic seizures and mild hypotonia. A history included neurological regression. After insignificant lab and imaging results, the patient underwent genetic testing, revealing a novel pathogenic mutation in the IRF2BPL gene (heterozygous variant), which had never been reported in the literature before. An autosomal dominant loss of function mutation was demonstrated, denoting in DNA as NM_0 24 496 c.911 C>T, which results in premature protein termination (p.Glu494). Conclusion Our case highlights the importance of early recognition of the neurological symptoms associated with various IRF2BPL gene mutations so that a timely multidisciplinary management approach can be provided.
Collapse
Affiliation(s)
- Wardah Javed Khan
- Northwest School of Medicine, Peshawar, Pakistan
- Khyber Girls Medical College, Peshawar, Pakistan
| | - Hamza Maqsood
- Neurology, Nishtar Medical College and Hospital, Multan, Punjab, Pakistan
| | - Shifa Younus
- Neurology, Nishtar Medical College and Hospital, Multan, Punjab, Pakistan
| |
Collapse
|
6
|
Costa C, Oliver KL, Calvello C, Cameron JM, Imperatore V, Tonelli L, Colavito D, Franceschetti S, Canafoglia L, Berkovic SF, Prontera P. IRF2BPL: A new genotype for progressive myoclonus epilepsies. Epilepsia 2023; 64:e164-e169. [PMID: 36810721 DOI: 10.1111/epi.17557] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 12/14/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
The progressive myoclonus epilepsies (PMEs) are a heterogeneous group of neurodegenerative disorders, typically presenting in late childhood. An etiologic diagnosis is achieved in about 80% of patients with PME, and genome-wide molecular studies on remaining, well-selected, undiagnosed cases can further dissect the underlying genetic heterogeneity. Through whole-exome sequencing (WES), we identified pathogenic truncating variants in the IRF2BPL gene in two, unrelated patients presenting with PME. IRF2BPL belongs to the transcriptional regulators family and it is expressed in multiple human tissues, including the brain. Recently missense and nonsense mutations in IRF2BPL were found in patients presenting with developmental delay and epileptic encephalopathy, ataxia, and movement disorders, but none with clear PME. We identified 13 other patients in the literature with myoclonic seizures and IRF2BPL variants. There was no clear genotype-phenotype correlation. With the description of these cases, the IRF2BPL gene should be considered in the list of genes to be tested in the presence of PME, in addition to patients with neurodevelopmental or movement disorders.
Collapse
Affiliation(s)
- Cinzia Costa
- Neurology Clinic, Department of Medicine and Surgery, University of Perugia-S. Maria Della Misericordia Hospital, Perugia, Italy
| | - Karen L Oliver
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Victoria, Australia
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Carmen Calvello
- Neurology Clinic, Department of Medicine and Surgery, University of Perugia-S. Maria Della Misericordia Hospital, Perugia, Italy
| | - Jillian M Cameron
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Victoria, Australia
| | - Valentina Imperatore
- Medical Genetics Unit, Maternal-Infantile Department, S. Maria della Misericordia Hospital, Perugia, Italy
| | - Laura Tonelli
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | | | - Silvana Franceschetti
- Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Canafoglia
- Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Samuel F Berkovic
- Department of Medicine (Austin Health), Epilepsy Research Centre, University of Melbourne, Heidelberg, Victoria, Australia
| | - Paolo Prontera
- Medical Genetics Unit, Maternal-Infantile Department, S. Maria della Misericordia Hospital, Perugia, Italy
| |
Collapse
|
7
|
Horovitz DDG, de Faria Domingues de Lima MA, Pires LDC, Campos Araujo ADQ, Vargas FR. Neurological Phenotypes of IRF2BPL Gene Variants: A Report of Four Novel Variants. J Cent Nerv Syst Dis 2023; 15:11795735231181467. [PMID: 37346291 PMCID: PMC10280516 DOI: 10.1177/11795735231181467] [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] [Indexed: 06/23/2023] Open
Abstract
IRF2BPL gene variants have recently been associated to developmental disability and epilepsy in children and movement disorders in adults. So far, only few cases have been reported; here we present four novel cases identified by exome sequencing, while investigating developmental delay, adult-onset cerebellar ataxia or regression.
Collapse
Affiliation(s)
- Dafne Dain Gandelman Horovitz
- Medical Genetics Department, Instituto Nacional de Saúde da
Mulher, da Criança e do Adolescente Fernandes Figueira/FIOCRUZ, Rio de
Janeiro, Brazil
| | | | | | - Abelardo de Queiroz Campos Araujo
- Associated Professor Neurology, Universidade Federal do Rio de
Janeiro, Rio de Janeiro, Brazil
- Researcher, Instituto Nacional de Infectologia Evandro
Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fernando Regla Vargas
- Medical Genetics, Gaffrée and Guinle University
Hospital, Rio de Janeiro, Brazil
- Genetics and Molecular Biology Department, Universidade Federal do Estado do Rio de
Janeiro, Rio de Janeiro, Brazil
- Epidemiology of congenital malformations
laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Nacional de Genética Médica
Populacional, Rio de Janeiro, Brazil
| |
Collapse
|
8
|
Li Y(J, Kresock E, Kuplicki R, Savitz J, McKinney BA. Differential expression of MDGA1 in major depressive disorder. Brain Behav Immun Health 2022; 26:100534. [PMID: 36247836 PMCID: PMC9563614 DOI: 10.1016/j.bbih.2022.100534] [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: 05/21/2022] [Revised: 09/08/2022] [Accepted: 10/09/2022] [Indexed: 11/09/2022] Open
Abstract
The identification of gene expression-based biomarkers for major depressive disorder (MDD) continues to be an important challenge. In order to identify candidate biomarkers and mechanisms, we apply statistical and machine learning feature selection to an RNA-Seq gene expression dataset of 78 unmedicated individuals with MDD and 79 healthy controls. We identify 49 genes by LASSO penalized logistic regression and 45 genes at the false discovery rate threshold 0.188. The MDGA1 gene has the lowest P-value (4.9e-5) and is expressed in the developing brain, involved in axon guidance, and associated with related mood disorders in previous studies of bipolar disorder (BD) and schizophrenia (SCZ). The expression of MDGA1 is associated with age and sex, but its association with MDD remains significant when adjusted for covariates. MDGA1 is in a co-expression cluster with another top gene, ATXN7L2 (ataxin 7 like 2), which was associated with MDD in a recent GWAS. The LASSO classification model of MDD includes MDGA1, and the model has a cross-validation accuracy of 79%. Another noteworthy top gene, IRF2BPL, is in a close co-expression cluster with MDGA1 and may be related to microglial inflammatory states in MDD. Future exploration of MDGA1 and its gene interactions may provide insights into mechanisms and heterogeneity of MDD. We use penalized regression to select differentially expressed genes and characterize their relationships through clustering. We identify MDGA1 as the most differentially expressed gene between MDD and healthy controls using RNA-Seq. Previous studies have implicated MDGA1 in psychiatric disorders, such as schizophrenia and bipolar disorder, but not in MDD. Different psychiatric disorders have some genetic associations in common due to shared neural pathways between disorders. A top gene, IRF2BPL, in a close co-expression cluster with MDGA1 may be related to microglial inflammatory states in MDD. Future investigation of interactions of MDGA1 and IRF2BPL may provide insights into mechanisms and heterogeneity of MDD.
Collapse
|
9
|
Straka B, Hermanovska B, Krskova L, Zamecnik J, Vlckova M, Balascakova M, Tesner P, Jezdik P, Tichy M, Kyncl M, Musilova A, Lassuthova P, Marusic P, Krsek P. Genetic Testing for Malformations of Cortical Development. Neurol Genet 2022; 8:e200032. [PMID: 36324633 PMCID: PMC9621608 DOI: 10.1212/nxg.0000000000200032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022]
Abstract
Background and Objectives Malformations of cortical development (MCD), though individually rare, constitute a significant burden of disease. The diagnostic yield of next-generation sequencing (NGS) in these patients varies across studies and methods, and novel genes and variants continue to emerge. Methods Patients (n = 123) with a definite radiologic or histopathologic diagnosis of MCD, with or without epilepsy were included in this study. They underwent NGS-based targeted gene panel (TGP) testing, whole-exome sequencing (WES), or WES-based virtual panel testing. Selected patients who underwent epilepsy surgery (n = 69) also had somatic gene testing of brain tissue–derived DNA. We analyzed predictors of positive germline genetic finding and diagnostic yield of respective methods. Results Pathogenic or likely pathogenic germline genetic variants were detected in 21% of patients (26/123). In the surgical subgroup (69/123), we performed somatic sequencing in 40% of cases (28/69) and detected causal variants in 18% (5/28). Diagnostic yield did not differ between TGP, WES-based virtual gene panel, and open WES (p = 0.69). Diagnosis of focal cortical dysplasia type 2A, epilepsy, and intellectual disability were associated with positive results of germline testing. We report previously unpublished variants in 16/26 patients and 4 cases of MCD with likely pathogenic variants in non-MCD genes. Discussion In this study, we are reporting genetic findings of a large cohort of MCD patients with epilepsy or potentially epileptogenic MCD. We determine predictors of successful ascertainment of a genetic diagnosis in real-life setting and report novel, likely pathogenic variants in MCD and non-MCD genes alike.
Collapse
|
10
|
Alkelai A, Greenbaum L, Docherty AR, Shabalin AA, Povysil G, Malakar A, Hughes D, Delaney SL, Peabody EP, McNamara J, Gelfman S, Baugh EH, Zoghbi AW, Harms MB, Hwang HS, Grossman-Jonish A, Aggarwal V, Heinzen EL, Jobanputra V, Pulver AE, Lerer B, Goldstein DB. The benefit of diagnostic whole genome sequencing in schizophrenia and other psychotic disorders. Mol Psychiatry 2022; 27:1435-1447. [PMID: 34799694 DOI: 10.1038/s41380-021-01383-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Schizophrenia has a multifactorial etiology, involving a polygenic architecture. The potential benefit of whole genome sequencing (WGS) in schizophrenia and other psychotic disorders is not well studied. We investigated the yield of clinical WGS analysis in 251 families with a proband diagnosed with schizophrenia (N = 190), schizoaffective disorder (N = 49), or other conditions involving psychosis (N = 48). Participants were recruited in Israel and USA, mainly of Jewish, Arab, and other European ancestries. Trio (parents and proband) WGS was performed for 228 families (90.8%); in the other families, WGS included parents and at least two affected siblings. In the secondary analyses, we evaluated the contribution of rare variant enrichment in particular gene sets, and calculated polygenic risk score (PRS) for schizophrenia. For the primary outcome, diagnostic rate was 6.4%; we found clinically significant, single nucleotide variants (SNVs) or small insertions or deletions (indels) in 14 probands (5.6%), and copy number variants (CNVs) in 2 (0.8%). Significant enrichment of rare loss-of-function variants was observed in a gene set of top schizophrenia candidate genes in affected individuals, compared with population controls (N = 6,840). The PRS for schizophrenia was significantly increased in the affected individuals group, compared to their unaffected relatives. Last, we were also able to provide pharmacogenomics information based on CYP2D6 genotype data for most participants, and determine their antipsychotic metabolizer status. In conclusion, our findings suggest that WGS may have a role in the setting of both research and genetic counseling for individuals with schizophrenia and other psychotic disorders and their families.
Collapse
Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna R Docherty
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrey A Shabalin
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Ayan Malakar
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Shannon L Delaney
- New York State Psychiatric Institute, Columbia University, New York City, NY, USA
| | - Emma P Peabody
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - James McNamara
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Sahar Gelfman
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Anthony W Zoghbi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, Columbia University, New York City, NY, USA
- New York State Psychiatric Institute, Office of Mental Health, New York, NY, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Harms
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Hann-Shyan Hwang
- Department of Medicine, National Taiwan University School of Medicine, Taipei, Taiwan
| | - Anat Grossman-Jonish
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Erin L Heinzen
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vaidehi Jobanputra
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bernard Lerer
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| |
Collapse
|
11
|
LeBlanc K, Kelley EG, Nagy A, Bater J, Berro T, McGuinness MA, Studwell C, Might M. Rare disease patient matchmaking: development and outcomes of an internet case-finding strategy in the Undiagnosed Diseases Network. Orphanet J Rare Dis 2021; 16:210. [PMID: 33971915 PMCID: PMC8108446 DOI: 10.1186/s13023-021-01825-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/28/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022] Open
Abstract
Background Although clinician, researcher, and patient resources for matchmaking exist, finding similar patients remains an obstacle for rare disease diagnosis. The goals of this study were to develop and test the effectiveness of an Internet case-finding strategy and identify factors associated with increased matching within a rare disease population. Methods Public web pages were created for consented participants. Matches made, time to each inquiry and match, and outcomes were recorded and analyzed using descriptive statistics. A Poisson regression model was run to identify characteristics associated with matches. Results 385 participants were referred to the project and 158 had pages posted. 579 inquiries were received; 89.0% were from the general public and 24.7% resulted in a match. 81.6% of pages received at least one inquiry and 15.0% had at least one patient match. Primary symptom category of neurology, diagnosis, gene page, and photo were associated with increased matches (p ≤ 0.05). Conclusions This Internet case-finding strategy was of interest to patients, families, and clinicians, and similar patients were identified using this approach. Extending matchmaking efforts to the general public resulted in matches and suggests including this population in matchmaking activities can improve identification of similar patients. Supplementary information The online version contains supplementary material available at 10.1186/s13023-021-01825-1.
Collapse
Affiliation(s)
- Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Emily G Kelley
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Anna Nagy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jorick Bater
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tala Berro
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Molly A McGuinness
- Bass Center for Childhood Cancer and Blood Diseases, Stanford Children's Health, Palo Alto, CA, USA
| | - Courtney Studwell
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Matthew Might
- Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|
12
|
Qian XH, Liu XY, Zhu ZY, Wang SG, Song XX, Chen G, Wu JY, Tang HD, Cao L. Neurodevelopmental disorder caused by a truncating de novo variant of IRF2BPL. Seizure 2020; 84:47-52. [PMID: 33278788 DOI: 10.1016/j.seizure.2020.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/15/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Mutations in the IRF2BPL gene can cause neurodevelopmental disorders. We describe the clinical and genetic characteristics of a Chinese patient with a novel abnormality in this gene, explore the potential pathogenic mechanism and summarize the clinical characteristics of 25 patients with IRF2BPL mutations. METHODS We identified the gene mutation sites by whole-exome and Sanger sequencing. The protein-protein interaction network of the IRF2BPL gene was constructed using bioinformatic techniques, and its function was enriched. We conducted a functional experiment to explore the potential pathogenicity of the identified IRF2BPL gene mutation. RESULTS An 8-year-old girl presented with progressive cerebellar ataxia, including involuntary tremor and slurred speech. Electroencephalography and electromyography revealed no abnormalities. Structural cranial MRI was also normal, but genetic analysis identified a truncating de novo variant in IRF2BPL. Bioinformatics predicted that IRF2BPL would be associated with IRF2 and 10 other genes and involved in ubiquitin binding and other pathways. The cellular location of IRF2BPL was altered, and compared to control cells, the level of ubiquitinated proteins was significantly decreased in cells harbouring the mutation. CONCLUSION In this study, we identified a truncating de novo variant of IRF2BPL as a causative gene in the neurodevelopmental disorder of a Chinese girl. Impairment of the ubiquitin-proteasome pathway caused by this IRF2BPL mutation may play an important role in this neurodevelopmental disorder.
Collapse
Affiliation(s)
- Xiao-Hang Qian
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xiao-Ying Liu
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Ze-Yu Zhu
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Shi-Ge Wang
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xiao-Xuan Song
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Guang Chen
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jing-Ying Wu
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hui-Dong Tang
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Li Cao
- Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Department of Neurology, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| |
Collapse
|
13
|
Vaisfeld A, Spartano S, Gobbi G, Vezzani A, Neri G. Chromosome 14 deletions, rings, and epilepsy genes: A riddle wrapped in a mystery inside an enigma. Epilepsia 2020; 62:25-40. [PMID: 33205446 DOI: 10.1111/epi.16754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/24/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 11/29/2022]
Abstract
The ring 14 syndrome is a rare condition caused by the rearrangement of one chromosome 14 into a ring-like structure. The formation of the ring requires two breakpoints and loss of material from the short and long arms of the chromosome. Like many other chromosome syndromes, it is characterized by multiple congenital anomalies and developmental delays. Typical of the condition are retinal anomalies and drug-resistant epilepsy. These latter manifestations are not found in individuals who are carriers of comparable 14q deletions without formation of a ring (linear deletions). To find an explanation for this apparent discrepancy and gain insight into the mechanisms leading to seizures, we reviewed and compared literature cases of both ring and linear deletion syndrome with respect to both their clinical manifestations and the role and function of potentially epileptogenic genes. Knowledge of the epilepsy-related genes in chromosome 14 is an important premise for the search of new and effective drugs to combat seizures. Current clinical and molecular evidence is not sufficient to explain the known discrepancies between ring and linear deletions.
Collapse
Affiliation(s)
- Alessandro Vaisfeld
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Serena Spartano
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Giuseppe Gobbi
- Residential Center for Rehabilitation Luce Sul Mare, Rimini, Italy
| | - Annamaria Vezzani
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Giovanni Neri
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy.,J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| |
Collapse
|
14
|
Kafantari E, Andréasson S, Säll T, Puschmann A. Do variants in IRF2BPL cause both neurological disorders and keratoconus 8? Parkinsonism Relat Disord 2020; 79:138-140. [PMID: 33069610 DOI: 10.1016/j.parkreldis.2020.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 11/25/2022]
Affiliation(s)
- Efthymia Kafantari
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Neurology, Lund, Sweden
| | - Sten Andréasson
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Ophthalmology, Lund, Sweden
| | - Torbjörn Säll
- Lund University, Department of Biology, Lund, Sweden
| | - Andreas Puschmann
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Neurology, Lund, Sweden.
| |
Collapse
|
15
|
Ansar M, Chung HL, Al-Otaibi A, Elagabani MN, Ravenscroft TA, Paracha SA, Scholz R, Abdel Magid T, Sarwar MT, Shah SF, Qaisar AA, Makrythanasis P, Marcogliese PC, Kamsteeg EJ, Falconnet E, Ranza E, Santoni FA, Aldhalaan H, Al-Asmari A, Faqeih EA, Ahmed J, Kornau HC, Bellen HJ, Antonarakis SE. Bi-allelic Variants in IQSEC1 Cause Intellectual Disability, Developmental Delay, and Short Stature. Am J Hum Genet 2019; 105:907-920. [PMID: 31607425 DOI: 10.1016/j.ajhg.2019.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022] Open
Abstract
We report two consanguineous families with probands that exhibit intellectual disability, developmental delay, short stature, aphasia, and hypotonia in which homozygous non-synonymous variants were identified in IQSEC1 (GenBank: NM_001134382.3). In a Pakistani family, the IQSEC1 segregating variant is c.1028C>T (p.Thr343Met), while in a Saudi Arabian family the variant is c.962G>A (p.Arg321Gln). IQSEC1-3 encode guanine nucleotide exchange factors for the small GTPase ARF6 and their loss affects a variety of actin-dependent cellular processes, including AMPA receptor trafficking at synapses. The ortholog of IQSECs in the fly is schizo and its loss affects growth cone guidance at the midline in the CNS, also an actin-dependent process. Overexpression of the reference IQSEC1 cDNA in wild-type flies is lethal, but overexpression of the two variant IQSEC1 cDNAs did not affect viability. Loss of schizo caused embryonic lethality that could be rescued to 2nd instar larvae by moderate expression of the human reference cDNA. However, the p.Arg321Gln and p.Thr343Met variants failed to rescue embryonic lethality. These data indicate that the variants behave as loss-of-function mutations. We also show that schizo in photoreceptors is required for phototransduction. Finally, mice with a conditional Iqsec1 deletion in cortical neurons exhibited an increased density of dendritic spines with an immature morphology. The phenotypic similarity of the affecteds and the functional experiments in flies and mice indicate that IQSEC1 variants are the cause of a recessive disease with intellectual disability, developmental delay, and short stature, and that axonal guidance and dendritic projection defects as well as dendritic spine dysgenesis may underlie disease pathogenesis.
Collapse
|
16
|
Li J, Gao K, Yan H, Xiangwei W, Liu N, Wang T, Xu H, Lin Z, Xie H, Wang J, Wu Y, Jiang Y. Reanalysis of whole exome sequencing data in patients with epilepsy and intellectual disability/mental retardation. Gene 2019; 700:168-175. [DOI: 10.1016/j.gene.2019.03.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022]
|
17
|
Mancini A, Howard SR, Cabrera CP, Barnes MR, David A, Wehkalampi K, Heger S, Lomniczi A, Guasti L, Ojeda SR, Dunkel L. EAP1 regulation of GnRH promoter activity is important for human pubertal timing. Hum Mol Genet 2019; 28:1357-1368. [PMID: 30608578 PMCID: PMC6452208 DOI: 10.1093/hmg/ddy451] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 11/23/2022] Open
Abstract
The initiation of puberty is orchestrated by an augmentation of gonadotropin-releasing hormone (GnRH) secretion from a few thousand hypothalamic neurons. Recent findings have indicated that the neuroendocrine control of puberty may be regulated by a hierarchically organized network of transcriptional factors acting upstream of GnRH. These include enhanced at puberty 1 (EAP1), which contributes to the initiation of female puberty through transactivation of the GnRH promoter. However, no EAP1 mutations have been found in humans with disorders of pubertal timing. We performed whole-exome sequencing in 67 probands and 93 relatives from a large cohort of familial self-limited delayed puberty (DP). Variants were analyzed for rare, potentially pathogenic variants enriched in case versus controls and relevant to the biological control of puberty. We identified one in-frame deletion (Ala221del) and one rare missense variant (Asn770His) in EAP1 in two unrelated families; these variants were highly conserved and potentially pathogenic. Expression studies revealed Eap1 mRNA abundance in peri-pubertal mouse hypothalamus. EAP1 binding to the GnRH1 promoter increased in monkey hypothalamus at the onset of puberty as determined by chromatin immunoprecipitation. Using a luciferase reporter assay, EAP1 mutants showed a reduced ability to trans-activate the GnRH promoter compared to wild-type EAP1, due to reduced protein levels caused by the Ala221del mutation and subcellular mislocation caused by the Asn770His mutation, as revealed by western blot and immunofluorescence, respectively. In conclusion, we have identified the first EAP1 mutations leading to reduced GnRH transcriptional activity resulting in a phenotype of self-limited DP.
Collapse
Affiliation(s)
- Alessandra Mancini
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sasha R Howard
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Claudia P Cabrera
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Michael R Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Alessia David
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK
| | - Karoliina Wehkalampi
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Sabine Heger
- Department of Pediatric Endocrinology, Children’s Hospital Auf der Bult, Hannover, Germany
| | - Alejandro Lomniczi
- Oregon National Primate Research Center/Oregon Health and Science University, Portland, OR, USA
| | - Leonardo Guasti
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sergio R Ojeda
- Oregon National Primate Research Center/Oregon Health and Science University, Portland, OR, USA
| | - Leo Dunkel
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| |
Collapse
|
18
|
Iwama K, Mizuguchi T, Takeshita E, Nakagawa E, Okazaki T, Nomura Y, Iijima Y, Kajiura I, Sugai K, Saito T, Sasaki M, Yuge K, Saikusa T, Okamoto N, Takahashi S, Amamoto M, Tomita I, Kumada S, Anzai Y, Hoshino K, Fattal-Valevski A, Shiroma N, Ohfu M, Moroto M, Tanda K, Nakagawa T, Sakakibara T, Nabatame S, Matsuo M, Yamamoto A, Yukishita S, Inoue K, Waga C, Nakamura Y, Watanabe S, Ohba C, Sengoku T, Fujita A, Mitsuhashi S, Miyatake S, Takata A, Miyake N, Ogata K, Ito S, Saitsu H, Matsuishi T, Goto YI, Matsumoto N. Genetic landscape of Rett syndrome-like phenotypes revealed by whole exome sequencing. J Med Genet 2019; 56:396-407. [DOI: 10.1136/jmedgenet-2018-105775] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 11/03/2022]
Abstract
BackgroundRett syndrome (RTT) is a characteristic neurological disease presenting with regressive loss of neurodevelopmental milestones. Typical RTT is generally caused by abnormality of methyl-CpG binding protein 2 (MECP2). Our objective to investigate the genetic landscape of MECP2-negative typical/atypical RTT and RTT-like phenotypes using whole exome sequencing (WES).MethodsWe performed WES on 77 MECP2-negative patients either with typical RTT (n=11), atypical RTT (n=22) or RTT-like phenotypes (n=44) incompatible with the RTT criteria.ResultsPathogenic or likely pathogenic single-nucleotide variants in 28 known genes were found in 39 of 77 (50.6%) patients. WES-based CNV analysis revealed pathogenic deletions involving six known genes (including MECP2) in 8 of 77 (10.4%) patients. Overall, diagnostic yield was 47 of 77 (61.0 %). Furthermore, strong candidate variants were found in four novel genes: a de novo variant in each of ATPase H+ transporting V0 subunit A1 (ATP6V0A1), ubiquitin-specific peptidase 8 (USP8) and microtubule-associated serine/threonine kinase 3 (MAST3), as well as biallelic variants in nuclear receptor corepressor 2 (NCOR2).ConclusionsOur study provides a new landscape including additional genetic variants contributing to RTT-like phenotypes, highlighting the importance of comprehensive genetic analysis.
Collapse
|