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Hussain SI, Muhammad N, Shah SA, Rehman AU, Khan SA, Saleha S, Khan YM, Muhammad N, Khan S, Wasif N. Variants in HCFC1 and MN1 genes causing intellectual disability in two Pakistani families. BMC Med Genomics 2024; 17:176. [PMID: 38956580 DOI: 10.1186/s12920-024-01943-2] [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: 03/25/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Intellectual disability (ID) is a neurodevelopmental condition affecting around 2% of children and young adults worldwide, characterized by deficits in intellectual functioning and adaptive behavior. Genetic factors contribute to the development of ID phenotypes, including mutations and structural changes in chromosomes. Pathogenic variants in the HCFC1 gene cause X-linked mental retardation syndrome, also known as Siderius type X-linked mental retardation. The MN1 gene is necessary for palate development, and mutations in this gene result in a genetic condition called CEBALID syndrome. METHODS Exome sequencing was used to identify the disease-causing variants in two affected families, A and B, from various regions of Pakistan. Affected individuals in these two families presented ID, developmental delay, and behavioral abnormalities. The validation and co-segregation analysis of the filtered variant was carried out using Sanger sequencing. RESULTS In an X-linked family A, a novel hemizygous missense variant (c.5705G > A; p.Ser1902Asn) in the HCFC1 gene (NM_005334.3) was identified, while in family B exome sequencing revealed a heterozygous nonsense variant (c.3680 G > A; p. Trp1227Ter) in exon-1 of the MN1 gene (NM_032581.4). Sanger sequencing confirmed the segregation of these variants with ID in each family. CONCLUSIONS The investigation of two Pakistani families revealed pathogenic genetic variants in the HCFC1 and MN1 genes, which cause ID and expand the mutational spectrum of these genes.
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Affiliation(s)
- Syeda Iqra Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Shahbaz Ali Shah
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Adil U Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
- Department of Computer Science and Bioinformatics, Khushal Khan Khatak University, Karak, Pakistan
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Yar Muhammad Khan
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan.
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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Torene RI, Guillen Sacoto MJ, Millan F, Zhang Z, McGee S, Oetjens M, Heise E, Chong K, Sidlow R, O'Grady L, Sahai I, Martin CL, Ledbetter DH, Myers SM, Mitchell KJ, Retterer K. Systematic analysis of variants escaping nonsense-mediated decay uncovers candidate Mendelian diseases. Am J Hum Genet 2024; 111:70-81. [PMID: 38091987 PMCID: PMC10806863 DOI: 10.1016/j.ajhg.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 01/07/2024] Open
Abstract
Protein-truncating variants (PTVs) near the 3' end of genes may escape nonsense-mediated decay (NMD). PTVs in the NMD-escape region (PTVescs) can cause Mendelian disease but are difficult to interpret given their varying impact on protein function. Previously, PTVesc burden was assessed in an epilepsy cohort, but no large-scale analysis has systematically evaluated these variants in rare disease. We performed a retrospective analysis of 29,031 neurodevelopmental disorder (NDD) parent-offspring trios referred for clinical exome sequencing to identify PTVesc de novo mutations (DNMs). We identified 1,376 PTVesc DNMs and 133 genes that were significantly enriched (binomial p < 0.001). The PTVesc-enriched genes included those with PTVescs previously described to cause dominant Mendelian disease (e.g., SEMA6B, PPM1D, and DAGLA). We annotated ClinVar variants for PTVescs and identified 948 genes with at least one high-confidence pathogenic variant. Twenty-two known Mendelian PTVesc-enriched genes had no prior evidence of PTVesc-associated disease. We found 22 additional PTVesc-enriched genes that are not well established to be associated with Mendelian disease, several of which showed phenotypic similarity between individuals harboring PTVesc variants in the same gene. Four individuals with PTVesc mutations in RAB1A had similar phenotypes including NDD and spasticity. PTVesc mutations in IRF2BP1 were found in two individuals who each had severe immunodeficiency manifesting in NDD. Three individuals with PTVesc mutations in LDB1 all had NDD and multiple congenital anomalies. Using a large-scale, systematic analysis of DNMs, we extend the mutation spectrum for known Mendelian disease-associated genes and identify potentially novel disease-associated genes.
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Affiliation(s)
| | | | | | | | | | - Matthew Oetjens
- Geisinger, Danville, PA, USA; Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | | | | | | | | | | | - Christa L Martin
- Geisinger, Danville, PA, USA; Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | - David H Ledbetter
- University of Florida, College of Medicine-Jacksonville, Jacksonville, FL, USA
| | - Scott M Myers
- Geisinger, Danville, PA, USA; Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | - Kevin J Mitchell
- Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Kyle Retterer
- GeneDx, Gaithersburg, MD, USA; Geisinger, Danville, PA, USA.
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Klonowski J, Liang Q, Coban-Akdemir Z, Lo C, Kostka D. aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants. Bioinformatics 2023; 39:btad556. [PMID: 37688563 PMCID: PMC10534055 DOI: 10.1093/bioinformatics/btad556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/13/2023] [Accepted: 09/07/2023] [Indexed: 09/11/2023] Open
Abstract
SUMMARY DNA changes that cause premature termination codons (PTCs) represent a large fraction of clinically relevant pathogenic genomic variation. Typically, PTCs induce transcript degradation by nonsense-mediated mRNA decay (NMD) and render such changes loss-of-function alleles. However, certain PTC-containing transcripts escape NMD and can exert dominant-negative or gain-of-function (DN/GOF) effects. Therefore, systematic identification of human PTC-causing variants and their susceptibility to NMD contributes to the investigation of the role of DN/GOF alleles in human disease. Here we present aenmd, a software for annotating PTC-containing transcript-variant pairs for predicted escape from NMD. aenmd is user-friendly and self-contained. It offers functionality not currently available in other methods and is based on established and experimentally validated rules for NMD escape; the software is designed to work at scale, and to integrate seamlessly with existing analysis workflows. We applied aenmd to variants in the gnomAD, Clinvar, and GWAS catalog databases and report the prevalence of human PTC-causing variants in these databases, and the subset of these variants that could exert DN/GOF effects via NMD escape. AVAILABILITY AND IMPLEMENTATION aenmd is implemented in the R programming language. Code is available on GitHub as an R-package (github.com/kostkalab/aenmd.git), and as a containerized command-line interface (github.com/kostkalab/aenmd_cli.git).
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Affiliation(s)
- Jonathan Klonowski
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Qianqian Liang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Zeynep Coban-Akdemir
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, United States
| | - Cecilia Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
- Department of Computational & Systems Biology and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260,United States
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Palma Milla C, Patricia PM, Lezana JM, Cruz J, Quesada JF, Vila S, Álvarez-Mora I, Arteche-López A, Gómez-Manjón I, Sánchez MT, Gómez-Rodríguez MJ, Sánchez J, Moreno-García M. A Novel Pathogenic Variant in the MN1 Gene in a Patient Presenting with Rhombencephalosynapsis and Craniofacial Anomalies, Expanding MN1 C-terminal Truncation Syndrome. J Pediatr Genet 2023; 12:254-257. [PMID: 37575653 PMCID: PMC10421676 DOI: 10.1055/s-0041-1728650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
Meningioma-1 is a transcription activator that regulates mammalian palate development and is required for appropriate osteoblast proliferation, motility, differentiation, and function. Microdeletions involving the MN1 gene have been linked to syndromes including craniofacial anomalies, such as Toriello-Carey syndrome. Recently, truncating variants in the C-terminal portion of the MN1 transcriptional factor have been linked to a characteristic and distinct phenotype presenting with craniofacial anomalies and partial rhombencephalosynapsis, a rare brain malformation characterized by midline fusion of the cerebellar hemispheres with partial or complete loss of the cerebellar vermis. It has been called MN1 C-terminal truncation (MCTT) syndrome or CEBALID (Craniofacial defects, dysmorphic Ears, Brain Abnormalities, Language delay, and Intellectual Disability) and suggested to be caused by dominantly acting truncated protein MN1 instead of haploinsufficiency. As a proto-oncogene, MN1 is also involved in familial meningioma. In this study, we present a novel case of MCTT syndrome in a female patient presenting with craniofacial anomalies and rhombencephalosynapsis, harboring a de novo pathogenic variant in the MN1 gene: c.3686_3698del, p.(Met1229Argfs*87).
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Affiliation(s)
- Carmen Palma Milla
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Pérez Mohand Patricia
- Department of Pediatric Endocrinology, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - José M. Lezana
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Jaime Cruz
- Department of Pediatric Endocrinology, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Juan F. Quesada
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Sara Vila
- Department of Pediatric Neurology, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Isabel Álvarez-Mora
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Ana Arteche-López
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Irene Gómez-Manjón
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - M. Teresa Sánchez
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | | | - Jaime Sánchez
- Department of Pediatric Endocrinology, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Marta Moreno-García
- Department of Genetics, Hospital Universitario Doce de Octubre, Madrid, Spain
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Klonowski J, Liang Q, Coban-Akdemir Z, Lo C, Kostka D. aenmd: Annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533185. [PMID: 36993377 PMCID: PMC10055276 DOI: 10.1101/2023.03.17.533185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
DNA changes that cause premature termination codons (PTCs) represent a large fraction of clinically relevant pathogenic genomic variation. Typically, PTCs induce a transcript's degradation by nonsense-mediated mRNA decay (NMD) and render such changes loss-of-function alleles. However, certain PTC-containing transcripts escape NMD and can exert dominant-negative or gain-of-function (DN/GOF) effects. Therefore, systematic identification of human PTC-causing variants and their susceptibility to NMD contributes to the investigation of the role of DN/GOF alleles in human disease. Here we present aenmd, a software for annotating PTC-containing transcript-variant pairs for predicted escape from NMD. aenmd is user-friendly and self-contained. It offers functionality not currently available in other methods and is based on established and experimentally validated rules for NMD escape; the software is designed to work at scale, and to integrate seamlessly with existing analysis workflows. We applied aenmd to variants in the gnomAD, Clinvar, and GWAS catalog databases and report the prevalence of human PTC-causing variants in these databases, and the subset of these that could exert DN/GOF effects via NMD escape. Availability and implementation: aenmd is implemented in the R programming language. Code is available on GitHub as an R package (github.com/kostkalab/aenmd.git), and as a containerized command-line interface (github.com/kostkalab/aenmd_cli.git).
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Affiliation(s)
- Jonathan Klonowski
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Qianqian Liang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zeynep Coban-Akdemir
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Cecilia Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Computational & Systems Biology and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Tran Mau-Them F, Overs A, Bruel AL, Duquet R, Thareau M, Denommé-Pichon AS, Vitobello A, Sorlin A, Safraou H, Nambot S, Delanne J, Moutton S, Racine C, Engel C, De Giraud d’Agay M, Lehalle D, Goldenberg A, Willems M, Coubes C, Genevieve D, Verloes A, Capri Y, Perrin L, Jacquemont ML, Lambert L, Lacaze E, Thevenon J, Hana N, Van-Gils J, Dubucs C, Bizaoui V, Gerard-Blanluet M, Lespinasse J, Mercier S, Guerrot AM, Maystadt I, Tisserant E, Faivre L, Philippe C, Duffourd Y, Thauvin-Robinet C. Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis. Front Genet 2023; 14:1122985. [PMID: 37152996 PMCID: PMC10157399 DOI: 10.3389/fgene.2023.1122985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: Exome sequencing has a diagnostic yield ranging from 25% to 70% in rare diseases and regularly implicates genes in novel disorders. Retrospective data reanalysis has demonstrated strong efficacy in improving diagnosis, but poses organizational difficulties for clinical laboratories. Patients and methods: We applied a reanalysis strategy based on intensive prospective bibliographic monitoring along with direct application of the GREP command-line tool (to "globally search for a regular expression and print matching lines") in a large ES database. For 18 months, we submitted the same five keywords of interest [(intellectual disability, (neuro)developmental delay, and (neuro)developmental disorder)] to PubMed on a daily basis to identify recently published novel disease-gene associations or new phenotypes in genes already implicated in human pathology. We used the Linux GREP tool and an in-house script to collect all variants of these genes from our 5,459 exome database. Results: After GREP queries and variant filtration, we identified 128 genes of interest and collected 56 candidate variants from 53 individuals. We confirmed causal diagnosis for 19/128 genes (15%) in 21 individuals and identified variants of unknown significance for 19/128 genes (15%) in 23 individuals. Altogether, GREP queries for only 128 genes over a period of 18 months permitted a causal diagnosis to be established in 21/2875 undiagnosed affected probands (0.7%). Conclusion: The GREP query strategy is efficient and less tedious than complete periodic reanalysis. It is an interesting reanalysis strategy to improve diagnosis.
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Affiliation(s)
- Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- *Correspondence: Frédéric Tran Mau-Them,
| | - Alexis Overs
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Romain Duquet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Mylene Thareau
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Arthur Sorlin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Camille Engel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | | | - Daphne Lehalle
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Marjolaine Willems
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Christine Coubes
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - David Genevieve
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Alain Verloes
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Department of Medical Genetics, AP-HPNord- Université de Paris, Hôpital Robert Debré, Paris, France
- INSERM UMR 1141, Paris, France
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Laurence Perrin
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pole Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, La Réunion, France
| | | | - Elodie Lacaze
- Unité de Génétique Médicale, Groupe Hospitalier du Havre, Le Havre, France
| | - Julien Thevenon
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nadine Hana
- Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France
- INSERM U1148, Laboratory for Vascular Translational Science, Université Paris de Paris, Hôpital Bichat, Paris, France
| | - Julien Van-Gils
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Charlotte Dubucs
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Varoona Bizaoui
- Service de Génétique, Centre Hospitalier Universitaire Caen Normandie, Caen, France
| | | | | | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Rouen, France
- Inserm U1245, FHU G4 Génomique, Rouen, France
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Emilie Tisserant
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
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Yu J, Li C, Chen J, Ran Q, Zhao Y, Cao Q, Chen X, Yu L, Li W, Zhao Z. Diagnosis and treatment of MN1 C-terminal truncation syndrome. Mol Genet Genomic Med 2022; 10:e1965. [PMID: 36124717 PMCID: PMC9651612 DOI: 10.1002/mgg3.1965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/03/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND MN1 C-terminal truncation (MCTT) is a rare syndrome; only 27 cases have been reported. We report the first case of an 8-year-old girl with MCTT syndrome complicated with moderate obstructive sleep apnea (OSA). METHODS MCTT syndrome was diagnosed by whole-exome sequencing (WES) and validated by Sanger sequencing. The patient received 2 years of treatment with continuous positive airway pressure (CPAP) to relieve sleep apnea and hypoxia, and a reverse sector fan-shaped expander for maxillary expansion. RESULTS WES revealed a de novo MN1 variant, c.3760C>T (p.[Q1254*]). An arachnoid cyst was found in the right occipital brain. The patient presented mild symptoms of classic MCTT syndrome. The patient did not experience hearing loss and only mild intellectual disability. Radiological examinations showed cleft secondary palate, narrow upper arch, narrow upper airway, and mandibular skeletal retrusion. Polysomnography indicated moderate OSA, with an apnea/hypopnea index of 6.8, which decreased to 1 after CPAP during the night. Two-year maxillary expansion widened the upper arch, and the cleft secondary palate became visible. The mandible moved forward spontaneously, resulting in the improvement of profile and upper airway widening. General physical conditions, such as motor delay, muscle weakness, and developmental delay, were significantly improved two years later. CONCLUSION In conclusion, we discovered a MN1 variant [NM_002430.2: c.3760C>T, p.Q1254*] that causes mild MCTT symptoms compared to other MN1 variants. For patients with MCTT complicated with OSA, multidisciplinary combination therapy can improve maxillofacial development, widen the upper airway and relieve sleep apnea, improving the general physical condition.
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Affiliation(s)
- Jingjia Yu
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Chen Li
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Jialin Chen
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Qiuchi Ran
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Yingya Zhao
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Qingxin Cao
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Ximeng Chen
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Linnan Yu
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
| | - Wenyang Li
- Institute of Respiratory Disease, The First Hospital of China Medical University, Shenyang, China
| | - Zhenjin Zhao
- The First Clinic, Orthodontic Department, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China
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8
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Perdomo-Sabogal A, Trakooljul N, Hadlich F, Murani E, Wimmers K, Ponsuksili S. DNA methylation landscapes from pig's limbic structures underline regulatory mechanisms relevant for brain plasticity. Sci Rep 2022; 12:16293. [PMID: 36175587 PMCID: PMC9522933 DOI: 10.1038/s41598-022-20682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Epigenetic dynamics are essential for reconciling stress-induced responses in neuro-endocrine routes between the limbic brain and adrenal gland. CpG methylation associates with the initiation and end of regulatory mechanisms underlying responses critical for survival, and learning. Using Reduced Representation Bisulfite Sequencing, we identified methylation changes of functional relevance for mediating tissue-specific responses in the hippocampus, amygdala, hypothalamus, and adrenal gland in pigs. We identified 4186 differentially methylated CpGs across all tissues, remarkably, enriched for promoters of transcription factors (TFs) of the homeo domain and zinc finger classes. We also detected 5190 differentially methylated regions (DMRs, 748 Mb), with about half unique to a single pairwise. Two structures, the hypothalamus and the hippocampus, displayed 860 unique brain-DMRs, with many linked to regulation of chromatin, nervous development, neurogenesis, and cell-to-cell communication. TF binding motifs for TFAP2A and TFAP2C are enriched amount DMRs on promoters of other TFs, suggesting their role as master regulators, especially for pathways essential in long-term brain plasticity, memory, and stress responses. Our results reveal sets of TF that, together with CpG methylation, may serve as regulatory switches to modulate limbic brain plasticity and brain-specific molecular genetics in pigs.
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Affiliation(s)
- Alvaro Perdomo-Sabogal
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Murani
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.,University Rostock, Faculty of Agricultural and Environmental Sciences, 18059, Rostock, Germany
| | - Siriluck Ponsuksili
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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9
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Yoshida A, Satomi K, Kobayashi E, Ryo E, Matsushita Y, Narita Y, Ichimura K, Kawai A, Mori T. Soft-tissue sarcoma with MN1-BEND2 fusion: A case report and comparison with astroblastoma. Genes Chromosomes Cancer 2022; 61:427-431. [PMID: 35094441 DOI: 10.1002/gcc.23028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
MN1-BEND2 is considered as a defining gene fusion of astroblastoma. Herein, we report the first case of soft-tissue sarcoma with this fusion. The tumor developed in the abdominal wall of an 87-year-old woman, and consisted of a striking storiform growth of low-grade spindle cells admixed with a dense proliferation of oval cells with a higher nuclear atypia and mitotic activity. The sarcoma was immunohistochemically positive for actin but negative for S100 protein, glial fibrillary acidic protein, and Olig2. Targeted RNA sequencing identified an in-frame MN1 (exon 1)-BEND2 (exon 11) fusion transcript, which was validated by reverse transcription polymerase chain reaction, Sanger sequencing, and MN1 break-apart fluorescence in situ hybridization. DNA methylation profiling revealed that the tumor did not match any sarcoma classes based on the DKFZ classifier. Using T-distributed stochastic neighbor embedding analysis, the sarcoma was plotted close to the provisional class "Sarcoma (malignant peripheral nerve sheath tumor-like)," despite no phenotypic resemblance. Copy number analysis using methylation data demonstrated losses at 2q, 8p, 9p, 11p, 14q, 19q, and 22q. When compared with a cerebral astroblastoma sample with MN1 (exon 1)-BEND2 (exon 9) fusion, the sarcoma showed no resemblance in histology, immunophenotype, or DNA methylation profile, although they shared copy number loss at 14q, 19q, and 22q. The present report demonstrated that MN1-BEND2 is another example of a pleiotropic fusion gene that is shared among different tumor types.
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Affiliation(s)
- Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Rare Cancer Center, National Cancer Center Hospital, Tokyo, Japan
| | - Kaishi Satomi
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Department of Pathology, Kyorin University, Tokyo, Japan
| | - Eisuke Kobayashi
- Rare Cancer Center, National Cancer Center Hospital, Tokyo, Japan.,Department of Musculoskeletal Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Eijitsu Ryo
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuko Matsushita
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Brain Disease Translational Research, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Yoshitaka Narita
- Department of Neurooncology, National Cancer Center Hospital, Tokyo, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Brain Disease Translational Research, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Akira Kawai
- Rare Cancer Center, National Cancer Center Hospital, Tokyo, Japan.,Department of Musculoskeletal Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Taisuke Mori
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
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10
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Lehman NL, Spassky N, Sak M, Webb A, Zumbar CT, Usubalieva A, Alkhateeb KJ, McElroy JP, Maclean KH, Fadda P, Liu T, Gangalapudi V, Carver J, Abdullaev Z, Timmers C, Parker JR, Pierson CR, Mobley BC, Gokden M, Hattab EM, Parrett T, Cooke RX, Lehman TD, Costinean S, Parwani A, Williams BJ, Jensen RL, Aldape K, Mistry AM. Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes. Nat Commun 2022; 13:2083. [PMID: 35440587 PMCID: PMC9018799 DOI: 10.1038/s41467-022-29302-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Astroblastomas (ABs) are rare brain tumors of unknown origin. We performed an integrative genetic and epigenetic analysis of AB-like tumors. Here, we show that tumors traceable to neural stem/progenitor cells (radial glia) that emerge during early to later brain development occur in children and young adults, respectively. Tumors with MN1-BEND2 fusion appear to present exclusively in females and exhibit overexpression of genes expressed prior to 25 post-conception weeks (pcw), including genes enriched in early ventricular zone radial glia and ependymal tumors. Other, histologically classic ABs overexpress or harbor mutations of mitogen-activated protein kinase pathway genes, outer and truncated radial glia genes, and genes expressed after 25 pcw, including neuronal and astrocyte markers. Findings support that AB-like tumors arise in the context of epigenetic and genetic changes in neural progenitors. Selective gene fusion, variable imprinting and/or chromosome X-inactivation escape resulting in biallelic overexpression may contribute to female predominance of AB molecular subtypes.
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Affiliation(s)
- Norman L Lehman
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA.
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA.
- The Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA.
| | - Nathalie Spassky
- Institut de Biologie de l'ENS (IBENS), Inserm, CNRS, École Normale Supérieure, PSL Research University, Paris, France
| | - Müge Sak
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Cory T Zumbar
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Aisulu Usubalieva
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Khaled J Alkhateeb
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Joseph P McElroy
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | | | - Paolo Fadda
- Department of Cancer Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Tom Liu
- Solid Tumor Translational Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Vineela Gangalapudi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jamie Carver
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Cynthia Timmers
- Solid Tumor Translational Science, The Ohio State University, Columbus, OH, 43210, USA
| | - John R Parker
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Christopher R Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
- Department of Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Bret C Mobley
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Murat Gokden
- Department of Pathology and Laboratory Services, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Eyas M Hattab
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Timothy Parrett
- Department of Pathology and Anatomic Sciences, University of Missouri, Columbia, MO, 65212, USA
| | - Ralph X Cooke
- Department of Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Trang D Lehman
- Department of Family and Community Medicine, Contra Costa County Health System, Martinez, CA, 94553, USA
| | - Stefan Costinean
- Department of Pathology, Banner Gateway Medical Center, MD Anderson Cancer Center, Tempe, AZ, 85284, USA
| | - Anil Parwani
- Department of Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Brian J Williams
- Department of Neurosurgery, University of Louisville, Louisville, KY, 40202, USA
| | - Randy L Jensen
- Department of Neurosurgery, University of Utah, Salt Lake City, UT, 84132, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Akshitkumar M Mistry
- Department of Neurological Surgery, Vanderbilt University, Nashville, TN, 37232, USA
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11
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Smogavec M, Gerykova Bujalkova M, Lehner R, Neesen J, Behunova J, Yerlikaya-Schatten G, Reischer T, Altmann R, Weis D, Duba HC, Laccone F. Singleton exome sequencing of 90 fetuses with ultrasound anomalies revealing novel disease-causing variants and genotype-phenotype correlations. Eur J Hum Genet 2022; 30:428-438. [PMID: 34974531 PMCID: PMC8991249 DOI: 10.1038/s41431-021-01012-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/25/2021] [Accepted: 11/15/2021] [Indexed: 11/08/2022] Open
Abstract
Exome sequencing has been increasingly implemented in prenatal genetic testing for fetuses with morphological abnormalities but normal rapid aneuploidy detection and microarray analysis. We present a retrospective study of 90 fetuses with different abnormal ultrasound findings, in which we employed the singleton exome sequencing (sES; 75 fetuses) or to a lesser extent (15 fetuses) a multigene panel analysis of 6713 genes as a primary tool for the detection of monogenic diseases. The detection rate of pathogenic or likely pathogenic variants in this study was 34.4%. The highest diagnostic rate of 56% was in fetuses with multiple anomalies, followed by cases with skeletal or renal abnormalities (diagnostic rate of 50%, respectively). We report 20 novel disease-causing variants in different known disease-associated genes and new genotype-phenotype associations for the genes KMT2D, MN1, CDK10, and EXOC3L2. Based on our data, we postulate that sES of fetal index cases with a concurrent sampling of parental probes for targeted testing of the origin of detected fetal variants could be a suitable tool to obtain reliable and rapid prenatal results, particularly in situations where a trio analysis is not possible.
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Affiliation(s)
- Mateja Smogavec
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria.
| | | | - Reinhard Lehner
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Jürgen Neesen
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Jana Behunova
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Gülen Yerlikaya-Schatten
- Division of Obstetrics and Feto-Maternal Medicine, Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Theresa Reischer
- Division of Obstetrics and Feto-Maternal Medicine, Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Reinhard Altmann
- Department of Prenatal Medicine, Kepler University Hospital, School of Medicine, Johannes Kepler University, Linz, Austria
| | - Denisa Weis
- Department of Medical Genetics, Kepler University Hospital, School of Medicine, Johannes Kepler University, Linz, Austria
| | - Hans-Christoph Duba
- Department of Medical Genetics, Kepler University Hospital, School of Medicine, Johannes Kepler University, Linz, Austria
| | - Franco Laccone
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
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12
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Identification of novel SSX1 fusions in synovial sarcoma. Mod Pathol 2022; 35:228-239. [PMID: 34504309 DOI: 10.1038/s41379-021-00910-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 12/28/2022]
Abstract
Synovial sarcoma is characterized by variable epithelial differentiation and specific SS18-SSX gene fusions. The diagnosis is primarily based on phenotype, but fusion gene detection is increasingly being considered indispensable, with SS18 break-apart fluorescence in situ hybridization (FISH) being favored in many laboratories. However, SS18 FISH assay produces negative or atypical results in a minority of cases, leaving uncertainties in diagnosis and management. Here, we analyzed this challenging subset of SS18 FISH-negative/atypical synovial sarcoma using RNA sequencing and monoclonal antibodies that recognize SS18-SSX and the SSX C-terminus. Among 99 synovial sarcoma cases that were previously subjected to SS18 break-apart FISH, eight cases were reported as negative and three cases were indeterminate, owing to atypical signal patterns. Three of these 11 tumors (two monophasic and one biphasic) harbored novel EWSR1-SSX1 fusions, were negative for SS18-SSX staining, and were positive for SSX C-terminus staining. One monophasic tumor harbored a novel MN1-SSX1 fusion, and showed negative SS18-SSX expression and positive SSX C-terminus staining. Another monophasic tumor carried an SS18L1-SSX1 fusion, and was weakly positive for SS18-SSX, while SMARCB1 expression was reduced. The presence of these novel and/or rare fusions was confirmed using RT-PCR and Sanger sequencing. EWSR1-SSX1 was further validated by EWSR1 FISH assay. The remaining six tumors (five monophasic and one biphasic) showed strong SS18-SSX expression, and RNA sequencing successfully performed in three cases identified canonical SS18-SSX2 fusions. Based on a DNA methylation-based unsupervised clustering, the tumors with EWSR1-SSX1 and SS18L1-SSX1 clustered with synovial sarcoma, while the MN1-SSX1-positive tumor was not co-clustered despite classic histology and immunoprofile. In summary, we discovered novel and rare SSX1 fusions to non-SS18 genes in synovial sarcoma. The expanded genetic landscape carries significant diagnostic implications and advances our understanding of the oncogenic mechanism.
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13
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Tian Q, Shu L, Zhang P, Zeng T, Cao Y, Xi H, Peng Y, Wang Y, Mao X, Wang H. MN1 Neurodevelopmental Disease-Atypical Phenotype Due to a Novel Frameshift Variant in the MN1 Gene. Front Mol Neurosci 2022; 14:789778. [PMID: 34975401 PMCID: PMC8716923 DOI: 10.3389/fnmol.2021.789778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background:MN1 C-terminal truncation (MCTT) syndrome is caused by variants in the C-terminal region of MN1, which were first described in 2020. The clinical features of MCTT syndrome includes severe neurodevelopmental and brain abnormalities. We reported on a patient who carried the MN1 variant in the C-terminal region with mild developmental delay and normal brain magnetic resonance image (MRI). Methods: Detailed clinical information was collected in the pedigree. Whole-exome sequencing (WES) accompanied with Sanger sequencing validation were performed. A functional study based on HEK239T cells was performed. Results: A de novo heterozygous c.3734delT: p.L1245fs variant was detected. HEK239T cells transinfected with the de novo variant showed decreased proliferation, enhanced apoptotic rate, and MN1 nuclear aggregation. Conclusion: Our study expended the clinical and genetic spectrum of MCTT which contributes to the genetic counseling of the MN1 gene.
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Affiliation(s)
- Qi Tian
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.,Department of Obstetrics and Gynecology, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Li Shu
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Pu Zhang
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Ting Zeng
- The Ministry of Education and Science, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Yang Cao
- Department of Radiology, Chenzhou First People's Hospital, Chenzhou, China
| | - Hui Xi
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Ying Peng
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Yaqin Wang
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Mao
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Hua Wang
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
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14
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Alhalabi KT, Stichel D, Sievers P, Peterziel H, Sommerkamp AC, Sturm D, Wittmann A, Sill M, Jäger N, Beck P, Pajtler KW, Snuderl M, Jour G, Delorenzo M, Martin AM, Levy A, Dalvi N, Hansford JR, Gottardo NG, Uro-Coste E, Maurage CA, Godfraind C, Vandenbos F, Pietsch T, Kramm C, Filippidou M, Kattamis A, Jones C, Øra I, Mikkelsen TS, Zapotocky M, Sumerauer D, Scheie D, McCabe M, Wesseling P, Tops BBJ, Kranendonk MEG, Karajannis MA, Bouvier N, Papaemmanuil E, Dohmen H, Acker T, von Hoff K, Schmid S, Miele E, Filipski K, Kitanovski L, Krskova L, Gojo J, Haberler C, Alvaro F, Ecker J, Selt F, Milde T, Witt O, Oehme I, Kool M, von Deimling A, Korshunov A, Pfister SM, Sahm F, Jones DTW. PATZ1 fusions define a novel molecularly distinct neuroepithelial tumor entity with a broad histological spectrum. Acta Neuropathol 2021; 142:841-857. [PMID: 34417833 PMCID: PMC8500868 DOI: 10.1007/s00401-021-02354-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022]
Abstract
Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens.
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Affiliation(s)
- Karam T Alhalabi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heike Peterziel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Alexander C Sommerkamp
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrea Wittmann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Martin Sill
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pengbo Beck
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matija Snuderl
- Division of Neuropathology, NYU Langone Health, New York, NY, USA
| | - George Jour
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | | | - Allison M Martin
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Adam Levy
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Nagma Dalvi
- Isabel Rapin Division of Child Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jordan R Hansford
- Department of Pediatrics, Children's Cancer Centre, Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas G Gottardo
- Department of Oncology and Haematology, Perth Children's Hospital, Perth, WA, Australia
| | - Emmanuelle Uro-Coste
- Department of Pathology, IUCT-Oncopole, Toulouse University Hospital, Toulouse, France
- INSERM U1037, Team 11, Cancer Research Center of Toulouse (CRCT), Toulouse, France
| | - Claude-Alain Maurage
- Department of Pathology, Lille University Hospital, Lille, France
- INSERM U837 UMR-S1172, Centre de Recherche Jean Pierre Aubert, Team 1, Lille, France
| | - Catherine Godfraind
- Laboratory of Pathology, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
- University Clermont-Auvergne, M2iSH UMR1071, Clermont-Ferrand, France
| | - Fanny Vandenbos
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Department of Pathology, CHU Gabriel Montpied, Clermont-Ferrand, France
| | - Torsten Pietsch
- Institute of Neuropathology, Brain Tumor Reference Center of the Society for Neuropathology and Neuroanatomy, University of Bonn Medical Center, Bonn, Germany
| | - Christof Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Gottingen, Germany
| | - Maria Filippidou
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonis Kattamis
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Ingrid Øra
- Children's Hospital, Paediatric Oncology, Skåne University Hospital, Lund, Sweden
| | - Torben Stamm Mikkelsen
- Paediatric and Adolescent Medicine, Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michal Zapotocky
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - David Sumerauer
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - David Scheie
- Department of Clinical Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Martin McCabe
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Pieter Wesseling
- Department of Pathology, Brain Tumor Center Amsterdam University Medical Center, Amsterdam Universities Medical Centers/VUmc, Amsterdam, The Netherlands
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bastiaan B J Tops
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mariëtte E G Kranendonk
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Nancy Bouvier
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hildegard Dohmen
- Department of Neuropathology, University Giessen, Giessen, Germany
| | - Till Acker
- Department of Neuropathology, University Giessen, Giessen, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Simone Schmid
- Department of Pediatric Oncology and Hematology, Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Evelina Miele
- Department of Oncology, Hematology, Cell Therapy, Gene Therapy and Haemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Katharina Filipski
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Lidija Kitanovski
- Division of Paediatrics, Department of Haematooncology, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Johannes Gojo
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Frank Alvaro
- University of Newcastle, Newcastle, NSW, Australia
- John Hunter Children's Hospital Newcastle, Newcastle, NSW, Australia
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Andreas von Deimling
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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15
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Zhao A, Shu D, Zhang D, Yang B, Hong L, Wang A, Yao R, Wang J, Lv H, Wang J, Shen Y, Wang H, Gu Q. Novel truncating variant of MN1 penultimate exon identified in a Chinese patient with newly recognized MN1 C-terminal truncation syndrome: Case report and literature review. Int J Dev Neurosci 2021; 82:96-103. [PMID: 34708882 DOI: 10.1002/jdn.10154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/01/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
MN1 C-terminal truncation (MCTT) syndrome is a newly recognized neurodevelopmental disorder due to heterozygous gain-of-function C-terminal truncating mutations clustering in the last or penultimate exon of MN1 gene (MIM: 156100). Up to date, only 25 affected patients have been reported. Here, we report a 2-year-old Chinese girl with MCTT syndrome. The girl presented with the characteristic features of the syndrome, including global developmental delay (GDD), facial dysmorphism and hearing impairment. Notably, the patient did not have other frequently observed symptoms such as hypotonia, cranial or brain abnormalities, indicating variability of the phenotype of patients with MN1 C-terminal truncating mutations. Trio whole-exome sequencing revealed a novel de novo heterozygous nonsense variant in the extreme 3' region of penultimate exon of MN1 (NM_002430.3: c.3743G > A, p.Trp1248*). This rare truncating variant was classified as pathogenic due to its predicted gain-of-function effect, given that the gain-of-function MN1 truncating variants producing C-terminally truncated proteins have been confirmed to cause the recognizable syndrome. Additionally, a systematic review of previously reported MN1 variants including C-terminal truncating variants and N-terminal truncating variants shows that different location of MN1 truncating variants causes two distinct clinical subtypes. To our knowledge, this is the first reported case of MCTT syndrome caused by a novel MN1 C-terminal truncating variant in a Chinese population, which enriched the mutation spectrum of MN1 gene and further supporting the association of the novel MCTT syndrome with MN1 C-terminal truncating variants.
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Affiliation(s)
- Arman Zhao
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, China
| | - Dandan Shu
- Department of Rehabilitation Medicine, Children's Hospital of Soochow University, Suzhou, China
| | - Daxue Zhang
- Department of Rehabilitation Medicine, Children's Hospital of Soochow University, Suzhou, China
| | - Bin Yang
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, China
| | - Liyi Hong
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, China
| | - Andi Wang
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, China
| | - Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haitao Lv
- Department of Cardiology, Children's Hospital of Soochow University, Suzhou, China
| | - Jian Wang
- Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, China
| | - Yiping Shen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Hongying Wang
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, China.,Department of Clinical Laboratory, Children's Hospital of Wujiang District, Suzhou, Suzhou, China
| | - Qin Gu
- Department of Rehabilitation Medicine, Children's Hospital of Soochow University, Suzhou, China
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16
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Sakamoto M, Sasaki K, Sugie A, Nitta Y, Kimura T, Gürsoy S, Cinleti T, Iai M, Sengoku T, Ogata K, Suzuki A, Okamoto N, Iwama K, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Hamanaka K, Miyatake S, Mizuguchi T, Taguri M, Ito S, Takahashi H, Miyake N, Matsumoto N. De novo ARF3 variants cause neurodevelopmental disorder with brain abnormality. Hum Mol Genet 2021; 31:69-81. [PMID: 34346499 DOI: 10.1093/hmg/ddab224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
An optimal Golgi transport system is important for mammalian cells. The adenosine diphosphate (ADP) ribosylation factors (ARF) are key proteins for regulating cargo sorting at the Golgi network. In this family, ARF3 mainly works at the trans-Golgi network (TGN), and no ARF3-related phenotypes have yet been described in humans. We here report the clinical and genetic evaluations of two unrelated children with de novo pathogenic variants in the ARF3 gene: c.200A > T (p.Asp67Val) and c.296G > T (p.Arg99Leu). Although the affected individuals presented commonly with developmental delay, epilepsy, and brain abnormalities, there were differences in severity, clinical course, and brain lesions. In vitro subcellular localization assays revealed that the p.Arg99Leu mutant localized to Golgi apparatus, similar to the wild-type, whereas the p.Asp67Val mutant tended to show a disperse cytosolic pattern together with abnormally dispersed Golgi localization, similar to that observed in a known dominant negative variant (p.Thr31Asn). Pull-down assays revealed that the p.Asp67Val had a loss-of-function effect and the p.Arg99Leu variant had increased binding of the adaptor protein, Golgi-localized, γ-adaptin ear-containing, ARF-binding protein 1 (GGA1), supporting the gain of function. Furthermore, in vivo studies revealed that p.Asp67Val transfection led to lethality in flies. In contrast, flies expressing p.Arg99Leu had abnormal rough eye, as observed in the gain-of-function variant p.Gln71Leu. These data indicate that two ARF3 variants, the possibly loss-of-function p.Asp67Val and the gain-of-function p.Arg99Leu, both impair the Golgi transport system. Therefore, it may not be unreasonable that they showed different clinical features like diffuse brain atrophy (p.Asp67Val) and cerebellar hypoplasia (p.Arg99Leu).
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazunori Sasaki
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Yohei Nitta
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Tetsuaki Kimura
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Semra Gürsoy
- Department of Pediatric Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, 35210, Turkey
| | - Tayfun Cinleti
- Department of Pediatric Genetics, Dokuz Eylul University, Faculty of Medicine, Izumir, 35340, Turkey
| | - Mizue Iai
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, 232-8555, Japan
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Suzuki
- Molecular Cellular Biology Laboratory, Yokohama City University Graduate School of Medical Life Science, Yokohama, 230-0045, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, 594-1101, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University School of Data Science, Yokohama, 236-0027, Japan
| | - Shuuichi Ito
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
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17
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Pintus SS, Akberdin IR, Yevshin I, Makhnovskii P, Tyapkina O, Nigmetzyanov I, Nurullin L, Devyatiyarov R, Shagimardanova E, Popov D, Kolpakov FA, Gusev O, Gazizova GR. Genome-Wide Atlas of Promoter Expression Reveals Contribution of Transcribed Regulatory Elements to Genetic Control of Disuse-Mediated Atrophy of Skeletal Muscle. BIOLOGY 2021; 10:biology10060557. [PMID: 34203013 PMCID: PMC8235325 DOI: 10.3390/biology10060557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/05/2022]
Abstract
Simple Summary The genetic process underlying the control of skeletal muscle homeostasis is a key factor in methods that develop technologies to prevent age and immobility-driven atrophy. In the current paper, using advanced methods for the whole-genome profiling of transcription starting sites in fast and slow muscle in rats, we developed an integrative database of transcribed regulatory elements. Employing methods of comparative transcriptomics, we demonstrate that cis-regulatory elements are actively involved in the control of atrophy and recovery, and that the differential use of promoters and enhancers is the one of the key mechanisms that distinguishes between specific processes in slow and fast skeletal muscles. Abstract The prevention of muscle atrophy carries with it clinical significance for the control of increased morbidity and mortality following physical inactivity. While major transcriptional events associated with muscle atrophy-recovery processes are the subject of active research on the gene level, the contribution of non-coding regulatory elements and alternative promoter usage is a major source for both the production of alternative protein products and new insights into the activity of transcription factors. We used the cap-analysis of gene expression (CAGE) to create a genome-wide atlas of promoter-level transcription in fast (m. EDL) and slow (m. soleus) muscles in rats that were subjected to hindlimb unloading and subsequent recovery. We found that the genetic regulation of the atrophy-recovery cycle in two types of muscle is mediated by different pathways, including a unique set of non-coding transcribed regulatory elements. We showed that the activation of “shadow” enhancers is tightly linked to specific stages of atrophy and recovery dynamics, with the largest number of specific regulatory elements being transcriptionally active in the muscles on the first day of recovery after a week of disuse. The developed comprehensive database of transcription of regulatory elements will further stimulate research on the gene regulation of muscle homeostasis in mammals.
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Affiliation(s)
- Sergey S. Pintus
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
| | - Ilya R. Akberdin
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ivan Yevshin
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
| | - Pavel Makhnovskii
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow 123007, Russia; (P.M.); (D.P.)
| | - Oksana Tyapkina
- Kazan Institute of Biochemistry and Biophysics FRC Kazan Scientific Center of RAS, 420007 Kazan, Russia; (O.T.); (L.N.)
- Department of Biology, Kazan State Medical University, 420012 Kazan, Russia
| | - Islam Nigmetzyanov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
| | - Leniz Nurullin
- Kazan Institute of Biochemistry and Biophysics FRC Kazan Scientific Center of RAS, 420007 Kazan, Russia; (O.T.); (L.N.)
- Department of Biology, Kazan State Medical University, 420012 Kazan, Russia
| | - Ruslan Devyatiyarov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
| | - Elena Shagimardanova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
| | - Daniil Popov
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow 123007, Russia; (P.M.); (D.P.)
| | - Fedor A. Kolpakov
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
- Correspondence: or (F.A.K.); (O.G.); (G.R.G.)
| | - Oleg Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
- RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- Department of Functional Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Correspondence: or (F.A.K.); (O.G.); (G.R.G.)
| | - Guzel R. Gazizova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
- Correspondence: or (F.A.K.); (O.G.); (G.R.G.)
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18
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Shu L, He D, Wu D, Peng Y, Xi H, Mao X, Wang H. MN1 gene loss-of-function mutation causes cleft palate in a pedigree. Brain 2021; 144:e18. [PMID: 33351070 PMCID: PMC7940500 DOI: 10.1093/brain/awaa431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Li Shu
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
- Department of School of Life Sciences, Central South University, Changsha, China
| | - Dinghua He
- Department of Otorhinolaryngology, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Dan Wu
- Department of Otorhinolaryngology, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Ying Peng
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Hui Xi
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Xiao Mao
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
- Correspondence may also be addressed to: Xiao Mao E-mail:
| | - Hua Wang
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
- Correspondence to: Hua Wang Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China E-mail:
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19
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Vegas N, Low K, Mak CCY, Fung JLF, Hing AV, Chung BHY, Doherty D, Amiel J, Gordon CT. Reply: MN1 gene loss-of-function mutation causes cleft palate in a pedigree. Brain 2021; 144:e19. [PMID: 33351141 DOI: 10.1093/brain/awaa432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nancy Vegas
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Université de Paris, 75015 Paris, France
| | - Karen Low
- Department of Clinical Genetics, St Michaels Hospital, University Hospitals Bristol and Weston NHS Trust, Bristol BS2 8EJ, UK
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jasmine L F Fung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Anne V Hing
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.,Seattle Craniofacial Center, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Université de Paris, 75015 Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), 75015 Paris, France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Université de Paris, 75015 Paris, France
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20
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Saida K, Fukuda T, Scott DA, Sengoku T, Ogata K, Nicosia A, Hernandez-Garcia A, Lalani SR, Azamian MS, Streff H, Liu P, Dai H, Mizuguchi T, Miyatake S, Asahina M, Ogata T, Miyake N, Matsumoto N. OTUD5 Variants Associated With X-Linked Intellectual Disability and Congenital Malformation. Front Cell Dev Biol 2021; 9:631428. [PMID: 33748114 PMCID: PMC7965969 DOI: 10.3389/fcell.2021.631428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND X-linked intellectual disability (XLID), which occurs predominantly in males, is a relatively common and genetically heterogeneous disorder in which over 100 mutated genes have been reported. The OTUD5 gene at Xp11.23 encodes ovarian tumor deubiquitinase 5 protein, which is a deubiquitinating enzyme member of the ovarian tumor family. LINKage-specific-deubiquitylation-deficiency-induced embryonic defects (LINKED) syndrome, arising from pathogenic OTUD5 variants, was recently reported as a new XLID with additional congenital anomalies. METHODS We investigated three affected males (49- and 47-year-old brothers [Individuals 1 and 2] and a 2-year-old boy [Individual 3]) from two families who showed developmental delay. Their common clinical features included developmental delay, hypotonia, short stature, and distinctive facial features, such as telecanthus and a depressed nasal bridge. Individuals 1 and 2 showed epilepsy and brain magnetic resonance imaging showed a thin corpus callosum and mild ventriculomegaly. Individual 3 showed congenital malformations, including tetralogy of Fallot, hypospadias, and bilateral cryptorchidism. To identify the genetic cause of these features, we performed whole-exome sequencing. RESULTS A hemizygous OTUD5 missense variant, c.878A>T, p.Asn293Ile [NM_017602.4], was identified in one family with Individuals 1 and 2, and another missense variant, c.1210 C>T, p.Arg404Trp, in the other family with Individual 3, respectively. The former variant has not been registered in public databases and was predicted to be pathogenic by multiple in silico prediction tools. The latter variant p.Arg404Trp was previously reported as a pathogenic OTUD5 variant, and Individual 3 showed a typical LINKED syndrome phenotype. However, Individuals 1 and 2, with the novel variant (p.Asn293Ile), showed no cardiac or genitourinary malformations. CONCLUSIONS Unlike previous reports of LINKED syndrome, which described early lethality with congenital cardiac anomalies, our three cases are still alive. Notably, the adult brothers with the novel missense OTUD5 variant have lived into their forties. This may be indicative of a milder phenotype as a possible genotype-phenotype correlation. These findings imply a possible long-term prognosis for individuals with this new XLID syndrome, and a wider phenotypic variation than initially thought.
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Affiliation(s)
- Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tokiko Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Texas Children’s Hospital, Houston, TX, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Annarita Nicosia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Texas Children’s Hospital, Houston, TX, United States
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Texas Children’s Hospital, Houston, TX, United States
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Baylor Genetics, Houston, TX, United States
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Baylor Genetics, Houston, TX, United States
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Miki Asahina
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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21
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Weng PL, Majmundar AJ, Khan K, Lim TY, Shril S, Jin G, Musgrove J, Wang M, Ahram DF, Aggarwal VS, Bier LE, Heinzen EL, Onuchic-Whitford AC, Mann N, Buerger F, Schneider R, Deutsch K, Kitzler TM, Klämbt V, Kolb A, Mao Y, Moufawad El Achkar C, Mitrotti A, Martino J, Beck BB, Altmüller J, Benz MR, Yano S, Mikati MA, Gunduz T, Cope H, Shashi V, Trachtman H, Bodria M, Caridi G, Pisani I, Fiaccadori E, AbuMaziad AS, Martinez-Agosto JA, Yadin O, Zuckerman J, Kim A, John-Kroegel U, Tyndall AV, Parboosingh JS, Innes AM, Bierzynska A, Koziell AB, Muorah M, Saleem MA, Hoefele J, Riedhammer KM, Gharavi AG, Jobanputra V, Pierce-Hoffman E, Seaby EG, O'Donnell-Luria A, Rehm HL, Mane S, D'Agati VD, Pollak MR, Ghiggeri GM, Lifton RP, Goldstein DB, Davis EE, Hildebrandt F, Sanna-Cherchi S. De novo TRIM8 variants impair its protein localization to nuclear bodies and cause developmental delay, epilepsy, and focal segmental glomerulosclerosis. Am J Hum Genet 2021; 108:357-367. [PMID: 33508234 PMCID: PMC7895901 DOI: 10.1016/j.ajhg.2021.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
Focal segmental glomerulosclerosis (FSGS) is the main pathology underlying steroid-resistant nephrotic syndrome (SRNS) and a leading cause of chronic kidney disease. Monogenic forms of pediatric SRNS are predominantly caused by recessive mutations, while the contribution of de novo variants (DNVs) to this trait is poorly understood. Using exome sequencing (ES) in a proband with FSGS/SRNS, developmental delay, and epilepsy, we discovered a nonsense DNV in TRIM8, which encodes the E3 ubiquitin ligase tripartite motif containing 8. To establish whether TRIM8 variants represent a cause of FSGS, we aggregated exome/genome-sequencing data for 2,501 pediatric FSGS/SRNS-affected individuals and 48,556 control subjects, detecting eight heterozygous TRIM8 truncating variants in affected subjects but none in control subjects (p = 3.28 × 10-11). In all six cases with available parental DNA, we demonstrated de novo inheritance (p = 2.21 × 10-15). Reverse phenotyping revealed neurodevelopmental disease in all eight families. We next analyzed ES from 9,067 individuals with epilepsy, yielding three additional families with truncating TRIM8 variants. Clinical review revealed FSGS in all. All TRIM8 variants cause protein truncation clustering within the last exon between residues 390 and 487 of the 551 amino acid protein, indicating a correlation between this syndrome and loss of the TRIM8 C-terminal region. Wild-type TRIM8 overexpressed in immortalized human podocytes and neuronal cells localized to nuclear bodies, while constructs harboring patient-specific variants mislocalized diffusely to the nucleoplasm. Co-localization studies demonstrated that Gemini and Cajal bodies frequently abut a TRIM8 nuclear body. Truncating TRIM8 DNVs cause a neuro-renal syndrome via aberrant TRIM8 localization, implicating nuclear bodies in FSGS and developmental brain disease.
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Affiliation(s)
- Patricia L Weng
- Division of Pediatric Nephrology, UCLA, Los Angeles, CA 90095, USA
| | - Amar J Majmundar
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kamal Khan
- Center for Disease Modeling, Duke University, Durham, NC 27701, USA; Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Tze Y Lim
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Gina Jin
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - John Musgrove
- Center for Disease Modeling, Duke University, Durham, NC 27701, USA; Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27705, USA
| | - Minxian Wang
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dina F Ahram
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Vimla S Aggarwal
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Louise E Bier
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Erin L Heinzen
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Ana C Onuchic-Whitford
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Florian Buerger
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ronen Schneider
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Konstantin Deutsch
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Thomas M Kitzler
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Verena Klämbt
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Amy Kolb
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Youying Mao
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christelle Moufawad El Achkar
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Adele Mitrotti
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Jeremiah Martino
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Bodo B Beck
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | | | - Shoji Yano
- Genetics Division, Department of Pediatrics, LAC+USC Medical Center, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology and Developmental Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Talha Gunduz
- Division of Pediatric Neurology and Developmental Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics. Duke University Medical Center, Durham, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics. Duke University Medical Center, Durham, NC 27710, USA
| | - Howard Trachtman
- Department of Pediatrics, Division of Nephrology, New York University Langone Health, New York, NY 10016, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova GE, Italy
| | - Gianluca Caridi
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova GE, Italy
| | - Isabella Pisani
- U.O. Nefrologia, Azienda Ospedaliero-Universitaria di Parma and Dipartimento di Medicina e Chirurgia, Università di Parma, 43126 Parma PR, Italy
| | - Enrico Fiaccadori
- U.O. Nefrologia, Azienda Ospedaliero-Universitaria di Parma and Dipartimento di Medicina e Chirurgia, Università di Parma, 43126 Parma PR, Italy
| | - Asmaa S AbuMaziad
- Division of Pediatric Nephrology, University of Arizona-Tucson, AZ 85724, USA
| | - Julian A Martinez-Agosto
- Department of Pediatrics, Division of Medical Genetics, UCLA, Los Angeles, CA 90095, USA; Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA; Department of Psychiatry, UCLA, Los Angeles, CA 90095, USA
| | - Ora Yadin
- Division of Pediatric Nephrology, UCLA, Los Angeles, CA 90095, USA
| | - Jonathan Zuckerman
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Arang Kim
- Department of Pediatrics, Division of Medical Genetics, UCLA, Los Angeles, CA 90095, USA
| | | | - Amanda V Tyndall
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Jillian S Parboosingh
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Agnieszka Bierzynska
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol BS2 8BJ, UK
| | - Ania B Koziell
- Department of Paediatric Nephrology, Evelina London, London SE1 7EH, UK; Faculty of Life Sciences, King's College London SE1 9RT, UK
| | - Mordi Muorah
- Renal Unit, Birmingham Children's Hospital, Birmingham, B4 6NH, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol BS2 8BJ, UK
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; New York Genome Center, New York, NY 10013, USA
| | - Emma Pierce-Hoffman
- Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Eleanor G Seaby
- Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anne O'Donnell-Luria
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Heidi L Rehm
- Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Vivette D D'Agati
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Martin R Pollak
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova GE, Italy
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, CT 06520, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Erica E Davis
- Center for Disease Modeling, Duke University, Durham, NC 27701, USA; Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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22
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MN1 Linked to Syndrome Characterized by Craniofacial Abnormalities and Severe Developmental Delay. Am J Med Genet A 2021; 182:615-616. [PMID: 32153127 DOI: 10.1002/ajmg.a.61229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Tsang B, Pritišanac I, Scherer SW, Moses AM, Forman-Kay JD. Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations. Cell 2020; 183:1742-1756. [DOI: 10.1016/j.cell.2020.11.050] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 02/08/2023]
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24
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Powers AK, Boggs TE, Gross JB. An Asymmetric Genetic Signal Associated with Mechanosensory Expansion in Cave-Adapted Fish. Symmetry (Basel) 2020; 12:1951. [PMID: 33614165 PMCID: PMC7894647 DOI: 10.3390/sym12121951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A key challenge in contemporary biology is connecting genotypic variation to phenotypic diversity. Quantitative genetics provides a powerful technique for identifying regions of the genome that covary with phenotypic variation. Here, we present a quantitative trait loci (QTL) analysis of a natural freshwater fish system, Astyanax mexicanus, that harbors two morphs corresponding to a cave and surface fish. Following their divergence ~500 Kya, cavefish have adapted to the extreme pressures of the subterranean biome. As a consequence, cavefish have lost numerous features, but evolved gains for a variety of constructive features including behavior. Prior work found that sensory tissues (neuromasts) present in the "eye orbit" region of the skull associate with sensitivity to vibrations in water. This augmented sensation is believed to facilitate foraging behavior in the complete darkness of a cave, and may impact on evolved lateral swimming preference. To this point, however, it has remained unclear how morphological variation integrates with behavioral variation through heritable factors. Using a QTL approach, we discovered the genetic architecture of neuromasts present in the eye orbit region, demonstrating that this feature is under genetic control. Interestingly, linked loci were asymmetric-signals were detected using only data collected from the right, but not left, side of the face. This finding may explain enhanced sensitivity and/or feedback of water movements mediating a lateral swimming preference. The locus we discovered based on neuromast position maps near established QTL for eye size and a facial bone morphology, raising the intriguing possibility that eye loss, sensory expansion, and the cranial skeleton may be integrated for evolving adaptive behaviors. Thus, this work will further our understanding of the functional consequence of key loci that influence the evolutionary origin of changes impacting morphology, behavior, and adaptation.
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Affiliation(s)
- Amanda K. Powers
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02138, USA
| | - Tyler E. Boggs
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45227, USA
| | - Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45227, USA
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25
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Sakamoto M, Iwama K, Sekiguchi F, Mashimo H, Kumada S, Ishigaki K, Okamoto N, Behnam M, Ghadami M, Koshimizu E, Miyatake S, Mitsuhashi S, Mizuguchi T, Takata A, Saitsu H, Miyake N, Matsumoto N. Novel EXOSC9 variants cause pontocerebellar hypoplasia type 1D with spinal motor neuronopathy and cerebellar atrophy. J Hum Genet 2020; 66:401-407. [PMID: 33040083 DOI: 10.1038/s10038-020-00853-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022]
Abstract
Pontocerebellar hypoplasia (PCH) is currently classified into 13 subgroups and many gene variants associated with PCH have been identified by next generation sequencing. PCH type 1 is a rare heterogeneous neurodegenerative disorder. The clinical presentation includes early-onset severe developmental delay, progressive motor neuronopathy, and cerebellar and pontine atrophy. Recently two variants in the EXOSC9 gene (MIM: 606180), NM_001034194.1: c.41T>C (p.Leu14Pro) and c.481C>T (p.Arg161*) were identified in four unrelated patients with PCH type 1D (PCH1D) (MIM: 618065). EXOSC9 encodes a component of the exosome complex, which is essential for correct processing and degradation of RNA. We report here two PCH1D families with biallelic EXOSC9 variants: c.239T>G (p.Leu80Arg) and c.484dupA (p.Arg162Lysfs*3) in one family and c.151G>C (p.Gly51Arg) in the other family. Although the patients studied here showed similar clinical features as previously described for PCH1D, relatively greater intellectual development (although still highly restricted) and normal pontine structure were recognized. Our findings expand the clinical consequences of biallelic EXOSC9 variants.
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Hideaki Mashimo
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Satoko Kumada
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Keiko Ishigaki
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Mahdiyeh Behnam
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohsen Ghadami
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Cardiac Primary Research Center, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Eriko Koshimizu
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriko Miyake
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.
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26
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A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis. NPJ Genom Med 2020; 5:37. [PMID: 32963807 PMCID: PMC7484757 DOI: 10.1038/s41525-020-00144-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Exome sequencing (ES) has become one of the important diagnostic tools in clinical genetics with a reported diagnostic rate of 25–58%. Many studies have illustrated the diagnostic and immediate clinical impact of ES. However, up to 75% of individuals remain undiagnosed and there is scarce evidence supporting clinical utility beyond a follow-up period of >1 year. This is a 3-year follow-up analysis to our previous publication by Mak et al. (NPJ Genom. Med. 3:19, 2018), to evaluate the long-term clinical utility of ES and the diagnostic potential of exome reanalysis. The diagnostic yield of the initial study was 41% (43/104). Exome reanalysis in 46 undiagnosed individuals has achieved 12 new diagnoses. The additional yield compared with the initial analysis was at least 12% (increased from 41% to at least 53%). After a median follow-up period of 3.4 years, change in clinical management was observed in 72.2% of the individuals (26/36), leading to positive change in clinical outcome in four individuals (11%). There was a minimum healthcare cost saving of HKD$152,078 (USD$19,497; €17,282) annually for these four individuals. There were a total of six pregnancies from five families within the period. Prenatal diagnosis was performed in four pregnancies; one fetus was affected and resulted in termination. None of the parents underwent preimplantation genetic diagnosis. This 3-year follow-up study demonstrated the long-term clinical utility of ES at individual, familial and health system level, and the promising diagnostic potential of subsequent reanalysis. This highlights the benefits of implementing ES and regular reanalysis in the clinical setting.
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