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Cesana D, Cicalese MP, Calabria A, Merli P, Caruso R, Volpin M, Rudilosso L, Migliavacca M, Barzaghi F, Fossati C, Gazzo F, Pizzi S, Ciolfi A, Bruselles A, Tucci F, Spinozzi G, Pais G, Benedicenti F, Barcella M, Merelli I, Gallina P, Giannelli S, Dionisio F, Scala S, Casiraghi M, Strocchio L, Vinti L, Pacillo L, Draghi E, Cesana M, Riccardo S, Colantuono C, Six E, Cavazzana M, Carlucci F, Schmidt M, Cancrini C, Ciceri F, Vago L, Cacchiarelli D, Gentner B, Naldini L, Tartaglia M, Montini E, Locatelli F, Aiuti A. A case of T-cell acute lymphoblastic leukemia in retroviral gene therapy for ADA-SCID. Nat Commun 2024; 15:3662. [PMID: 38688902 PMCID: PMC11061298 DOI: 10.1038/s41467-024-47866-5] [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: 10/13/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Hematopoietic stem cell gene therapy (GT) using a γ-retroviral vector (γ-RV) is an effective treatment for Severe Combined Immunodeficiency due to Adenosine Deaminase deficiency. Here, we describe a case of GT-related T-cell acute lymphoblastic leukemia (T-ALL) that developed 4.7 years after treatment. The patient underwent chemotherapy and haploidentical transplantation and is currently in remission. Blast cells contain a single vector insertion activating the LIM-only protein 2 (LMO2) proto-oncogene, confirmed by physical interaction, and low Adenosine Deaminase (ADA) activity resulting from methylation of viral promoter. The insertion is detected years before T-ALL in multiple lineages, suggesting that further hits occurred in a thymic progenitor. Blast cells contain known and novel somatic mutations as well as germline mutations which may have contributed to transformation. Before T-ALL onset, the insertion profile is similar to those of other ADA-deficient patients. The limited incidence of vector-related adverse events in ADA-deficiency compared to other γ-RV GT trials could be explained by differences in transgenes, background disease and patient's specific factors.
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Affiliation(s)
- Daniela Cesana
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Merli
- IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Monica Volpin
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Rudilosso
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maddalena Migliavacca
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Fossati
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Gazzo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Tucci
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Pais
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Pierangela Gallina
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Giannelli
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Dionisio
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Miriam Casiraghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Lucia Pacillo
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Eleonora Draghi
- Immunogenetics, Leukemia Genomics and Immunobiology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Naples, Italy
| | - Sara Riccardo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA S.r.l., Pozzuoli, Italy
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA S.r.l., Pozzuoli, Italy
| | - Emmanuelle Six
- Laboratory of Human Lympho-hematopoiesis, INSERM, Paris, France
| | | | - Filippo Carlucci
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Caterina Cancrini
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
- Department of Systems Medicine University of Rome Tor Vergata, Rome, Italy
| | - Fabio Ciceri
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
- Haematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Luca Vago
- Università Vita-Salute San Raffaele, Milan, Italy
- Immunogenetics, Leukemia Genomics and Immunobiology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132, Milan, Italy
- Haematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Haematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Università Vita-Salute San Raffaele, Milan, Italy.
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Abu Alhaija AA, Lone IN, Sekeroglu EO, Batur T, Angelov D, Dimitrov S, Hamiche A, Firat Karalar EN, Ercan ME, Yagci T, Alotaibi H, Diril MK. Development of a mouse embryonic stem cell model for investigating the functions of the linker histone H1-4. FEBS Open Bio 2024; 14:309-321. [PMID: 38098212 PMCID: PMC10839353 DOI: 10.1002/2211-5463.13750] [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: 08/29/2023] [Revised: 11/11/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024] Open
Abstract
The linker histone H1 C-terminal domain (CTD) plays a pivotal role in chromatin condensation. De novo frameshift mutations within the CTD coding region of H1.4 have recently been reported to be associated with Rahman syndrome, a neurological disease that causes intellectual disability and overgrowth. To investigate the mechanisms and pathogenesis of Rahman syndrome, we developed a cellular model using murine embryonic stem cells (mESCs) and CRISPR/Cas9 genome engineering. Our engineered mES cells facilitate detailed investigations, such as H1-4 dynamics, immunoprecipitation, and nuclear localization; in addition, we tagged the mutant H1-4 with a photoactivatable GFP (PA-GFP) and an HA tag to facilitate pulldown assays. We anticipate that these engineered cells could also be used for the development of a mouse model to study the in vivo role of the H1-4 protein.
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Affiliation(s)
- Abed Alkarem Abu Alhaija
- Department of Molecular Biology and Genetics, Faculty of Basic SciencesGebze Technical UniversityTurkey
- Izmir Biomedicine and Genome CenterTurkey
| | | | - Esin Ozkuru Sekeroglu
- Izmir Biomedicine and Genome CenterTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTurkey
| | | | - Dimitar Angelov
- Izmir Biomedicine and Genome CenterTurkey
- Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239Université de Lyon, Ecole Normale Supérieure de LyonFrance
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome CenterTurkey
- Roumen Tsanev Institute of Molecular BiologyBulgarian Academy of SciencesSofiaBulgaria
- Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309Université Grenoble AlpesFrance
| | - Ali Hamiche
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)UdS, CNRS, INSERMStrasbourgFrance
| | | | | | - Tamer Yagci
- Department of Molecular Biology and Genetics, Faculty of Basic SciencesGebze Technical UniversityTurkey
| | - Hani Alotaibi
- Izmir Biomedicine and Genome CenterTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTurkey
| | - Muhammed Kasim Diril
- Izmir Biomedicine and Genome CenterTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTurkey
- Department of Medical Biology, Faculty of MedicineDokuz Eylül UniversityIzmirTurkey
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Zhao W, Zhang Y, Lv T, He J, Zhu B. A case report of a novel HIST1H1E mutation and a review of the bibliography to evaluate the genotype-phenotype correlations. Mol Genet Genomic Med 2023; 11:e2273. [PMID: 37605493 PMCID: PMC10724515 DOI: 10.1002/mgg3.2273] [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: 01/19/2023] [Revised: 04/14/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND HIST1H1E is a member of the H1 gene family. Excess de novo likely gene-disruptive variants involving the C-terminal tail of HIST1H1E have been reported in neurodevelopmental disorders. Although clinical phenotypes in some patients have been described in single studies, few studies have reviewed the genotype and phenotype relationships using a relatively large cohort of patients with HIST1H1E variants. METHODS Whole-exome sequencing (WES) was performed on the proband. The variant was validated using Sanger sequencing in both proband and parents. Published HIST1H1E variants in neuropsychiatric disorders were reviewed. RESULTS Herein, we reported a new de novo frameshift mutation in HIST1H1E (NM_005321.2, c.416_419dupAGAA, p.Ala141GlufsTer56) in an individual with Rahman syndrome. To explore the genotype-phenotype correlations for HIST1H1E variants in neurodevelopmental disorders, we comprehensively curated and summarized 23 variants and the clinical features from 52 patients. Our findings revealed that likely gene-disrupting variants in HIST1H1E contribute to a wide range of neurodevelopmental phenotypes. We observed the common phenotypes including craniofacial features, ID, hypotonia, and autism/behavior problem in patients with HIST1H1E variants. While the different genotypes corresponding to different phenotypes or the same phenotype were also observed. CONCLUSION These data provide scientific evidence for the genetic diagnosis and precision clinical management.
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Affiliation(s)
- Wenjing Zhao
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Yinhong Zhang
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Tao Lv
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Jing He
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Baosheng Zhu
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
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Yüksel Ülker A, Uludağ Alkaya D, Çağlayan AO, Usluer E, Aykut A, Aslanger A, Vural M, Tüysüz B. An investigation of the etiology and follow-up findings in 35 children with overgrowth syndromes, including biallelic SUZ12 variant. Am J Med Genet A 2023; 191:1530-1545. [PMID: 36919607 DOI: 10.1002/ajmg.a.63180] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/01/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023]
Abstract
Overgrowth-intellectual disability (OGID) syndromes are clinically and genetically heterogeneous group of disorders. The aim of this study was to examine the molecular etiology and long-term follow-up findings of Turkish OGID cohort. Thirty-five children with OGID were included in the study. Single gene sequencing, clinical exome analysis, chromosomal microarray analysis and whole exome sequencing were performed. Five pathogenic copy number variants were detected in the patients; three of them located on chromosome 5q35.2 (encompassing NSD1), others on 9q22.3 and 22q13.31. In 19 of 35 patients; we identified pathogenic variants in OGID genes associated with epigenetic regulation, NSD1 (n = 15), HIST1H1E (n = 1), SETD1B (n = 1), and SUZ12 (n = 2). The pathogenic variants in PIK3CA (n = 2), ABCC9 (n = 1), GPC4 (n = 2), FIBP (n = 1), and TMEM94 (n = 1) which had a role in other growth pathways were detected in seven patients. The diagnostic yield was 31/35(88%). Twelve pathogenic variants were novel. The common facial feature of the patients was prominent forehead. The patients with Sotos syndrome were observed to have milder intellectual disability than patients with other OGID syndromes. In conclusion, this study showed, for the first time, that biallelic variants of SUZ12 caused Imagawa-Matsumoto syndrome, monoallelic variants in SETDIB resulted in OGID. Besides expanded the phenotypes of very rare OGID syndromes caused by FIBP and TMEM94.
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Affiliation(s)
- Aylin Yüksel Ülker
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ahmet Okay Çağlayan
- Departments of Neurosurgery, Neurobiology and Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Esra Usluer
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ayça Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ayça Aslanger
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Mehmet Vural
- Department of Neonatology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
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Kumar A, Maurya P, Hayes JJ. Post-Translation Modifications and Mutations of Human Linker Histone Subtypes: Their Manifestation in Disease. Int J Mol Sci 2023; 24:ijms24021463. [PMID: 36674981 PMCID: PMC9860689 DOI: 10.3390/ijms24021463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Linker histones (LH) are a critical component of chromatin in addition to the canonical histones (H2A, H2B, H3, and H4). In humans, 11 subtypes (7 somatic and 4 germinal) of linker histones have been identified, and their diverse cellular functions in chromatin structure, DNA replication, DNA repair, transcription, and apoptosis have been explored, especially for the somatic subtypes. Delineating the unique role of human linker histone (hLH) and their subtypes is highly tedious given their high homology and overlapping expression patterns. However, recent advancements in mass spectrometry combined with HPLC have helped in identifying the post-translational modifications (PTMs) found on the different LH subtypes. However, while a number of PTMs have been identified and their potential nuclear and non-nuclear functions explored in cellular processes, there are very few studies delineating the direct relevance of these PTMs in diseases. In addition, recent whole-genome sequencing of clinical samples from cancer patients and individuals afflicted with Rahman syndrome have identified high-frequency mutations and therefore broadened the perspective of the linker histone mutations in diseases. In this review, we compile the identified PTMs of hLH subtypes, current knowledge of the relevance of hLH PTMs in human diseases, and the correlation of PTMs coinciding with mutations mapped in diseases.
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Affiliation(s)
- Ashok Kumar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
- Correspondence:
| | - Preeti Maurya
- Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY 14642, USA
| | - Jeffrey J. Hayes
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
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Whiwon L, Salma S, Daniel A, Stephanie L, Marc C, Cherith S, Abby T, Angela S, Robin H, Yvonne B. Patient-facing digital tools for delivering genetic services: a systematic review. J Med Genet 2023; 60:1-10. [PMID: 36137613 DOI: 10.1136/jmg-2022-109085] [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: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 01/24/2023]
Abstract
This study systematically reviewed the literature on the impact of digital genetics tools on patient care and system efficiencies. MEDLINE and Embase were searched for articles published between January 2010 and March 2021. Studies evaluating the use of patient-facing digital tools in the context of genetic service delivery were included. Two reviewers screened and extracted patient-reported and system-focused outcomes from each study. Data were synthesised using a descriptive approach. Of 3226 unique studies identified, 87 were included. A total of 70 unique digital tools were identified. As a result of using digital tools, 84% of studies reported a positive outcome in at least one of the following patient outcomes: knowledge, psychosocial well-being, behavioural/management changes, family communication, decision-making or level of engagement. Digital tools improved workflow and efficiency for providers and reduced the amount of time they needed to spend with patients. However, we identified a misalignment between study purpose and patient-reported outcomes measured and a lack of tools that encompass the entire genetic counselling and testing trajectory. Given increased demand for genetic services and the shift towards virtual care, this review provides evidence that digital tools can be used to efficiently deliver patient-centred care. Future research should prioritise development, evaluation and implementation of digital tools that can support the entire patient trajectory across a range of clinical settings. PROSPERO registration numberCRD42020202862.
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Affiliation(s)
- Lee Whiwon
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shickh Salma
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Assamad Daniel
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Luca Stephanie
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Clausen Marc
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Somerville Cherith
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Tafler Abby
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shaw Angela
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Hayeems Robin
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Bombard Yvonne
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
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Wu H, Liang C. Pan-Cancer Analysis of the Tumorigenic Effect and Prognostic Diagnostic Value of FAM111B in Human Carcinomas. Int J Gen Med 2023; 16:1845-1865. [PMID: 37213474 PMCID: PMC10199687 DOI: 10.2147/ijgm.s409690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction FAM111B (FAM111 trypsin-like peptidase B) gene mutations have been linked to a hereditary fibrosing poikiloderma disorder known to cause poikiloderma, tendon contracture, myopathy, and pulmonary fibrosis (POIKTMP). Overexpression of FAM111B has been associated with an increased risk of certain cancers with a poor prognosis, although the relationship between FAM111B and other tumors is still unclear, and the molecular mechanism of its action is not fully understood. Methods We investigated the biological functions of FAM111B in 33 solid tumors using multi-omics data. We further recruited 109 gastric cancer (GC) patients for a clinical cohort study to confirm the effect of FAM111B on early tumor recurrence. Furthermore, we assessed the role of FAM111B in GC cell proliferation and migration via EdU incorporation, CCK8 and transwell assays in vitro. Results We found that FAM111B can enhance oncogenesis and progression in multiple tumor types. The clinical cohort of GC showed that upregulation of FAM111B is associated with early recurrence of GC, and knockdown of the FAM111B gene can inhibit the proliferation and migration of GC cells. Gene enrichment analysis indicates that FAM111B promotes cancer through immune system process, chromosome instability, DNA repair, and apoptosis regulation. Mechanistically, FAM111B appears to promote the growth cycle of malignant tumor cells while inhibiting apoptosis. Conclusion FAM111B may serve as a potential pan-cancer biomarker for predicting the prognosis and survival of malignant tumor patients. Our study elucidates the role of FAM111B in the occurrence and development of various cancers, and highlights the need for future research on FAM111B in cancers.
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Affiliation(s)
- Hengmiao Wu
- Department of General Surgery, the Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315000, People’s Republic of China
| | - Chao Liang
- Department of General Surgery, the Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315000, People’s Republic of China
- Correspondence: Chao Liang, Department of General Surgery, the Affiliated Lihuili Hospital, Ningbo University, 57 Xingning Road, Ningbo, 315000, People’s Republic of China, Tel +86-574-87018607, Email
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Sokolova V, Sarkar S, Tan D. Histone variants and chromatin structure, update of advances. Comput Struct Biotechnol J 2022; 21:299-311. [PMID: 36582440 PMCID: PMC9764139 DOI: 10.1016/j.csbj.2022.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Histone proteins are highly conserved among all eukaryotes. They have two important functions in the cell: to package the genomic DNA and to regulate gene accessibility. Fundamental to these functions is the ability of histone proteins to interact with DNA and to form the nucleoprotein complex called chromatin. One of the mechanisms the cells use to regulate chromatin and gene expression is through replacing canonical histones with their variants at specific loci to achieve functional consequence. Recent cryo-electron microscope (cryo-EM) studies of chromatin containing histone variants reveal new details that shed light on how variant-specific features influence the structures and functions of chromatin. In this article, we review the current state of knowledge on histone variants biochemistry and discuss the implication of these new structural information on histone variant biology and their functions in transcription.
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9
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Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
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10
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Feng H, Zhou BR, Schwieters CD, Bai Y. Structural Mechanism of TAF-Iβ Chaperone Function on Linker Histone H1.10. J Mol Biol 2022; 434:167755. [PMID: 35870650 PMCID: PMC9489631 DOI: 10.1016/j.jmb.2022.167755] [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: 05/10/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022]
Abstract
Linker histone H1, facilitated by its chaperones, plays an essential role in regulating gene expression by maintaining chromatin's higher-order structure and epigenetic state. However, we know little about the structural mechanism of how the chaperones recognize linker histones and conduct their function. Here, we used biophysical and biochemical methods to investigate the recognition of human linker histone isoform H1.10 by the TAF-Iβ chaperone. Both H1.10 and TAF-Iβ proteins consist of folded cores and disordered tails. We found that H1.10 formed a complex with TAF-Iβ in a 2:2 stoichiometry. Using distance restraints obtained from methyl-TROSY NMR and spin labels, we built a structural model for the core region of the complex. In the model, the TAF-Iβ core interacts with the globular domain of H1.10 mainly through electrostatic interactions. We confirmed the interactions by measuring the effects of mutations on the binding affinity. A comparison of our structural model with the chromatosome structure shows that TAF-Iβ blocks the DNA binding sites of H1.10. Our study provides insights into the structural mechanism whereby TAF-Iβ functions as a chaperone by preventing H1.10 from interacting with DNA directly.
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Affiliation(s)
- Haniqao Feng
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles D Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Flex E, Albadri S, Radio FC, Cecchetti S, Lauri A, Priolo M, Kissopoulos M, Carpentieri G, Fasano G, Venditti M, Magliocca V, Bellacchio E, Welch CL, Colombo PC, Kochav SM, Chang R, Barrick R, Trivisano M, Micalizzi A, Borghi R, Messina E, Mancini C, Pizzi S, De Santis F, Rosello M, Specchio N, Compagnucci C, McWalter K, Chung WK, Del Bene F, Tartaglia M. Dominantly acting KIF5B variants with pleiotropic cellular consequences cause variable clinical phenotypes. Hum Mol Genet 2022; 32:473-488. [PMID: 36018820 PMCID: PMC9851748 DOI: 10.1093/hmg/ddac213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/05/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023] Open
Abstract
Kinesins are motor proteins involved in microtubule (MT)-mediated intracellular transport. They contribute to key cellular processes, including intracellular trafficking, organelle dynamics and cell division. Pathogenic variants in kinesin-encoding genes underlie several human diseases characterized by an extremely variable clinical phenotype, ranging from isolated neurodevelopmental/neurodegenerative disorders to syndromic phenotypes belonging to a family of conditions collectively termed as 'ciliopathies.' Among kinesins, kinesin-1 is the most abundant MT motor for transport of cargoes towards the plus end of MTs. Three kinesin-1 heavy chain isoforms exist in mammals. Different from KIF5A and KIF5C, which are specifically expressed in neurons and established to cause neurological diseases when mutated, KIF5B is an ubiquitous protein. Three de novo missense KIF5B variants were recently described in four subjects with a syndromic skeletal disorder characterized by kyphomelic dysplasia, hypotonia and DD/ID. Here, we report three dominantly acting KIF5B variants (p.Asn255del, p.Leu498Pro and p.Leu537Pro) resulting in a clinically wide phenotypic spectrum, ranging from dilated cardiomyopathy with adult-onset ophthalmoplegia and progressive skeletal myopathy to a neurodevelopmental condition characterized by severe hypotonia with or without seizures. In vitro and in vivo analyses provide evidence that the identified disease-associated KIF5B variants disrupt lysosomal, autophagosome and mitochondrial organization, and impact cilium biogenesis. All variants, and one of the previously reported missense changes, were shown to affect multiple developmental processes in zebrafish. These findings document pleiotropic consequences of aberrant KIF5B function on development and cell homeostasis, and expand the phenotypic spectrum resulting from altered kinesin-mediated processes.
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Affiliation(s)
- Elisabetta Flex
- To whom correspondence should be addressed at: Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy. Tel: +39 06 4990 2866; ; Marco Tartaglia, Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy. Tel: +39 06 6859 3742;
| | | | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Serena Cecchetti
- Core Facilities, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Manuela Priolo
- UOSD Genetica Medica, Grande Ospedale Metropolitano "Bianchi Melacrino Morelli", 89124 Reggio Calabria, Italy
| | - Marta Kissopoulos
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Giovanna Carpentieri
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Magliocca
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, NY, New York 10032, USA
| | - Paolo C Colombo
- Department of Medicine, Columbia University Irving Medical Center, NY, New York 10032, USA
| | - Stephanie M Kochav
- Department of Medicine, Columbia University Irving Medical Center, NY, New York 10032, USA
| | - Richard Chang
- Division of Metabolic Disorders, Children's Hospital of Orange County (CHOC), CA, Orange 92868, USA
| | - Rebekah Barrick
- Division of Metabolic Disorders, Children's Hospital of Orange County (CHOC), CA, Orange 92868, USA
| | - Marina Trivisano
- Department of Neuroscience, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Alessia Micalizzi
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Rossella Borghi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Elena Messina
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Flavia De Santis
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215 Paris, France
| | - Marion Rosello
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, F-75012 Paris, France
| | - Nicola Specchio
- Department of Neuroscience, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Claudia Compagnucci
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, NY, New York 10032, USA,Department of Medicine, Columbia University Irving Medical Center, NY, New York 10032, USA
| | | | - Marco Tartaglia
- To whom correspondence should be addressed at: Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy. Tel: +39 06 4990 2866; ; Marco Tartaglia, Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy. Tel: +39 06 6859 3742;
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12
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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13
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Priolo M, Mancini C, Pizzi S, Chiriatti L, Radio FC, Cordeddu V, Pintomalli L, Mammì C, Dallapiccola B, Tartaglia M. Complex Presentation of Hao-Fountain Syndrome Solved by Exome Sequencing Highlighting Co-Occurring Genomic Variants. Genes (Basel) 2022; 13:genes13050889. [PMID: 35627274 PMCID: PMC9141324 DOI: 10.3390/genes13050889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/02/2022] [Accepted: 05/11/2022] [Indexed: 01/05/2023] Open
Abstract
Objective: The co-occurrence of pathogenic variants has emerged as a relatively common finding underlying complex phenotypes. Here, we used whole-exome sequencing (WES) to solve an unclassified multisystem clinical presentation. Patients and Methods: A 20-year-old woman affected by moderate intellectual disability (ID), dysmorphic features, hypertrichosis, scoliosis, recurrent bronchitis, and pneumonia with bronchiectasis, colelithiasis, chronic severe constipation, and a family history suggestive of autosomal dominant recurrence of polycystic kidney disease was analyzed by WES to identify the genomic events underlying the condition. Results: Four co-occurring genomic events fully explaining the proband’s clinical features were identified. A de novo truncating USP7 variant was disclosed as the cause of Hao–Fountain syndrome, a disorder characterized by syndromic ID and distinctive behavior. Compound heterozygosity for a major cystic fibrosis-causing variant and the modulator allele, IVS8-5T, in CFTR explained the recurrent upper and lower respiratory way infections, bronchiectasis, cholelithiasis, and chronic constipation. Finally, a truncating PKD2 variant co-segregating with polycystic kidney disease in the family allowed presymptomatic disease diagnosis. Conclusions: The co-occurring variants in USP7 and CFTR variants explained the multisystem disorder of the patient. The comprehensive dissection of the phenotype and early diagnosis of autosomal dominant polycystic kidney disease allowed us to manage the CFTR-related disorder symptoms and monitor renal function and other complications associated with PKD2 haploinsufficiency, addressing proper care and surveillance.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
- Correspondence: ; Tel.: +39-09-6539-7319
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Luigi Chiriatti
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
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14
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Tremblay MW, Green MV, Goldstein BM, Aldridge AI, Rosenfeld JA, Streff H, Tan WD, Craigen W, Bekheirnia N, Al Tala S, West AE, Jiang YH. Mutations of the histone linker H1-4 in neurodevelopmental disorders and functional characterization of neurons expressing C-terminus frameshift mutant H1.4. Hum Mol Genet 2022; 31:1430-1442. [PMID: 34788807 PMCID: PMC9271223 DOI: 10.1093/hmg/ddab321] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 12/29/2022] Open
Abstract
Rahman syndrome (RMNS) is a rare genetic disorder characterized by mild to severe intellectual disability, hypotonia, anxiety, autism spectrum disorder, vision problems, bone abnormalities and dysmorphic facies. RMNS is caused by de novo heterozygous mutations in the histone linker gene H1-4; however, mechanisms underlying impaired neurodevelopment in RMNS are not understood. All reported mutations associated with RMNS in H1-4 are small insertions or deletions that create a shared frameshift, resulting in a H1.4 protein that is both truncated and possessing an abnormal C-terminus frameshifted tail (H1.4 CFT). To expand understanding of mutations and phenotypes associated with mutant H1-4, we identified new variants at both the C- and N-terminus of H1.4. The clinical features of mutations identified at the C-terminus are consistent with other reports and strengthen the support of pathogenicity of H1.4 CFT. To understand how H1.4 CFT may disrupt brain function, we exogenously expressed wild-type or H1.4 CFT protein in rat hippocampal neurons and assessed neuronal structure and function. Genome-wide transcriptome analysis revealed ~ 400 genes altered in the presence of H1.4 CFT. Neuronal genes downregulated by H1.4 CFT were enriched for functional categories involved in synaptic communication and neuropeptide signaling. Neurons expressing H1.4 CFT also showed reduced neuronal activity on multielectrode arrays. These data are the first to characterize the transcriptional and functional consequence of H1.4 CFT in neurons. Our data provide insight into causes of neurodevelopmental impairments associated with frameshift mutations in the C-terminus of H1.4 and highlight the need for future studies on the function of histone H1.4 in neurons.
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Affiliation(s)
- Martine W Tremblay
- University Program in Genetics and Genomics, Duke University, Durham NC 27710, USA
- Department of Neurobiology, Duke University, Durham NC 27710, USA
| | - Matthew V Green
- Department of Neurobiology, Duke University, Durham NC 27710, USA
| | | | - Andrew I Aldridge
- University Program in Genetics and Genomics, Duke University, Durham NC 27710, USA
- Department of Neurobiology, Duke University, Durham NC 27710, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
- Baylor Genetics Laboratories, Baylor College of Medicine, Houston TX 77030, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Wendy D Tan
- Department of Neurobiology, Duke University, Durham NC 27710, USA
| | - William Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Nasim Bekheirnia
- Department of Pediatrics, Renal section, Baylor College of Medicine, Houston TX 77030, USA
| | - Saeed Al Tala
- Department of Pediatrics, Armed Forces Hospital SR, Khamis Mushayt 61961, Saudi Arabia
| | - Anne E West
- University Program in Genetics and Genomics, Duke University, Durham NC 27710, USA
- Department of Neurobiology, Duke University, Durham NC 27710, USA
| | - Yong-hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven CT 06520, USA
- Neuroscience, Yale University School of Medicine, New Haven CT 06520, USA
- Pediatrics, Yale University School of Medicine, New Haven CT 06520, USA
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15
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Tessadori F, Duran K, Knapp K, Fellner M, Smithson S, Beleza Meireles A, Elting MW, Waisfisz Q, O’Donnell-Luria A, Nowak C, Douglas J, Ronan A, Brunet T, Kotzaeridou U, Svihovec S, Saenz MS, Thiffault I, Del Viso F, Devine P, Rego S, Tenney J, van Haeringen A, Ruivenkamp CA, Koene S, Robertson SP, Deshpande C, Pfundt R, Verbeek N, van de Kamp JM, Weiss JM, Ruiz A, Gabau E, Banne E, Pepler A, Bottani A, Laurent S, Guipponi M, Bijlsma E, Bruel AL, Sorlin A, Willis M, Powis Z, Smol T, Vincent-Delorme C, Baralle D, Colin E, Revencu N, Calpena E, Wilkie AO, Chopra M, Cormier-Daire V, Keren B, Afenjar A, Niceta M, Terracciano A, Specchio N, Tartaglia M, Rio M, Barcia G, Rondeau S, Colson C, Bakkers J, Mace PD, Bicknell LS, van Haaften G, van Haaften G. Recurrent de novo missense variants across multiple histone H4 genes underlie a neurodevelopmental syndrome. Am J Hum Genet 2022; 109:750-758. [PMID: 35202563 PMCID: PMC9069069 DOI: 10.1016/j.ajhg.2022.02.003] [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: 11/24/2021] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Chromatin is essentially an array of nucleosomes, each of which consists of the DNA double-stranded fiber wrapped around a histone octamer. This organization supports cellular processes such as DNA replication, DNA transcription, and DNA repair in all eukaryotes. Human histone H4 is encoded by fourteen canonical histone H4 genes, all differing at the nucleotide level but encoding an invariant protein. Here, we present a cohort of 29 subjects with de novo missense variants in six H4 genes (H4C3, H4C4, H4C5, H4C6, H4C9, and H4C11) identified by whole-exome sequencing and matchmaking. All individuals present with neurodevelopmental features of intellectual disability and motor and/or gross developmental delay, while non-neurological features are more variable. Ten amino acids are affected, six recurrently, and are all located within the H4 core or C-terminal tail. These variants cluster to specific regions of the core H4 globular domain, where protein-protein interactions occur with either other histone subunits or histone chaperones. Functional consequences of the identified variants were evaluated in zebrafish embryos, which displayed abnormal general development, defective head organs, and reduced body axis length, providing compelling evidence for the causality of the reported disorder(s). While multiple developmental syndromes have been linked to chromatin-associated factors, missense-bearing histone variants (e.g., H3 oncohistones) are only recently emerging as a major cause of pathogenicity. Our findings establish a broader involvement of H4 variants in developmental syndromes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 Utrecht, the Netherlands.
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16
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González-Tarancón R, Salvador-Rupérez E, Goñi-Ros N, Álvarez SI, Sánchez-Navarro I, García MM, Segura JLP, Lafuente AL. A novel likely pathogenic variant in the H1-4 gene c.139G > C p.(Ala47Pro) associated with Rahman syndrome: a clinical report. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00265-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Rahman syndrome (RMNS) is a rare genetic disorder inherited in an autosomal dominant manner caused by a de novo mutation in H1-4 gene. Since there are few cases described in the literature, the prevalence of the syndrome is unknown. RMNS should be suspected in individuals presenting mild to severe intellectual disability associated with behavioural problems.
Case presentation
A novel variant in the H1-4 gene: c.139G > C p.(Ala47Pro), classified as likely pathogenic, was identified in a patient with a phenotype compatible with RMNS. Clubfoot and obesity were described in our patient and should be considered in future reviews of the disease.
Conclusions
This case is added to the reduced number of publications previously reported regarding RMNS and contributes to understanding the genetic characteristics, clinical features and diagnosis of this syndrome.
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17
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Zhao J, Lyu G, Ding C, Wang X, Li J, Zhang W, Yang X, Zhang VW. Expanding the mutational spectrum of Rahman syndrome: A rare disorder with severe intellectual disability and particular facial features in two Chinese patients. Mol Genet Genomic Med 2022; 10:e1825. [PMID: 35156329 PMCID: PMC8922969 DOI: 10.1002/mgg3.1825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/28/2022] Open
Abstract
Background The study aimed to investigate the clinical and genetic features of Rahman syndrome caused by HIST1H1E gene mutations. Methods We retrospectively analyzed the clinical information and genetic testing results of a Rahman syndrome family in an outpatient clinic in August 2020 and summarized the clinical characteristics of the HIST1H1E gene mutations in conjunction with peer‐reviewed reports. Results A 4‐year‐old boy was diagnosed with severe developmental delay and with specific features (large head, full cheeks, high hairline, low‐set ear, sparse eyebrows, and short neck) similar to his mother (mild intellectual disability, high hairline, reduced hair, ptosis, sagging skin, and hyperkeratosis) and premature aging. Trio whole exome sequencing (WES) revealed a novel maternal c.368dup (p.G124Rfs*72) heterozygous mutation in the HIST1H1E gene. There have been only a few reported cases with mainly de novo mutations. Only six peer‐reviewed articles in English and one in Chinese have been published regarding this syndrome. From 48 children with Rahman syndrome, 21 were males and 27 were females encompassing 25 mutations in the HIST1H1E gene. All mutations located in C‐terminal tail were frameshift mutations leading to premature protein termination. Conclusion Rahman syndrome, caused by the HIST1H1E gene mutation, is a rare autosomal dominant disorder in which the patient has an unusual facial appearance with high hairline and full cheeks, and clinical manifestations of mild to severe intellectual disability, motor delay and speech delay. Genetic testing may assist in the diagnosis of these patients. This diagnosis will permit early speech rehabilitation to improve their quality of life.
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Affiliation(s)
- Jianbo Zhao
- Department of Neurology Beijing Children’s Hospital National Center for Children’s Health Capital Medical University Beijing China
| | | | - Changhong Ding
- Department of Neurology Beijing Children’s Hospital National Center for Children’s Health Capital Medical University Beijing China
| | - Xiaohui Wang
- Department of Neurology Beijing Children’s Hospital National Center for Children’s Health Capital Medical University Beijing China
| | - Jiuwei Li
- Department of Neurology Beijing Children’s Hospital National Center for Children’s Health Capital Medical University Beijing China
| | - Weihua Zhang
- Department of Neurology Beijing Children’s Hospital National Center for Children’s Health Capital Medical University Beijing China
| | - Xinying Yang
- Department of Neurology Beijing Children’s Hospital National Center for Children’s Health Capital Medical University Beijing China
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18
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [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] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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19
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Pavinato L, Villamor-Payà M, Sanchiz-Calvo M, Andreoli C, Gay M, Vilaseca M, Arauz-Garofalo G, Ciolfi A, Bruselles A, Pippucci T, Prota V, Carli D, Giorgio E, Radio FC, Antona V, Giuffrè M, Ranguin K, Colson C, De Rubeis S, Dimartino P, Buxbaum JD, Ferrero GB, Tartaglia M, Martinelli S, Stracker TH, Brusco A. Functional analysis of TLK2 variants and their proximal interactomes implicates impaired kinase activity and chromatin maintenance defects in their pathogenesis. J Med Genet 2022; 59:170-179. [PMID: 33323470 PMCID: PMC10631451 DOI: 10.1136/jmedgenet-2020-107281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/19/2020] [Accepted: 11/14/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The Tousled-like kinases 1 and 2 (TLK1 and TLK2) are involved in many fundamental processes, including DNA replication, cell cycle checkpoint recovery and chromatin remodelling. Mutations in TLK2 were recently associated with 'Mental Retardation Autosomal Dominant 57' (MRD57, MIM# 618050), a neurodevelopmental disorder characterised by a highly variable phenotype, including mild-to-moderate intellectual disability, behavioural abnormalities, facial dysmorphisms, microcephaly, epilepsy and skeletal anomalies. METHODS We re-evaluate whole exome sequencing and array-CGH data from a large cohort of patients affected by neurodevelopmental disorders. Using spatial proteomics (BioID) and single-cell gel electrophoresis, we investigated the proximity interaction landscape of TLK2 and analysed the effects of p.(Asp551Gly) and a previously reported missense variant (c.1850C>T; p.(Ser617Leu)) on TLK2 interactions, localisation and activity. RESULTS We identified three new unrelated MRD57 families. Two were sporadic and caused by a missense change (c.1652A>G; p.(Asp551Gly)) or a 39 kb deletion encompassing TLK2, and one was familial with three affected siblings who inherited a nonsense change from an affected mother (c.1423G>T; p.(Glu475Ter)). The clinical phenotypes were consistent with those of previously reported cases. The tested mutations strongly impaired TLK2 kinase activity. Proximal interactions between TLK2 and other factors implicated in neurological disorders, including CHD7, CHD8, BRD4 and NACC1, were identified. Finally, we demonstrated a more relaxed chromatin state in lymphoblastoid cells harbouring the p.(Asp551Gly) variant compared with control cells, conferring susceptibility to DNA damage. CONCLUSION Our study identified novel TLK2 pathogenic variants, confirming and further expanding the MRD57-related phenotype. The molecular characterisation of missense variants increases our knowledge about TLK2 function and provides new insights into its role in neurodevelopmental disorders.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, Torino, Italy
- Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marina Villamor-Payà
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Maria Sanchiz-Calvo
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Cristina Andreoli
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Marina Gay
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Marta Vilaseca
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Tommaso Pippucci
- Medical Genetics Unity, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Valentina Prota
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Diana Carli
- Department of Pediatrics and Public Health and Pediatric Sciences, University of Turin, Torino, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Turin, Torino, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Vincenzo Antona
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Mario Giuffrè
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Kara Ranguin
- Department of Genetics, Reference center for Rare Diseases and Developmental Anomalies, Caen, France
| | - Cindy Colson
- Department of Genetics, Reference center for Rare Diseases and Developmental Anomalies, Caen, France
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Giovanni Battista Ferrero
- Department of Pediatrics and Public Health and Pediatric Sciences, University of Turin, Torino, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Roma, Italy
| | - Travis H Stracker
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Torino, Italy
- Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, Torino, Italy
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20
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Indugula SR, Ayala SS, Vetrini F, Belonis A, Zhang W. Exome sequencing identified a novel HIST1H1E heterozygous protein-truncating variant in a 6-month-old male patient with Rahman syndrome: A case report. Clin Case Rep 2022; 10:e05370. [PMID: 35154720 PMCID: PMC8822259 DOI: 10.1002/ccr3.5370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/28/2021] [Accepted: 01/14/2022] [Indexed: 11/11/2022] Open
Abstract
Rahman syndrome is a rare congenital anomaly syndrome recently described, which results from pathogenic variants in the HIST1H1E gene. The condition is characterized by variable somatic overgrowth, macrocephaly, distinctive facial features, intellectual disability, and behavioral problems. This report extends the genotype and clinical phenotype of HIST1H1E-associated Rahman syndrome.
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Affiliation(s)
- Subba Rao Indugula
- Division of Human GeneticsCincinnati Children’s Hospital Medical CenterCincinnatiOhioUSA
| | - Sofia Saenz Ayala
- Division of Human GeneticsCincinnati Children’s Hospital Medical CenterCincinnatiOhioUSA
| | - Francesco Vetrini
- Department of Medical and Molecular GeneticsUndiagnosed Rare Disease ClinicIndiana University School of MedicineIndianapolisIndianaUSA
| | - Alyce Belonis
- Division of Human GeneticsCincinnati Children’s Hospital Medical CenterCincinnatiOhioUSA
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Wenying Zhang
- Division of Human GeneticsCincinnati Children’s Hospital Medical CenterCincinnatiOhioUSA
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
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21
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Analysis of histone variant constraint and tissue expression suggests five potential novel human disease genes: H2AFY2, H2AFZ, H2AFY, H2AFV, H1F0. Hum Genet 2022; 141:1409-1421. [DOI: 10.1007/s00439-022-02432-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/07/2022] [Indexed: 11/26/2022]
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22
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Broggi G, Tirrò E, Alzoubi H, Arcella A, Gianno F, Antonelli M, Minasi S, Vigneri P, Certo F, Altieri R, Barbagallo GMV, Miele E, Caltabiano R, Giangaspero F. Cerebellar liponeurocytoma: clinical, histopathological and molecular features of a series of three cases, including one recurrent tumor. Neuropathology 2022; 42:169-180. [PMID: 35042275 DOI: 10.1111/neup.12799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/10/2021] [Accepted: 11/21/2021] [Indexed: 12/11/2022]
Abstract
Cerebellar liponeurocytoma (CL) is an unusual tumor, histologically composed of a mixture of small to medium-sized, rounded neurocytic cells and a variable lipomatous component. Although CL was originally considered as a subtype of medulloblastoma, subsequent molecular studies demonstrated that this tumor was a distinct entity, exhibiting the tumor protein p53 gene (TP53) missense mutations in 20% of cases, chromosome 17 deletion, and the absence of mutations in the adenomatous polyposis coli gene (APC), the protein patched homolog gene (PTCH), the kinase insert domain receptor gene (KDR), and the β-catenin gene (CTNNB). Apart from these molecular features, little is known about the pathogenesis and the genetic landscape of CL to date. In order to characterize the mutational landscape of CL and identify alterations that are driving tumorigenesis, we report a series of three cases, including one recurrent tumor, analysed by next-generation sequencing (NGS), which identified a total of 22 variants, of which four were missense mutations, nine were synonymous variants, and nine were located on intronic regions. In particular, DNA sequencing identified missense mutations in APC, KDR, and TP53 that could be implicated in promoting tumor progression and angiogenesis of CL. Furthermore, the NGS analysis revealed that recurrent CL did not have additional genetic changes compared with the primary tumor. Moreover, the high frequencies of detected mutations suggested that the identified alterations are germline variants. Indeed, an additional NGS on the genomic DNA obtained from one of the three patients confirmed the presence of the variants in the germline DNA. In conclusion, the obtained data support the hypothesis that CL is a distinct pathological entity that does not show specific somatic alterations driving tumorigenesis.
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Affiliation(s)
- Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania, Italy
| | - Elena Tirrò
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", Catania, Italy.,Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Hiba Alzoubi
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | | | - Francesca Gianno
- IRCCS Neuromed, Pozzilli, Italy.,Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Manila Antonelli
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Simone Minasi
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Paolo Vigneri
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", Catania, Italy
| | - Francesco Certo
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy
| | - Roberto Altieri
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy
| | - Giuseppe Maria Vincenzo Barbagallo
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania, Italy
| | - Felice Giangaspero
- IRCCS Neuromed, Pozzilli, Italy.,Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
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23
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Fathi A, Mathivanan S, Kong L, Petersen AJ, Harder CK, Block J, Miller JM, Bhattacharyya A, Wang D, Zhang S. Chemically induced senescence in human stem cell-derived neurons promotes phenotypic presentation of neurodegeneration. Aging Cell 2022; 21:e13541. [PMID: 34953016 PMCID: PMC8761019 DOI: 10.1111/acel.13541] [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: 07/08/2021] [Revised: 11/18/2021] [Accepted: 12/10/2021] [Indexed: 01/10/2023] Open
Abstract
Modeling age‐related neurodegenerative disorders with human stem cells are difficult due to the embryonic nature of stem cell‐derived neurons. We developed a chemical cocktail to induce senescence of iPSC‐derived neurons to address this challenge. We first screened small molecules that induce embryonic fibroblasts to exhibit features characteristic of aged fibroblasts. We then optimized a cocktail of small molecules that induced senescence in fibroblasts and cortical neurons without causing DNA damage. The utility of the “senescence cocktail” was validated in motor neurons derived from ALS patient iPSCs which exhibited protein aggregation and axonal degeneration substantially earlier than those without cocktail treatment. Our “senescence cocktail” will likely enhance the manifestation of disease‐related phenotypes in neurons derived from iPSCs, enabling the generation of reliable drug discovery platforms.
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Affiliation(s)
- Ali Fathi
- Waisman Center University of Wisconsin‐Madison Madison Wisconsin USA
| | | | - Linghai Kong
- Waisman Center University of Wisconsin‐Madison Madison Wisconsin USA
| | | | - Cole R. K. Harder
- Waisman Center University of Wisconsin‐Madison Madison Wisconsin USA
| | - Jasper Block
- Waisman Center University of Wisconsin‐Madison Madison Wisconsin USA
| | | | - Anita Bhattacharyya
- Waisman Center University of Wisconsin‐Madison Madison Wisconsin USA
- Department of Cell and Regenerative Biology School of Medicine and Public Health University of Wisconsin‐Madison Madison Wisconsin USA
| | - Daifeng Wang
- Waisman Center University of Wisconsin‐Madison Madison Wisconsin USA
| | - Su‐Chun Zhang
- Waisman Center University of Wisconsin‐Madison Madison Wisconsin USA
- Department of Neuroscience School of Medicine and Public Health University of Wisconsin Madison Wisconsin USA
- Department of Neurology School of Medicine and Public Health University of Wisconsin Madison Wisconsin USA
- Program in Neuroscience and Behavioral Disorders Duke‐NUS Medical School Singapore Singapore
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24
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A Rare Case of Brachyolmia with Amelogenesis Imperfecta Caused by a New Pathogenic Splicing Variant in LTBP3. Genes (Basel) 2021; 12:genes12091406. [PMID: 34573388 PMCID: PMC8470690 DOI: 10.3390/genes12091406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
In recent years, a rare form of autosomal recessive brachyolmia associated with amelogenesis imperfecta (AI) has been described as a novel nosologic entity. This disorder is characterized by skeletal dysplasia (e.g., platyspondyly, short trunk, scoliosis, broad ilia, elongated femoral necks with coxa valga) and severe enamel and dental anomalies. Pathogenic variants in the latent transforming growth factor-β binding protein 3 (LTBP3) gene have been found implicated in the pathogenesis of this disorder. So far, biallelic pathogenic LTBP3 variants have been identified in less than 10 families. We here report a young boy born from consanguineous parents with a complex phenotype including skeletal dysplasia associated with aortic stenosis, hypertrophic cardiomyopathy, hypodontia and amelogenesis imperfecta caused by a previously unreported homozygous LTBP3 splice site variant. We also compare the genotypes and phenotypes of patients reported to date. This work provides further evidence that brachyolmia with amelogenesis imperfecta is a distinct nosologic entity and that variations in LTBP3 are involved in its pathogenesis.
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25
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Contrò G, Micalizzi A, Giangiobbe S, Caraffi SG, Zuntini R, Rosato S, Pollazzon M, Terracciano A, Napoli M, Rizzi S, Salerno GG, Radio FC, Niceta M, Parrini E, Fusco C, Gargano G, Guerrini R, Tartaglia M, Novelli A, Zuffardi O, Garavelli L. Posterior Lissencephaly Associated with Subcortical Band Heterotopia Due to a Variation in the CEP85L Gene: A Case Report and Refining of the Phenotypic Spectrum. Genes (Basel) 2021; 12:genes12081208. [PMID: 34440382 PMCID: PMC8391275 DOI: 10.3390/genes12081208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/23/2022] Open
Abstract
Lissencephaly describes a group of conditions characterized by the absence of normal cerebral convolutions and abnormalities of cortical development. To date, at least 20 genes have been identified as involved in the pathogenesis of this condition. Variants in CEP85L, encoding a protein involved in the regulation of neuronal migration, have been recently described as causative of lissencephaly with a posterior-prevalent involvement of the cerebral cortex and an autosomal dominant pattern of inheritance. Here, we describe a 3-year-old boy with slightly delayed psychomotor development and mild dysmorphic features, including bitemporal narrowing, protruding ears with up-lifted lobes and posterior plagiocephaly. Brain MRI at birth identified type 1 lissencephaly, prevalently in the temporo–occipito–parietal regions of both hemispheres with “double-cortex” (Dobyns’ 1–2 degree) periventricular band alterations. Whole-exome sequencing revealed a previously unreported de novo pathogenic variant in the CEP85L gene (NM_001042475.3:c.232+1del). Only 20 patients have been reported as carriers of pathogenic CEP85L variants to date. They show lissencephaly with prevalent posterior involvement, variable cognitive deficits and epilepsy. The present case report indicates the clinical variability associated with CEP85L variants that are not invariantly associated with severe phenotypes and poor outcome, and underscores the importance of including this gene in diagnostic panels for lissencephaly.
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Affiliation(s)
- Gianluca Contrò
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.C.); (S.G.C.); (R.Z.); (S.R.); (M.P.)
| | - Alessia Micalizzi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.M.); (A.T.); (A.N.)
| | - Sara Giangiobbe
- Clinical Genomics, Medical Genetics Service, San Raffaele Hospital, 20132 Milan, Italy;
| | - Stefano Giuseppe Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.C.); (S.G.C.); (R.Z.); (S.R.); (M.P.)
| | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.C.); (S.G.C.); (R.Z.); (S.R.); (M.P.)
| | - Simonetta Rosato
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.C.); (S.G.C.); (R.Z.); (S.R.); (M.P.)
| | - Marzia Pollazzon
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.C.); (S.G.C.); (R.Z.); (S.R.); (M.P.)
| | - Alessandra Terracciano
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.M.); (A.T.); (A.N.)
| | - Manuela Napoli
- Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Susanna Rizzi
- Child Neurology and Psychiatry Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (S.R.); (G.G.S.); (C.F.)
| | - Grazia Gabriella Salerno
- Child Neurology and Psychiatry Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (S.R.); (G.G.S.); (C.F.)
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (F.C.R.); (M.N.); (M.T.)
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (F.C.R.); (M.N.); (M.T.)
| | - Elena Parrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy; (E.P.); (R.G.)
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (S.R.); (G.G.S.); (C.F.)
| | - Giancarlo Gargano
- Neonatal Intensive Care Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy; (E.P.); (R.G.)
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (F.C.R.); (M.N.); (M.T.)
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.M.); (A.T.); (A.N.)
| | - Orsetta Zuffardi
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy;
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.C.); (S.G.C.); (R.Z.); (S.R.); (M.P.)
- Correspondence: ; Tel.: +39-0522-296244 or +39-0522-295463
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26
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Ahmed MSO, Rafey M, McDonnell T, Smith D. HIST1H1E syndrome with type 2 diabetes. BMJ Case Rep 2021; 14:14/7/e241907. [PMID: 34290007 DOI: 10.1136/bcr-2021-241907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A 20-year-old woman was referred to the diabetes clinic with type 2 diabetes diagnosed at the age of 19. Her body mass index was 31.4 kg/m2, HbA1C was 76 mmol/mol, GAD antibodies were negative with a detectable C-peptide. She had a characteristic facial appearance with widespread eyes, posterior hairline suggesting a facial gestalt and abnormal dentition. She also had hypothyroidism, mild intellectual disability, primary amenorrhoea and patent ductus arteriosus. Karyotyping reported normal 46XX karyotype. Genetic testing revealed a pathogenic variant in the gene encoding the HIST1H1E protein which confirmed her diagnosis of HIST1H1E syndrome. Type 2 diabetes has not been reported in previous cases of HIST1H1E and so this is the first reported case of type 2 diabetes with HIST1H1E syndrome.
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Affiliation(s)
- Mohammed S O Ahmed
- Academic Department of Endocrinology, Beaumont Hospital, Dublin, Ireland
| | - Mohammed Rafey
- Academic Department of Endocrinology, Beaumont Hospital, Dublin, Ireland
| | - Tara McDonnell
- Academic Department of Endocrinology, Beaumont Hospital, Dublin, Ireland
| | - Diarmuid Smith
- Academic Department of Endocrinology, Beaumont Hospital, Dublin, Ireland.,Royal College of Surgeons in Ireland, Dublin, Ireland
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27
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Priolo M, Radio FC, Pizzi S, Pintomalli L, Pantaleoni F, Mancini C, Cordeddu V, Africa E, Mammì C, Dallapiccola B, Tartaglia M. Co-Occurring Heterozygous CNOT3 and SMAD6 Truncating Variants: Unusual Presentation and Refinement of the IDDSADF Phenotype. Genes (Basel) 2021; 12:genes12071009. [PMID: 34208845 PMCID: PMC8303239 DOI: 10.3390/genes12071009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objective, the application of genomic sequencing in clinical practice has allowed us to appreciate the contribution of co-occurring pathogenic variants to complex and unclassified clinical phenotypes. Besides the clinical relevance, these findings have provided evidence of previously unrecognized functional links between genes in the context of developmental processes and physiology. Patients and Methods, a 5-year-old patient showing an unclassified phenotype characterized by developmental delay, speech delay, peculiar behavioral features, facial dysmorphism and severe cardiopathy was analyzed by trio-based whole exome sequencing (WES) analysis to identify the genomic events underlying the condition. Results, two co-occurring heterozygous truncating variants in CNOT3 and SMAD6 were identified. Heterozygous loss-of-function variants in CNOT3, encoding a subunit of the CCR4-NOT protein complex, have recently been reported to cause a syndromic condition known as intellectual developmental disorder with speech delay, autism and dysmorphic facies (IDDSADF). Enrichment of rare/private variants in the SMAD6 gene, encoding a protein negatively controlling transforming growth factor β/bone morphogenetic protein (TGFB/BMP) signaling, has been described in association with a wide spectrum of congenital heart defects. We dissected the contribution of individual variants to the complex clinical manifestations and profiled a previously unappreciated set of facial features and signs characterizing IDDSADF. Conclusions, two concomitant truncating variants in CNOT3 and SMAD6 are the cause of the combination of features documented in the patient resulting in the unique multisystem neurodevelopmental condition. These findings provide evidence for a functional link between the CCR4-NOT complex and TGFB/BMP signaling in processes controlling cardiac development. Finally, the present revision provides evidence that IDDSADF is characterized by a distinctive facial gestalt.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Francesca Pantaleoni
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Emilio Africa
- UOC di Neuroradiologia, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy;
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
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28
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Leoni C, Tedesco M, Radio FC, Chillemi G, Leone A, Bruselles A, Ciolfi A, Stellacci E, Pantaleoni F, Butera G, Rigante D, Onesimo R, Tartaglia M, Zampino G. Broadening the phenotypic spectrum of Beta3GalT6-associated phenotypes. Am J Med Genet A 2021; 185:3153-3160. [PMID: 34159694 DOI: 10.1002/ajmg.a.62399] [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: 02/11/2021] [Revised: 04/27/2021] [Accepted: 06/05/2021] [Indexed: 11/11/2022]
Abstract
Biallelic mutations in B3GALT6, coding for a galactosyltransferase involved in the synthesis of glycosaminoglycans (GAGs), have been associated with various clinical conditions, causing spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMDJL1 or SEMDJL Beighton type), Al-Gazali syndrome (ALGAZ), and a severe progeroid form of Ehlers-Danlos syndrome (EDSSPD2). In the 2017 Ehlers-Danlos syndrome (EDS) classification, Beta3GalT6-related disorders were grouped in the spondylodysplastic EDSs together with spondylodysplastic EDSs due to B4GALT7 and SLC39A13 mutations. Herein, we describe a patient with a previously unreported homozygous pathogenic B3GALT6 variant resulting in a complex phenotype more severe than spondyloepimetaphyseal dysplasia with joint laxity type 1, and having dural ectasia and aortic dilation as additionally associated features, further broadening the phenotypic spectrum of the Beta3GalT6-related syndromes. We also document the utility of repeating sequencing in patients with uninformative exomes, particularly when performed by using "first generations" enrichment capture methods.
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Affiliation(s)
- Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Marta Tedesco
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Dipartimento di Scienze Della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Chillemi
- Dipartimento per la Innovazione Nei Sistemi Biologici, Agroalimentari e Forestali, Università Della Tuscia, Viterbo, Italy.,Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Centro Nazionale Delle Ricerche, Bari, Italy
| | - Antonio Leone
- Dipartimento di Scienze Della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze Radiologiche ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Emilia Stellacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Gianfranco Butera
- Department of Pediatric Cardiology, Cardiac Surgery and Heart Lung Transplantation, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Donato Rigante
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Dipartimento di Scienze Della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roberta Onesimo
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Dipartimento di Scienze Della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
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29
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Trimarchi G, Caraffi SG, Radio FC, Barresi S, Contrò G, Pizzi S, Maini I, Pollazzon M, Fusco C, Sassi S, Nicoli D, Napoli M, Pascarella R, Gargano G, Zuffardi O, Tartaglia M, Garavelli L. Adducted Thumb and Peripheral Polyneuropathy: Diagnostic Supports in Suspecting White-Sutton Syndrome: Case Report and Review of the Literature. Genes (Basel) 2021; 12:genes12070950. [PMID: 34206215 PMCID: PMC8303405 DOI: 10.3390/genes12070950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/04/2021] [Accepted: 06/19/2021] [Indexed: 01/01/2023] Open
Abstract
One of the recently described syndromes emerging from the massive study of cohorts of undiagnosed patients with autism spectrum disorders (ASD) and syndromic intellectual disability (ID) is White–Sutton syndrome (WHSUS) (MIM #616364), caused by variants in the POGZ gene (MIM *614787), located on the long arm of chromosome 1 (1q21.3). So far, more than 50 individuals have been reported worldwide, although phenotypic features and natural history have not been exhaustively characterized yet. The phenotypic spectrum of the WHSUS is broad and includes moderate to severe ID, microcephaly, variable cerebral malformations, short stature, brachydactyly, visual abnormalities, sensorineural hearing loss, hypotonia, sleep difficulties, autistic features, self-injurious behaviour, feeding difficulties, gastroesophageal reflux, and other less frequent features. Here, we report the case of a girl with microcephaly, brain malformations, developmental delay (DD), peripheral polyneuropathy, and adducted thumb—a remarkable clinical feature in the first years of life—and heterozygous for a previously unreported, de novo splicing variant in POGZ. This report contributes to strengthen and expand the knowledge of the clinical spectrum of WHSUS, pointing out the importance of less frequent clinical signs as diagnostic handles in suspecting this condition.
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Affiliation(s)
- Gabriele Trimarchi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.T.); (S.G.C.); (G.C.); (M.P.)
| | - Stefano Giuseppe Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.T.); (S.G.C.); (G.C.); (M.P.)
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.B.); (S.P.)
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.B.); (S.P.)
| | - Gianluca Contrò
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.T.); (S.G.C.); (G.C.); (M.P.)
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.B.); (S.P.)
| | - Ilenia Maini
- Unità Operativa di Psichiatria e Psicologia dell’Infanzia e dell’Adolescenza, DAI-SMDP, AUSL Parma, 43121 Parma, Italy;
| | - Marzia Pollazzon
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.T.); (S.G.C.); (G.C.); (M.P.)
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Silvia Sassi
- Rehabilitation Pediatric Unit, Azienda USL-IRCCS of Reggio Emilia, 42123 Reggio Emilia, Italy; (S.S.); (M.T.)
| | - Davide Nicoli
- Molecular Biology Laboratory, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Manuela Napoli
- Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (M.N.); (R.P.)
| | - Rosario Pascarella
- Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (M.N.); (R.P.)
| | - Giancarlo Gargano
- Neonatal Intensive Care Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Orsetta Zuffardi
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy;
| | - Marco Tartaglia
- Rehabilitation Pediatric Unit, Azienda USL-IRCCS of Reggio Emilia, 42123 Reggio Emilia, Italy; (S.S.); (M.T.)
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (G.T.); (S.G.C.); (G.C.); (M.P.)
- Correspondence: ; Tel.: +39-0522-296244
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Pavinato L, Nematian-Ardestani E, Zonta A, De Rubeis S, Buxbaum J, Mancini C, Bruselles A, Tartaglia M, Pessia M, Tucker SJ, D’Adamo MC, Brusco A. KCNK18 Biallelic Variants Associated with Intellectual Disability and Neurodevelopmental Disorders Alter TRESK Channel Activity. Int J Mol Sci 2021; 22:ijms22116064. [PMID: 34199759 PMCID: PMC8200030 DOI: 10.3390/ijms22116064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
The TWIK-related spinal cord potassium channel (TRESK) is encoded by KCNK18, and variants in this gene have previously been associated with susceptibility to familial migraine with aura (MIM #613656). A single amino acid substitution in the same protein, p.Trp101Arg, has also been associated with intellectual disability (ID), opening the possibility that variants in this gene might be involved in different disorders. Here, we report the identification of KCNK18 biallelic missense variants (p.Tyr163Asp and p.Ser252Leu) in a family characterized by three siblings affected by mild-to-moderate ID, autism spectrum disorder (ASD) and other neurodevelopment-related features. Functional characterization of the variants alone or in combination showed impaired channel activity. Interestingly, Ser252 is an important regulatory site of TRESK, suggesting that alteration of this residue could lead to additive downstream effects. The functional relevance of these mutations and the observed co-segregation in all the affected members of the family expand the clinical variability associated with altered TRESK function and provide further insight into the relationship between altered function of this ion channel and human disease.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
- Center for Molecular Medicine Cologne, Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Ehsan Nematian-Ardestani
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD-2080 Msida, Malta; (E.N.-A.); (M.P.)
| | - Andrea Zonta
- Unit of Medical Genetics, “Città della Salute e della Scienza” University Hospital, 10126 Turin, Italy;
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (S.D.R.); (J.B.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (S.D.R.); (J.B.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (C.M.); (M.T.)
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (C.M.); (M.T.)
| | - Mauro Pessia
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD-2080 Msida, Malta; (E.N.-A.); (M.P.)
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 4BH, UK;
| | - Maria Cristina D’Adamo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD-2080 Msida, Malta; (E.N.-A.); (M.P.)
- Correspondence: (M.C.D.); (A.B.)
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
- Unit of Medical Genetics, “Città della Salute e della Scienza” University Hospital, 10126 Turin, Italy;
- Correspondence: (M.C.D.); (A.B.)
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Abstract
In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome-nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. In this review, we provide a summary of recent progress on the structure of chromatin fibers in vitro and in the nucleus, highlight studies on the dynamic regulation of chromatin fibers, and discuss their related biological functions and abnormal organization in diseases.
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Affiliation(s)
- Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China; .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Wei Li
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; .,Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; .,University of Chinese Academy of Sciences, Beijing 100049, China
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de Lima Camillo LP, Quinlan RBA. A ride through the epigenetic landscape: aging reversal by reprogramming. GeroScience 2021; 43:463-485. [PMID: 33825176 PMCID: PMC8110674 DOI: 10.1007/s11357-021-00358-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Aging has become one of the fastest-growing research topics in biology. However, exactly how the aging process occurs remains unknown. Epigenetics plays a significant role, and several epigenetic interventions can modulate lifespan. This review will explore the interplay between epigenetics and aging, and how epigenetic reprogramming can be harnessed for age reversal. In vivo partial reprogramming holds great promise as a possible therapy, but several limitations remain. Rejuvenation by reprogramming is a young but rapidly expanding subfield in the biology of aging.
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Pavinato L, Trajkova S, Grosso E, Giorgio E, Bruselles A, Radio FC, Pippucci T, Dimartino P, Tartaglia M, Petlichkovski A, De Rubeis S, Buxbaum J, Ferrero GB, Keller R, Brusco A. Expanding the clinical phenotype of the ultra-rare Skraban-Deardorff syndrome: Two novel individuals with WDR26 loss-of-function variants and a literature review. Am J Med Genet A 2021; 185:1712-1720. [PMID: 33675273 DOI: 10.1002/ajmg.a.62157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/23/2022]
Abstract
De novo variants in the WDR26 gene leading to haploinsufficiency have recently been associated with Skraban-Deardorff syndrome. This condition is an ultra-rare autosomal dominant neurodevelopmental disorder characterized by a broad range of clinical signs, including intellectual disability (ID), developmental delay (DD), seizures, abnormal facial features, feeding difficulties, and minor skeletal anomalies. Currently, 18 cases have been reported in the literature and for only 15 of them a clinical description is available. Here, we describe a child with Skraban-Deardorff syndrome associated with the WDR26 pathogenic de novo variant NM_025160.6:c.69dupC, p.(Gly24ArgfsTer48), and an adult associated with the pathogenic de novo variant c.1076G > A, p.(Trp359Ter). The adult patient was a 29-year-old female with detailed information on clinical history and pharmacological treatments since birth, providing an opportunity to map disease progression and patient management. By comparing our cases with published reports of Skraban-Deardorff syndrome, we provide a genetic and clinical summary of this ultrarare condition, describe the clinical management from childhood to adult age, and further expand on the clinical phenotype.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, Turin, Italy.,Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Enrico Grosso
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Tommaso Pippucci
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Aleksandar Petlichkovski
- Institute for Immunobiology and Human Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje, Macedonia
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joseph Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giovanni Battista Ferrero
- Department of Clinical and Biological Sciences, School of Medicine, University of Turin, Orbassano, Torino, Italy
| | - Roberto Keller
- Adult autism center, Mental Health Department, Local Health Unit ASL Città di Torino, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
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Etanercept as a successful therapy in autoinflammatory syndrome related to TRNT1 mutations: a case-based review. Clin Rheumatol 2021; 40:4341-4348. [PMID: 33646446 DOI: 10.1007/s10067-021-05653-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 01/31/2021] [Accepted: 02/14/2021] [Indexed: 10/22/2022]
Abstract
Mutations in the gene encoding tRNA nucleotidyltransferase 1 (TRNT1) are associated with heterogeneous phenotypes and multisystem involvement of variable severity and progression. Immunodeficiency and inflammation are recurrent-associated features. The use of cytokine inhibitors in suppressing the inflammatory phenotype has been recently reported, with a 3-year follow-up for patients treated with Etanercept. We report on two unrelated patients sharing the same clinical condition, who had been referred to our Pediatric Rheumatology Unit because of recurrent fever associated with cutaneous lesions and increased levels of inflammatory markers since their first months of life. Whole exome sequencing allowed to identify compound heterozygosity for functionally relevant variants in TRNT1 as the only molecular event shared by the two patients. Both patients have been treated with Etanercept during 11 years, documenting normalization of inflammatory indexes and resolution of recurrent fever and associated symptoms. This is the longest follow-up assessment of Etanercept treatment in patients with TRNT1 mutations. Our findings confirm efficacy and safety of the treatment. Key Points • Mutations in TRNT1 have been associated with phenotypic heterogeneity. • We report on two patients with early-onset autoinflammatory syndrome. • Whole exome sequencing led to reveal compound heterozygosity for two variants in TRNT1 in both patients. • The patients were successfully treated with Etanercept for more than 10 years, the longest follow-up described in literature.
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35
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Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell 2021; 81:166-182.e6. [PMID: 33238161 PMCID: PMC7796963 DOI: 10.1016/j.molcel.2020.10.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/21/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022]
Abstract
The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Tara Fox
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Htet Khant
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Natalia de Val
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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36
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Jena SR, Nayak J, Kumar S, Kar S, Dixit A, Samanta L. Paternal contributors in recurrent pregnancy loss: Cues from comparative proteome profiling of seminal extracellular vesicles. Mol Reprod Dev 2020; 88:96-112. [PMID: 33345401 DOI: 10.1002/mrd.23445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 11/04/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022]
Abstract
Recent evidence entail paternal factors as plausible contributors in spontaneous recurrent pregnancy loss (RPL). Seminal extracellular vesicles secreted from cells of male reproductive tract carry regulatory proteins and RNAs. They are proposed to regulate sperm maturation and function while their fusion to endometrial stromal cells helps in decidualization. Nevertheless, the mechanism(s) involved in these processes are poorly understood. This study aims at elucidating the molecular basis of paternal contribution by comparative proteomics (label-free LC-MS/MS) of isolated seminal extracellular vesicles from fertile men and partners of patients with RPL (n = 21 per group). Bioinformatics analysis revealed the identified differentially expressed proteins to be involved in DNA replication, recombination and repair, gene expression, cellular assembly and organization, cell death, and survival. Major disease pathways affected were identified as developmental, hereditary, and immunological disorders. Of the three identified hub genes regulating the above disease pathways, two (HNRNPC and HNRNPU) are overexpressed while RUVBL1 is underexpressed along with over expression of HIST1H1C, DDX1, surmising defective chromatin packaging, and histone removal in spermatozoa resulting in improper expression in paternal genes thereby leading to abnormal embryo development. Besides, alteration in GSTP1 expression points oxidative predominance in RPL group. Differential expression of C3, C4a/C4b, CFB, and GDF 15 may be involved in altered maternal immune response to paternal antigens resulting in impaired decidualization.
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Affiliation(s)
- Soumya R Jena
- Department of Zoology, Redox Biology Laboratory, School of Life Sciences, Ravenshaw University, Odisha, India.,Centre for Excellence in Environment and Public Health, Ravenshaw University, Odisha, India
| | - Jasmine Nayak
- Department of Zoology, Redox Biology Laboratory, School of Life Sciences, Ravenshaw University, Odisha, India.,Centre for Excellence in Environment and Public Health, Ravenshaw University, Odisha, India
| | - Sugandh Kumar
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Sujata Kar
- Department of Obstetrics & Gynaecology, Kar Clinic and Hospital Pvt. Ltd., Bhubaneswar, India
| | - Anshuman Dixit
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Luna Samanta
- Department of Zoology, Redox Biology Laboratory, School of Life Sciences, Ravenshaw University, Odisha, India.,Centre for Excellence in Environment and Public Health, Ravenshaw University, Odisha, India
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37
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Polovitskaya MM, Barbini C, Martinelli D, Harms FL, Cole FS, Calligari P, Bocchinfuso G, Stella L, Ciolfi A, Niceta M, Rizza T, Shinawi M, Sisco K, Johannsen J, Denecke J, Carrozzo R, Wegner DJ, Kutsche K, Tartaglia M, Jentsch TJ. A Recurrent Gain-of-Function Mutation in CLCN6, Encoding the ClC-6 Cl -/H +-Exchanger, Causes Early-Onset Neurodegeneration. Am J Hum Genet 2020; 107:1062-1077. [PMID: 33217309 PMCID: PMC7820737 DOI: 10.1016/j.ajhg.2020.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022] Open
Abstract
Dysfunction of the endolysosomal system is often associated with neurodegenerative disease because postmitotic neurons are particularly reliant on the elimination of intracellular aggregates. Adequate function of endosomes and lysosomes requires finely tuned luminal ion homeostasis and transmembrane ion fluxes. Endolysosomal CLC Cl-/H+ exchangers function as electric shunts for proton pumping and in luminal Cl- accumulation. We now report three unrelated children with severe neurodegenerative disease, who carry the same de novo c.1658A>G (p.Tyr553Cys) mutation in CLCN6, encoding the late endosomal Cl-/H+-exchanger ClC-6. Whereas Clcn6-/- mice have only mild neuronal lysosomal storage abnormalities, the affected individuals displayed severe developmental delay with pronounced generalized hypotonia, respiratory insufficiency, and variable neurodegeneration and diffusion restriction in cerebral peduncles, midbrain, and/or brainstem in MRI scans. The p.Tyr553Cys amino acid substitution strongly slowed ClC-6 gating and increased current amplitudes, particularly at the acidic pH of late endosomes. Transfection of ClC-6Tyr553Cys, but not ClC-6WT, generated giant LAMP1-positive vacuoles that were poorly acidified. Their generation strictly required ClC-6 ion transport, as shown by transport-deficient double mutants, and depended on Cl-/H+ exchange, as revealed by combination with the uncoupling p.Glu200Ala substitution. Transfection of either ClC-6Tyr553Cys/Glu200Ala or ClC-6Glu200Ala generated slightly enlarged vesicles, suggesting that p.Glu200Ala, previously associated with infantile spasms and microcephaly, is also pathogenic. Bafilomycin treatment abrogated vacuole generation, indicating that H+-driven Cl- accumulation osmotically drives vesicle enlargement. Our work establishes mutations in CLCN6 associated with neurological diseases, whose spectrum of clinical features depends on the differential impact of the allele on ClC-6 function.
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Affiliation(s)
- Maya M Polovitskaya
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
| | - Carlo Barbini
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
| | - Diego Martinelli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Frederike L Harms
- Institute for Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - F Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, and St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University "Tor Vergata," 00133 Rome, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University "Tor Vergata," 00133 Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University "Tor Vergata," 00133 Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Teresa Rizza
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, and St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - Kathleen Sisco
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, and St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - Jessika Johannsen
- Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Rosalba Carrozzo
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Daniel J Wegner
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, and St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - Kerstin Kutsche
- Institute for Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
| | - Thomas J Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany; NeuroCure Cluster of Excellence, Charité Universitätsmedizin, 10117 Berlin, Germany.
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38
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Rodger C, Flex E, Allison RJ, Sanchis-Juan A, Hasenahuer MA, Cecchetti S, French CE, Edgar JR, Carpentieri G, Ciolfi A, Pantaleoni F, Bruselles A, Onesimo R, Zampino G, Marcon F, Siniscalchi E, Lees M, Krishnakumar D, McCann E, Yosifova D, Jarvis J, Kruer MC, Marks W, Campbell J, Allen LE, Gustincich S, Raymond FL, Tartaglia M, Reid E. De Novo VPS4A Mutations Cause Multisystem Disease with Abnormal Neurodevelopment. Am J Hum Genet 2020; 107:1129-1148. [PMID: 33186545 PMCID: PMC7820634 DOI: 10.1016/j.ajhg.2020.10.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022] Open
Abstract
The endosomal sorting complexes required for transport (ESCRTs) are essential for multiple membrane modeling and membrane-independent cellular processes. Here we describe six unrelated individuals with de novo missense variants affecting the ATPase domain of VPS4A, a critical enzyme regulating ESCRT function. Probands had structural brain abnormalities, severe neurodevelopmental delay, cataracts, growth impairment, and anemia. In cultured cells, overexpression of VPS4A mutants caused enlarged endosomal vacuoles resembling those induced by expression of known dominant-negative ATPase-defective forms of VPS4A. Proband-derived fibroblasts had enlarged endosomal structures with abnormal accumulation of the ESCRT protein IST1 on the limiting membrane. VPS4A function was also required for normal endosomal morphology and IST1 localization in iPSC-derived human neurons. Mutations affected other ESCRT-dependent cellular processes, including regulation of centrosome number, primary cilium morphology, nuclear membrane morphology, chromosome segregation, mitotic spindle formation, and cell cycle progression. We thus characterize a distinct multisystem disorder caused by mutations affecting VPS4A and demonstrate that its normal function is required for multiple human developmental and cellular processes.
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Affiliation(s)
- Catherine Rodger
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Rachel J Allison
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alba Sanchis-Juan
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0XY, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Marcia A Hasenahuer
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK; European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Serena Cecchetti
- Microscopy Area, Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Courtney E French
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Giovanna Carpentieri
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00161, Italy; Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Roberta Onesimo
- Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome 00168, Italy
| | - Giuseppe Zampino
- Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome 00168, Italy; Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Francesca Marcon
- Unit of Mechanisms, Biomarkers and Models, Department of Environment and Health, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Ester Siniscalchi
- Unit of Mechanisms, Biomarkers and Models, Department of Environment and Health, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Melissa Lees
- Department of Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Deepa Krishnakumar
- Department of Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Emma McCann
- Department of Clinical Genetics, Liverpool Women's Hospital, Liverpool L8 7SS, UK
| | - Dragana Yosifova
- Department of Medical Genetics, Guys' and St Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Joanna Jarvis
- Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham B15 2TG, UK
| | | | - Warren Marks
- Cook Children's Medical Centre, Fort Worth, TX 76104, USA
| | - Jonathan Campbell
- Colchester Hospital, East Suffolk and North Essex NHS Foundation Trust, Essex CO4 5JL, UK
| | - Louise E Allen
- Ophthalmology Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova 16163, Italy; Area of Neuroscience, SISSA, Trieste 34136, Italy
| | - F Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.
| | - Evan Reid
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK.
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39
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Benetti E, Tita R, Spiga O, Ciolfi A, Birolo G, Bruselles A, Doddato G, Giliberti A, Marconi C, Musacchia F, Pippucci T, Torella A, Trezza A, Valentino F, Baldassarri M, Brusco A, Asselta R, Bruttini M, Furini S, Seri M, Nigro V, Matullo G, Tartaglia M, Mari F, Renieri A, Pinto AM. ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population. Eur J Hum Genet 2020; 28:1602-1614. [PMID: 32681121 PMCID: PMC7366459 DOI: 10.1038/s41431-020-0691-z] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/01/2020] [Accepted: 06/30/2020] [Indexed: 11/17/2022] Open
Abstract
In December 2019, an initial cluster of interstitial bilateral pneumonia emerged in Wuhan, China. A human-to-human transmission was assumed and a previously unrecognized entity, termed coronavirus disease-19 (COVID-19) due to a novel coronavirus (SARS-CoV-2) was described. The infection has rapidly spread out all over the world and Italy has been the first European country experiencing the endemic wave with unexpected clinical severity in comparison with Asian countries. It has been shown that SARS-CoV-2 utilizes angiotensin converting enzyme 2 (ACE2) as host receptor and host proteases for cell surface binding and internalization. Thus, a predisposing genetic background can give reason for interindividual disease susceptibility and/or severity. Taking advantage of the Network of Italian Genomes (NIG), here we mined whole-exome sequencing data of 6930 Italian control individuals from five different centers looking for ACE2 variants. A number of variants with a potential impact on protein stability were identified. Among these, three more common missense changes, p.(Asn720Asp), p.(Lys26Arg), and p.(Gly211Arg) were predicted to interfere with protein structure and stabilization. Rare variants likely interfering with the internalization process, namely p.(Leu351Val) and p.(Pro389His), predicted to interfere with SARS-CoV-2 spike protein binding, were also observed. Comparison of ACE2 WES data between a cohort of 131 patients and 258 controls allowed identifying a statistically significant (P value < 0.029) higher allelic variability in controls compared with patients. These findings suggest that a predisposing genetic background may contribute to the observed interindividual clinical variability associated with COVID-19, allowing an evidence-based risk assessment leading to personalized preventive measures and therapeutic options.
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Affiliation(s)
- Elisa Benetti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Caterina Marconi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | | | - Annalaura Torella
- Dipartimento di Medicina di Precisione, Università della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy
- Genetica Medica, Città della Salute e della Scienza, Torino, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Mirella Bruttini
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Seri
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Dipartimento di Medicina di Precisione, Università della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- Genetica Medica, Città della Salute e della Scienza, Torino, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Francesca Mari
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
- Medical Genetics, University of Siena, Siena, Italy.
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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40
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Schnabel F, Kornak U, Wollnik B. Premature aging disorders: A clinical and genetic compendium. Clin Genet 2020; 99:3-28. [PMID: 32860237 DOI: 10.1111/cge.13837] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022]
Abstract
Progeroid disorders make up a heterogeneous group of very rare hereditary diseases characterized by clinical signs that often mimic physiological aging in a premature manner. Apart from Hutchinson-Gilford progeria syndrome, one of the best-investigated progeroid disorders, a wide spectrum of other premature aging phenotypes exist, which differ significantly in their clinical presentation and molecular pathogenesis. Next-generation sequencing (NGS)-based approaches have made it feasible to determine the molecular diagnosis in the early stages of a disease. Nevertheless, a broad clinical knowledge on these disorders and their associated symptoms is still fundamental for a comprehensive patient management and for the interpretation of variants of unknown significance from NGS data sets. This review provides a detailed overview on characteristic clinical features and underlying molecular genetics of well-known as well as only recently identified premature aging disorders and also highlights novel findings towards future therapeutic options.
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Affiliation(s)
- Franziska Schnabel
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany
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41
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Motta M, Pannone L, Pantaleoni F, Bocchinfuso G, Radio FC, Cecchetti S, Ciolfi A, Di Rocco M, Elting MW, Brilstra EH, Boni S, Mazzanti L, Tamburrino F, Walsh L, Payne K, Fernández-Jaén A, Ganapathi M, Chung WK, Grange DK, Dave-Wala A, Reshmi SC, Bartholomew DW, Mouhlas D, Carpentieri G, Bruselles A, Pizzi S, Bellacchio E, Piceci-Sparascio F, Lißewski C, Brinkmann J, Waclaw RR, Waisfisz Q, van Gassen K, Wentzensen IM, Morrow MM, Álvarez S, Martínez-García M, De Luca A, Memo L, Zampino G, Rossi C, Seri M, Gelb BD, Zenker M, Dallapiccola B, Stella L, Prada CE, Martinelli S, Flex E, Tartaglia M. Enhanced MAPK1 Function Causes a Neurodevelopmental Disorder within the RASopathy Clinical Spectrum. Am J Hum Genet 2020; 107:499-513. [PMID: 32721402 DOI: 10.1016/j.ajhg.2020.06.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/24/2020] [Indexed: 12/23/2022] Open
Abstract
Signal transduction through the RAF-MEK-ERK pathway, the first described mitogen-associated protein kinase (MAPK) cascade, mediates multiple cellular processes and participates in early and late developmental programs. Aberrant signaling through this cascade contributes to oncogenesis and underlies the RASopathies, a family of cancer-prone disorders. Here, we report that de novo missense variants in MAPK1, encoding the mitogen-activated protein kinase 1 (i.e., extracellular signal-regulated protein kinase 2, ERK2), cause a neurodevelopmental disease within the RASopathy phenotypic spectrum, reminiscent of Noonan syndrome in some subjects. Pathogenic variants promote increased phosphorylation of the kinase, which enhances translocation to the nucleus and boosts MAPK signaling in vitro and in vivo. Two variant classes are identified, one of which directly disrupts binding to MKP3, a dual-specificity protein phosphatase negatively regulating ERK function. Importantly, signal dysregulation driven by pathogenic MAPK1 variants is stimulus reliant and retains dependence on MEK activity. Our data support a model in which the identified pathogenic variants operate with counteracting effects on MAPK1 function by differentially impacting the ability of the kinase to interact with regulators and substrates, which likely explains the minor role of these variants as driver events contributing to oncogenesis. After nearly 20 years from the discovery of the first gene implicated in Noonan syndrome, PTPN11, the last tier of the MAPK cascade joins the group of genes mutated in RASopathies.
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42
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Rigante D, Stellacci E, Leoni C, Onesimo R, Radio FC, Pizzi S, Giorgio V, Tornesello A, Tartaglia M, Zampino G. Biallelic TRNT1 variants in a child with B cell immunodeficiency, periodic fever and developmental delay without sideroblastic anemia (SIFD variant). Immunol Lett 2020; 225:64-65. [PMID: 32592741 DOI: 10.1016/j.imlet.2020.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 10/24/2022]
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43
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Alzoubi H, Gianno F, Giangaspero F, Bartolini D, Riccioni L, Miele E, Antonelli M. Dural-based atypical teratoid/rhabdoid tumor in an adult: DNA methylation profiling as a tool for the diagnosis. CNS Oncol 2020; 9:CNS54. [PMID: 32602741 PMCID: PMC7341157 DOI: 10.2217/cns-2020-0006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Atypical teratoid/rhabdoid tumor (ATRT) is a malignant CNS embryonal tumor that mostly occurs in childhood, adult cases are rare. We report a case of a 23-year-old male with an extra-axial dura-based lesion in the left frontal area, previously diagnosed as gliosarcoma. After 6 years, the patient had a recurrence and the previous slides were reviewed. Tumor was positive for vimentin and negative for INI1. The differential diagnosis for this extra-axial tumor with long survival was rhabdoid meningioma with INI1 loss or ATRT. DNA methylation profiling was performed to reach the final and the most definitive diagnosis; the result was ATRT. Our case suggests the usefulness of DNA methylation profiling for diagnosing challenging CNS tumors.
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Affiliation(s)
- Hiba Alzoubi
- Department of Basic Medical Sciences, Faculty of medicine, Yarmouk University, Irbid, Jordan.,Department of Radiological, Oncological & Anatomopathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological & Anatomopathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological & Anatomopathological Sciences, Sapienza University of Rome, Rome, Italy.,IRCCS Neuromed-Mediterranean Neurological Institute, Pozzilli, Italy
| | | | - Luca Riccioni
- Department of Pathology, Bufalini Hospital, Cesena, Italy
| | - Evelina Miele
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Manila Antonelli
- Department of Radiological, Oncological & Anatomopathological Sciences, Sapienza University of Rome, Rome, Italy
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44
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Miele E, De Vito R, Ciolfi A, Pedace L, Russo I, De Pasquale MD, Di Giannatale A, Crocoli A, Angelis BD, Tartaglia M, Alaggio R, Milano GM. DNA Methylation Profiling for Diagnosing Undifferentiated Sarcoma with Capicua Transcriptional Receptor ( CIC) Alterations. Int J Mol Sci 2020; 21:ijms21051818. [PMID: 32155762 PMCID: PMC7084764 DOI: 10.3390/ijms21051818] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/15/2020] [Accepted: 03/03/2020] [Indexed: 12/31/2022] Open
Abstract
Undifferentiated soft tissue sarcomas are a group of diagnostically challenging tumors in the pediatric population. Molecular techniques are instrumental for the categorization and differential diagnosis of these tumors. A subgroup of recently identified soft tissue sarcomas with undifferentiated round cell morphology was characterized by Capicua transcriptional receptor (CIC) rearrangements. Recently, an array-based DNA methylation analysis of undifferentiated tumors with small blue round cell histology was shown to provide a highly robust and reproducible approach for precisely classifying this diagnostically challenging group of tumors. We describe the case of an undifferentiated sarcoma of the abdominal wall in a 12-year-old girl. The patient presented with a voluminous mass of the abdominal wall, and multiple micro-nodules in the right lung. The tumor was unclassifiable with current immunohistochemical and molecular approaches. However, DNA methylation profiling allowed us to classify this neoplasia as small blue round cell tumor with CIC alterations. The patient was treated with neoadjuvant chemotherapy followed by complete surgical resection and adjuvant chemotherapy. After 22 months, the patient is disease-free and in good clinical condition. To put our experience in context, we conducted a literature review, analyzing current knowledge and state-of-the-art diagnosis, prognosis, and clinical management of CIC rearranged sarcomas. Our findings further support the use of DNA methylation profiling as an important tool to improve diagnosis of non-Ewing small round cell tumors.
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Affiliation(s)
- Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
- Correspondence:
| | - Rita De Vito
- Department of Laboratories, Pathology Unit, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (R.D.V.); (R.A.)
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.C.); (M.T.)
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Ida Russo
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Maria Debora De Pasquale
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Angela Di Giannatale
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Alessandro Crocoli
- Department of Surgery, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy;
| | - Biagio De Angelis
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.C.); (M.T.)
| | - Rita Alaggio
- Department of Laboratories, Pathology Unit, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (R.D.V.); (R.A.)
| | - Giuseppe Maria Milano
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
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45
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Ciolfi A, Aref-Eshghi E, Pizzi S, Pedace L, Miele E, Kerkhof J, Flex E, Martinelli S, Radio FC, Ruivenkamp CAL, Santen GWE, Bijlsma E, Barge-Schaapveld D, Ounap K, Siu VM, Kooy RF, Dallapiccola B, Sadikovic B, Tartaglia M. Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature. Clin Epigenetics 2020; 12:7. [PMID: 31910894 PMCID: PMC6947958 DOI: 10.1186/s13148-019-0804-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND We previously associated HIST1H1E mutations causing Rahman syndrome with a specific genome-wide methylation pattern. RESULTS Methylome analysis from peripheral blood samples of six affected subjects led us to identify a specific hypomethylated profile. This "episignature" was enriched for genes involved in neuronal system development and function. A computational classifier yielded full sensitivity and specificity in detecting subjects with Rahman syndrome. Applying this model to a cohort of undiagnosed probands allowed us to reach diagnosis in one subject. CONCLUSIONS We demonstrate an epigenetic signature in subjects with Rahman syndrome that can be used to reach molecular diagnosis.
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Affiliation(s)
- Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5C1, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, Canada
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5C1, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, Canada
| | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Emilia Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Daniela Barge-Schaapveld
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Katrin Ounap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, 50406, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Victoria Mok Siu
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2650, Antwerp, Belgium
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5C1, Canada. .,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, Canada.
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy.
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