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Ryan CW, Regan SL, Mills EF, McGrath BT, Gong E, Lai YT, Sheingold JB, Patel K, Horowitz T, Moccia A, Tsan YC, Srivastava A, Bielas SL. RING1 missense variants reveal sensitivity of DNA damage repair to H2A monoubiquitination dosage during neurogenesis. Nat Commun 2024; 15:7931. [PMID: 39256363 PMCID: PMC11387726 DOI: 10.1038/s41467-024-52292-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/30/2024] [Indexed: 09/12/2024] Open
Abstract
Polycomb repressive complex 1 (PRC1) modifies chromatin through catalysis of histone H2A lysine 119 monoubiquitination (H2AK119ub1). RING1 and RNF2 interchangeably serve as the catalytic subunit within PRC1. Pathogenic missense variants in PRC1 core components reveal functions of these proteins that are obscured in knockout models. While Ring1a knockout models remain healthy, the microcephaly and neuropsychiatric phenotypes associated with a pathogenic RING1 missense variant implicate unappreciated functions. Using an in vitro model of neurodevelopment, we observe that RING1 contributes to the broad placement of H2AK119ub1, and that its targets overlap with those of RNF2. PRC1 complexes harboring hypomorphic RING1 bind target loci but do not catalyze H2AK119ub1, reducing H2AK119ub1 by preventing catalytically active complexes from accessing the locus. This results in delayed DNA damage repair and cell cycle progression in neural progenitor cells (NPCs). Conversely, reduced H2AK119ub1 due to hypomorphic RING1 does not generate differential expression that impacts NPC differentiation. In contrast, hypomorphic RNF2 generates a greater reduction in H2AK119ub1 that results in both delayed DNA repair and widespread transcriptional changes. These findings suggest that the DNA damage response is more sensitive to H2AK119ub1 dosage change than is regulation of gene expression.
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Affiliation(s)
- C W Ryan
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
- Medical Science Training Program, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - S L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - E F Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - B T McGrath
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - E Gong
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Y T Lai
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - J B Sheingold
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - K Patel
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - T Horowitz
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - A Moccia
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Y C Tsan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - A Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Department of Medical Genetics, Lucknow, India
| | - S L Bielas
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Kannan B, Jayaseelan VP, Arumugam P, Navamani HK, Dv L. Biallelic loss-of-function variations in BTD cause profound biotinidase deficiency in an Indian patient. Mol Biol Rep 2024; 51:900. [PMID: 39120718 DOI: 10.1007/s11033-024-09827-5] [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: 05/20/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Biotinidase deficiency (BD) is a rare, autosomal recessive metabolic disorder characterized by neurocutaneous symptoms. This study investigates a case of profound BD in an Indian infant and the underlying genetic basis. METHODS A 10-month-old male presenting with seizures, hypotonia, ataxia, visual impairments, and developmental delay underwent biochemical and genetic analysis. Biotinidase activity was measured using an ELISA kit. Sanger sequencing of the biotinidase (BTD) gene was performed to identify genetic variations. In silico analysis was employed to assess the potential impact of the identified variants. RESULTS The infant biotinidase activity was undetectable and its suggest profound biotinidase deficiency. Novel biallelic loss-of-function variations (c.903G > A and c.946 C > T) in the BTD gene were identified, leading to premature stop codons and truncated, non-functional protein fragments. CONCLUSION This case expands our knowledge of BD genetic diversity and underscores the critical role of early diagnosis and newborn screening programs in managing this treatable condition.
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Affiliation(s)
- Balachander Kannan
- Molecular Biology Laboratory, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, TN, India
| | - Vijayashree Priyadharsini Jayaseelan
- Clinical Genetics Laboratory, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, TN, India
| | - Paramasivam Arumugam
- Molecular Biology Laboratory, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, TN, India.
| | - Hephzibah Kirubamani Navamani
- Department of Obstetrics and Gynecology, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Medical College and Hospital, Saveetha University, Chennai, 602 105, TN, India
| | - Lal Dv
- Department of Pediatrics, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 602 105, TN, India
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3
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Ghasemi MR, Sadeghi H, Hashemi-Gorji F, Mirfakhraie R, Gupta V, Ben-Mahmoud A, Bagheri S, Razjouyan K, Salehpour S, Tonekaboni SH, Dianatpour M, Omrani D, Jang MH, Layman LC, Miryounesi M, Kim HG. Exome sequencing reveals neurodevelopmental genes in simplex consanguineous Iranian families with syndromic autism. BMC Med Genomics 2024; 17:196. [PMID: 39103847 DOI: 10.1186/s12920-024-01969-6] [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: 05/16/2023] [Accepted: 07/23/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Autosomal recessive genetic disorders pose significant health challenges in regions where consanguineous marriages are prevalent. The utilization of exome sequencing as a frequently employed methodology has enabled a clear delineation of diagnostic efficacy and mode of inheritance within multiplex consanguineous families. However, these aspects remain less elucidated within simplex families. METHODS In this study involving 12 unrelated simplex Iranian families presenting syndromic autism, we conducted singleton exome sequencing. The identified genetic variants were validated using Sanger sequencing, and for the missense variants in FOXG1 and DMD, 3D protein structure modeling was carried out to substantiate their pathogenicity. To examine the expression patterns of the candidate genes in the fetal brain, adult brain, and muscle, RT-qPCR was employed. RESULTS In four families, we detected an autosomal dominant gene (FOXG1), an autosomal recessive gene (CHKB), and two X-linked autism genes (IQSEC2 and DMD), indicating diverse inheritance patterns. In the remaining eight families, we were unable to identify any disease-associated genes. As a result, our variant detection rate stood at 33.3% (4/12), surpassing rates reported in similar studies of smaller cohorts. Among the four newly identified coding variants, three are de novo (heterozygous variant p.Trp546Ter in IQSEC2, heterozygous variant p.Ala188Glu in FOXG1, and hemizygous variant p.Leu211Met in DMD), while the homozygous variant p.Glu128Ter in CHKB was inherited from both healthy heterozygous parents. 3D protein structure modeling was carried out for the missense variants in FOXG1 and DMD, which predicted steric hindrance and spatial inhibition, respectively, supporting the pathogenicity of these human mutants. Additionally, the nonsense variant in CHKB is anticipated to influence its dimerization - crucial for choline kinase function - and the nonsense variant in IQSEC2 is predicted to eliminate three functional domains. Consequently, these distinct variants found in four unrelated individuals with autism are likely indicative of loss-of-function mutations. CONCLUSIONS In our two syndromic autism families, we discovered variants in two muscular dystrophy genes, DMD and CHKB. Given that DMD and CHKB are recognized for their participation in the non-cognitive manifestations of muscular dystrophy, it indicates that some genes transcend the boundary of apparently unrelated clinical categories, thereby establishing a novel connection between ASD and muscular dystrophy. Our findings also shed light on the complex inheritance patterns observed in Iranian consanguineous simplex families and emphasize the connection between autism spectrum disorder and muscular dystrophy. This underscores a likely genetic convergence between neurodevelopmental and neuromuscular disorders.
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Affiliation(s)
- Mohammad-Reza Ghasemi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Saman Bagheri
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Katayoon Razjouyan
- Psychiatric Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shadab Salehpour
- Department of Pediatric Endocrinology & Metabolism, School of Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Hassan Tonekaboni
- Department of Pediatric Neurology, School of Medicine, Pediatric Neurology Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Dianatpour
- Department of Medical Genetics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Davood Omrani
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mi-Hyeon Jang
- Department of Neurosurgery, Robert Wood Johnson Medical School, The State University of New Jersey, Rutgers, Piscataway, NJ, 08854, USA
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hyung-Goo Kim
- Department of Neurosurgery, Robert Wood Johnson Medical School, The State University of New Jersey, Rutgers, Piscataway, NJ, 08854, USA.
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Zhang X, Theotokis PI, Li N, Wright CF, Samocha KE, Whiffin N, Ware JS. Genetic constraint at single amino acid resolution in protein domains improves missense variant prioritisation and gene discovery. Genome Med 2024; 16:88. [PMID: 38992748 PMCID: PMC11238507 DOI: 10.1186/s13073-024-01358-9] [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: 09/18/2023] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND One of the major hurdles in clinical genetics is interpreting the clinical consequences associated with germline missense variants in humans. Recent significant advances have leveraged natural variation observed in large-scale human populations to uncover genes or genomic regions that show a depletion of natural variation, indicative of selection pressure. We refer to this as "genetic constraint". Although existing genetic constraint metrics have been demonstrated to be successful in prioritising genes or genomic regions associated with diseases, their spatial resolution is limited in distinguishing pathogenic variants from benign variants within genes. METHODS We aim to identify missense variants that are significantly depleted in the general human population. Given the size of currently available human populations with exome or genome sequencing data, it is not possible to directly detect depletion of individual missense variants, since the average expected number of observations of a variant at most positions is less than one. We instead focus on protein domains, grouping homologous variants with similar functional impacts to examine the depletion of natural variations within these comparable sets. To accomplish this, we develop the Homologous Missense Constraint (HMC) score. We utilise the Genome Aggregation Database (gnomAD) 125 K exome sequencing data and evaluate genetic constraint at quasi amino-acid resolution by combining signals across protein homologues. RESULTS We identify one million possible missense variants under strong negative selection within protein domains. Though our approach annotates only protein domains, it nonetheless allows us to assess 22% of the exome confidently. It precisely distinguishes pathogenic variants from benign variants for both early-onset and adult-onset disorders. It outperforms existing constraint metrics and pathogenicity meta-predictors in prioritising de novo mutations from probands with developmental disorders (DD). It is also methodologically independent of these, adding power to predict variant pathogenicity when used in combination. We demonstrate utility for gene discovery by identifying seven genes newly significantly associated with DD that could act through an altered-function mechanism. CONCLUSIONS Grouping variants of comparable functional impacts is effective in evaluating their genetic constraint. HMC is a novel and accurate predictor of missense consequence for improved variant interpretation.
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Affiliation(s)
- Xiaolei Zhang
- National Heart & Lung Institute, Imperial College London, London, UK.
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK.
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
- Present address: European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Pantazis I Theotokis
- National Heart & Lung Institute, Imperial College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Nicholas Li
- National Heart & Lung Institute, Imperial College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Kaitlin E Samocha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Whiffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - James S Ware
- National Heart & Lung Institute, Imperial College London, London, UK.
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK.
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Ghaffar A, Akhter T, Strømme P, Misceo D, Khan A, Frengen E, Umair M, Isidor B, Cogné B, Khan AA, Bruel AL, Sorlin A, Kuentz P, Chiaverini C, Innes AM, Zech M, Baláž M, Havrankova P, Jech R, Ahmed ZM, Riazuddin S, Riazuddin S. Variants of NAV3, a neuronal morphogenesis protein, cause intellectual disability, developmental delay, and microcephaly. Commun Biol 2024; 7:831. [PMID: 38977784 PMCID: PMC11231287 DOI: 10.1038/s42003-024-06466-1] [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: 01/04/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
Microtubule associated proteins (MAPs) are widely expressed in the central nervous system, and have established roles in cell proliferation, myelination, neurite formation, axon specification, outgrowth, dendrite, and synapse formation. We report eleven individuals from seven families harboring predicted pathogenic biallelic, de novo, and heterozygous variants in the NAV3 gene, which encodes the microtubule positive tip protein neuron navigator 3 (NAV3). All affected individuals have intellectual disability (ID), microcephaly, skeletal deformities, ocular anomalies, and behavioral issues. In mouse brain, Nav3 is expressed throughout the nervous system, with more prominent signatures in postmitotic, excitatory, inhibiting, and sensory neurons. When overexpressed in HEK293T and COS7 cells, pathogenic variants impaired NAV3 ability to stabilize microtubules. Further, knocking-down nav3 in zebrafish led to severe morphological defects, microcephaly, impaired neuronal growth, and behavioral impairment, which were rescued with co-injection of WT NAV3 mRNA and not by transcripts encoding the pathogenic variants. Our findings establish the role of NAV3 in neurodevelopmental disorders, and reveal its involvement in neuronal morphogenesis, and neuromuscular responses.
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Affiliation(s)
- Amama Ghaffar
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tehmeena Akhter
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Petter Strømme
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Amjad Khan
- Faculty of Biological Sciences, Department of Zoology, University of Lakki Marwat, 28420, Khyber, Pakhtunkhwa, Pakistan
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübinge, 72076, Germany
- Alexander von Humboldt Fellowship Foundation, Berlin, 10117, Germany
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France
| | - Asma A Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ange-Line Bruel
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, Université de Bourgogne Franche-Comté, Dijon, France
| | - Arthur Sorlin
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, Université de Bourgogne Franche-Comté, Dijon, France
- National Center of Genetics (NCG), Laboratoire national de santé (LNS), 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Paul Kuentz
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, Université de Bourgogne Franche-Comté, Dijon, France
| | | | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, D-85748, Garching, Germany
| | - Marek Baláž
- First Department of Neurology, Faculty of Medicine, St. Anne's University Hospital, and CEITEC, Masaryk University, Brno, Czech Republic
| | - Petra Havrankova
- Department of Neurology, Charles University, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Robert Jech
- Department of Neurology, Charles University, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Zubair M Ahmed
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA
| | - Sheikh Riazuddin
- Jinnah Burn and Reconstructive Surgery Centre, Allama Iqbal Medical Research, University of Health Sciences, Lahore, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, USA.
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Kronzer VL, Sparks JA, Raychaudhuri S, Cerhan JR. Low-frequency and rare genetic variants associated with rheumatoid arthritis risk. Nat Rev Rheumatol 2024; 20:290-300. [PMID: 38538758 DOI: 10.1038/s41584-024-01096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 04/28/2024]
Abstract
Rheumatoid arthritis (RA) has an estimated heritability of nearly 50%, which is particularly high in seropositive RA. HLA alleles account for a large proportion of this heritability, in addition to many common single-nucleotide polymorphisms with smaller individual effects. Low-frequency and rare variants, such as those captured by next-generation sequencing, can also have a large role in heritability in some individuals. Rare variant discovery has informed the development of drugs such as inhibitors of PCSK9 and Janus kinases. Some 34 low-frequency and rare variants are currently associated with RA risk. One variant (19:10352442G>C in TYK2) was identified in five separate studies, and might therefore represent a promising therapeutic target. Following a set of best practices in future studies, including studying diverse populations, using large sample sizes, validating RA and serostatus, replicating findings, adjusting for other variants and performing functional assessment, could help to ensure the relevance of identified variants. Exciting opportunities are now on the horizon for genetics in RA, including larger datasets and consortia, whole-genome sequencing and direct applications of findings in the management, and especially treatment, of RA.
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Affiliation(s)
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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Michaels JR, Husami A, Vontell AM, Brugmann SA, Stottmann RW. Genetic Analysis and Functional Assessment of a TGFBR2 Variant in Micrognathia and Cleft Palate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588524. [PMID: 38645005 PMCID: PMC11030355 DOI: 10.1101/2024.04.08.588524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Cleft lip and cleft palate are among the most common congenital anomalies and are the result of incomplete fusion of embryonic craniofacial processes or palatal shelves, respectively. We know that genetics play a large role in these anomalies but the list of known causal genes is far from complete. As part of a larger sequencing effort of patients with micrognathia and cleft palate we identified a candidate variant in transforming growth factor beta receptor 2 ( TGFBR2 ) which is rare, changing a highly conserved amino acid, and predicted to be pathogenic by a number of metrics. The family history and population genetics would suggest this specific variant would be incompletely penetrant, but this gene has been convincingly implicated in craniofacial development. In order to test the hypothesis this might be a causal variant, we used genome editing to create the orthologous variant in a new mouse model. Surprisingly, Tgfbr2 V387M mice did not exhibit craniofacial anomalies or have reduced survival suggesting this is, in fact, not a causal variant for cleft palate/ micrognathia. The discrepancy between in silico predictions and mouse phenotypes highlights the complexity of translating human genetic findings to mouse models. We expect these findings will aid in interpretation of future variants seen in TGFBR2 from ongoing sequencing of patients with congenital craniofacial anomalies.
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8
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MacGowan SA, Madeira F, Britto-Borges T, Barton GJ. A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites. Commun Biol 2024; 7:447. [PMID: 38605212 PMCID: PMC11009406 DOI: 10.1038/s42003-024-06117-5] [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: 07/26/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference. Here, we map 2.4 million population variants to 5885 protein families and quantify residue-level constraint with a new Missense Enrichment Score (MES). Analysis of 61,214 structures from the PDB spanning 3661 families shows that missense depleted sites are enriched in buried residues or those involved in small-molecule or protein binding. MES is complementary to evolutionary conservation and a combined analysis allows a new classification of residues according to a conservation plane. This approach finds functional residues that are evolutionarily diverse, which can be related to specificity, as well as family-wide conserved sites that are critical for folding or function. We also find a possible contrast between lethal and non-lethal pathogenic sites, and a surprising clinical variant hot spot at a subset of missense enriched positions.
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Affiliation(s)
- Stuart A MacGowan
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK
| | - Fábio Madeira
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Thiago Britto-Borges
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Geoffrey J Barton
- Division of Computational Biology School of Life Sciences University of Dundee, Dow Street Dundee, DD1 5EH, Scotland, UK.
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9
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Herbst C, Bothe V, Wegler M, Axer-Schaefer S, Audebert-Bellanger S, Gecz J, Cogne B, Feldman HB, Horn AHC, Hurst ACE, Kelly MA, Kruer MC, Kurolap A, Laquerriere A, Li M, Mark PR, Morawski M, Nizon M, Pastinen T, Polster T, Saugier-Veber P, SeSong J, Sticht H, Stieler JT, Thifffault I, van Eyk CL, Marcorelles P, Vezain-Mouchard M, Abou Jamra R, Oppermann H. Heterozygous loss-of-function variants in DOCK4 cause neurodevelopmental delay and microcephaly. Hum Genet 2024; 143:455-469. [PMID: 38526744 PMCID: PMC11043173 DOI: 10.1007/s00439-024-02655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024]
Abstract
Neurons form the basic anatomical and functional structure of the nervous system, and defects in neuronal differentiation or formation of neurites are associated with various psychiatric and neurodevelopmental disorders. Dynamic changes in the cytoskeleton are essential for this process, which is, inter alia, controlled by the dedicator of cytokinesis 4 (DOCK4) through the activation of RAC1. Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay. Additional symptoms include coordination or gait abnormalities, microcephaly, nonspecific brain malformations, hypotonia and seizures. Four individuals carry missense variants (three of them detected de novo) and three individuals carry null variants (two of them maternally inherited). Molecular modeling of the heterozygous missense variants suggests that the majority of them affect the globular structure of DOCK4. In vitro functional expression studies in transfected Neuro-2A cells showed that all missense variants impaired neurite outgrowth. Furthermore, Dock4 knockout Neuro-2A cells also exhibited defects in promoting neurite outgrowth. Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
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Affiliation(s)
- Charlotte Herbst
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Viktoria Bothe
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Meret Wegler
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Susanne Axer-Schaefer
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Performance Computing Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital University of Arizona College of Medicine, Phoenix, USA
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Annie Laquerriere
- Department of Anatomy, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Megan Li
- Invitae Corp, San Francisco, CA, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Markus Morawski
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Tilman Polster
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Jang SeSong
- Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jens T Stieler
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Isabelle Thifffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Clare L van Eyk
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Myriam Vezain-Mouchard
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
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10
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Stegmann JD, Kalanithy JC, Dworschak GC, Ishorst N, Mingardo E, Lopes FM, Ho YM, Grote P, Lindenberg TT, Yilmaz Ö, Channab K, Seltzsam S, Shril S, Hildebrandt F, Boschann F, Heinen A, Jolly A, Myers K, McBride K, Bekheirnia MR, Bekheirnia N, Scala M, Morleo M, Nigro V, Torella A, Pinelli M, Capra V, Accogli A, Maitz S, Spano A, Olson RJ, Klee EW, Lanpher BC, Jang SS, Chae JH, Steinbauer P, Rieder D, Janecke AR, Vodopiutz J, Vogel I, Blechingberg J, Cohen JL, Riley K, Klee V, Walsh LE, Begemann M, Elbracht M, Eggermann T, Stoppe A, Stuurman K, van Slegtenhorst M, Barakat TS, Mulhern MS, Sands TT, Cytrynbaum C, Weksberg R, Isidori F, Pippucci T, Severi G, Montanari F, Kruer MC, Bakhtiari S, Darvish H, Reutter H, Hagelueken G, Geyer M, Woolf AS, Posey JE, Lupski JR, Odermatt B, Hilger AC. Bi-allelic variants in CELSR3 are implicated in central nervous system and urinary tract anomalies. NPJ Genom Med 2024; 9:18. [PMID: 38429302 PMCID: PMC10907620 DOI: 10.1038/s41525-024-00398-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024] Open
Abstract
CELSR3 codes for a planar cell polarity protein. We describe twelve affected individuals from eleven independent families with bi-allelic variants in CELSR3. Affected individuals presented with an overlapping phenotypic spectrum comprising central nervous system (CNS) anomalies (7/12), combined CNS anomalies and congenital anomalies of the kidneys and urinary tract (CAKUT) (3/12) and CAKUT only (2/12). Computational simulation of the 3D protein structure suggests the position of the identified variants to be implicated in penetrance and phenotype expression. CELSR3 immunolocalization in human embryonic urinary tract and transient suppression and rescue experiments of Celsr3 in fluorescent zebrafish reporter lines further support an embryonic role of CELSR3 in CNS and urinary tract formation.
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Affiliation(s)
- Jil D Stegmann
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, 53127, Germany.
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany.
| | - Jeshurun C Kalanithy
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, 53127, Germany
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Gabriel C Dworschak
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, 53127, Germany
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, 53115, Germany
- Department of Neuropediatrics, University Hospital Bonn, Bonn, 53127, Germany
| | - Nina Ishorst
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, 53127, Germany
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Enrico Mingardo
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Filipa M Lopes
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Yee Mang Ho
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Phillip Grote
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596, Frankfurt am Main, Germany
| | - Tobias T Lindenberg
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Öznur Yilmaz
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Khadija Channab
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - André Heinen
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Angad Jolly
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Katherine Myers
- Center for Cardiovascular Research, Nationwide Children's Hospital, Department of Pediatrics, Ohio State University, Columbus, OH, USA
| | - Kim McBride
- Center for Cardiovascular Research, Nationwide Children's Hospital, Department of Pediatrics, Ohio State University, Columbus, OH, USA
| | - Mir Reza Bekheirnia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Renal Service, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Nasim Bekheirnia
- Department of Pediatrics, Renal Service, Texas Children's Hospital, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132, Genoa, Italy
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Manuela Morleo
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania 'Luigi Vanvitelli', via Luigi De Crecchio 7, 80138, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Vincenzo Nigro
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania 'Luigi Vanvitelli', via Luigi De Crecchio 7, 80138, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Annalaura Torella
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania 'Luigi Vanvitelli', via Luigi De Crecchio 7, 80138, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, Naples, Italy
| | - Valeria Capra
- Genomics and Clinical Genetics, IRCCS Gaslini, Genoa, Italy
| | - Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Silvia Maitz
- Medical Genetics Service, Oncology Department of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Rory J Olson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Genomics Medicine, Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Philipp Steinbauer
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, 6020, Innsbruck, Austria
- Division of Human Genetics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Pulmonology, Allergology and Endocrinology, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090, Vienna, Austria
| | - Ida Vogel
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Jenny Blechingberg
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Jennifer L Cohen
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kacie Riley
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Victoria Klee
- Pediatric Neurology, Riley Hospital for Children Indiana University Health, Indianapolis, IN, USA
| | - Laurence E Walsh
- Pediatric Neurology, Riley Hospital for Children Indiana University Health, Indianapolis, IN, USA
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Arzu Stoppe
- Division of Neuropediatrics and Social Pediatrics, Department of Pediatrics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
| | - Kyra Stuurman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Maureen S Mulhern
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Tristan T Sands
- Division of Child Neurology, Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons and NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY, USA
- Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Cheryl Cytrynbaum
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Rosanna Weksberg
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Federica Isidori
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giulia Severi
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Francesca Montanari
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Heiko Reutter
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, 53127, Germany
- Division Neonatology and Pediatric Intensive Care, Department of Pediatric and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Gregor Hagelueken
- Institute of Structural Biology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - Benjamin Odermatt
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Alina C Hilger
- Department of Pediatric and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, 91054, Germany.
- Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, 91054, Erlangen, Germany.
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11
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Zech M, Winkelmann J. Next-generation sequencing and bioinformatics in rare movement disorders. Nat Rev Neurol 2024; 20:114-126. [PMID: 38172289 DOI: 10.1038/s41582-023-00909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
The ability to sequence entire exomes and genomes has revolutionized molecular testing in rare movement disorders, and genomic sequencing is becoming an integral part of routine diagnostic workflows for these heterogeneous conditions. However, interpretation of the extensive genomic variant information that is being generated presents substantial challenges. In this Perspective, we outline multidimensional strategies for genetic diagnosis in patients with rare movement disorders. We examine bioinformatics tools and computational metrics that have been developed to facilitate accurate prioritization of disease-causing variants. Additionally, we highlight community-driven data-sharing and case-matchmaking platforms, which are designed to foster the discovery of new genotype-phenotype relationships. Finally, we consider how multiomic data integration might optimize diagnostic success by combining genomic, epigenetic, transcriptomic and/or proteomic profiling to enable a more holistic evaluation of variant effects. Together, the approaches that we discuss offer pathways to the improved understanding of the genetic basis of rare movement disorders.
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Affiliation(s)
- Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany.
- DZPG, Deutsches Zentrum für Psychische Gesundheit, Munich, Germany.
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12
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Dharmadhikari AV, Abad MA, Khan S, Maroofian R, Sands TT, Ullah F, Samejima I, Wear MA, Moore KE, Kondakova E, Mitina N, Schaub T, Lee GK, Umandap CH, Berger SM, Iglesias AD, Popp B, Jamra RA, Gabriel H, Rentas S, Rippert AL, Izumi K, Conlin LK, Koboldt DC, Mosher TM, Hickey SE, Albert DVF, Norwood H, Lewanda AF, Dai H, Liu P, Mitani T, Marafi D, Pehlivan D, Posey JE, Lippa N, Vena N, Heinzen EL, Goldstein DB, Mignot C, de Sainte Agathe JM, Al-Sannaa NA, Zamani M, Sadeghian S, Azizimalamiri R, Seifia T, Zaki MS, Abdel-Salam GMH, Abdel-Hamid M, Alabdi L, Alkuraya FS, Dawoud H, Lofty A, Bauer P, Zifarelli G, Afzal E, Zafar F, Efthymiou S, Gossett D, Towne MC, Yeneabat R, Wontakal SN, Aggarwal VS, Rosenfeld JA, Tarabykin V, Ohta S, Lupski JR, Houlden H, Earnshaw WC, Davis EE, Jeyaprakash AA, Liao J. RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.09.23300329. [PMID: 38260255 PMCID: PMC10802637 DOI: 10.1101/2024.01.09.23300329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, we identified 24 individuals with neurodevelopmental delays from 18 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants showed reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicated that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 revealed that most disease-associated missense variants mapped to the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants had reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS ( SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.
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13
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Accogli A, Shakya S, Yang T, Insinna C, Kim SY, Bell D, Butov KR, Severino M, Niceta M, Scala M, Lee HS, Yoo T, Stauffer J, Zhao H, Fiorillo C, Pedemonte M, Diana MC, Baldassari S, Zakharova V, Shcherbina A, Rodina Y, Fagerberg C, Roos LS, Wierzba J, Dobosz A, Gerard A, Potocki L, Rosenfeld JA, Lalani SR, Scott TM, Scott D, Azamian MS, Louie R, Moore HW, Champaigne NL, Hollingsworth G, Torella A, Nigro V, Ploski R, Salpietro V, Zara F, Pizzi S, Chillemi G, Ognibene M, Cooney E, Do J, Linnemann A, Larsen MJ, Specht S, Walters KJ, Choi HJ, Choi M, Tartaglia M, Youkharibache P, Chae JH, Capra V, Park SG, Westlake CJ. Variants in the WDR44 WD40-repeat domain cause a spectrum of ciliopathy by impairing ciliogenesis initiation. Nat Commun 2024; 15:365. [PMID: 38191484 PMCID: PMC10774338 DOI: 10.1038/s41467-023-44611-2] [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: 11/09/2022] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
WDR44 prevents ciliogenesis initiation by regulating RAB11-dependent vesicle trafficking. Here, we describe male patients with missense and nonsense variants within the WD40 repeats (WDR) of WDR44, an X-linked gene product, who display ciliopathy-related developmental phenotypes that we can model in zebrafish. The patient phenotypic spectrum includes developmental delay/intellectual disability, hypotonia, distinct craniofacial features and variable presence of brain, renal, cardiac and musculoskeletal abnormalities. We demonstrate that WDR44 variants associated with more severe disease impair ciliogenesis initiation and ciliary signaling. Because WDR44 negatively regulates ciliogenesis, it was surprising that pathogenic missense variants showed reduced abundance, which we link to misfolding of WDR autonomous repeats and degradation by the proteasome. We discover that disease severity correlates with increased RAB11 binding, which we propose drives ciliogenesis initiation dysregulation. Finally, we discover interdomain interactions between the WDR and NH2-terminal region that contains the RAB11 binding domain (RBD) and show patient variants disrupt this association. This study provides new insights into WDR44 WDR structure and characterizes a new syndrome that could result from impaired ciliogenesis.
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Affiliation(s)
- Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre (MUHC), Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Saurabh Shakya
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Taewoo Yang
- Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 08826, Seoul, Republic of Korea
| | - Christine Insinna
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, 03080, Seoul, Republic of Korea
| | - David Bell
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kirill R Butov
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | | | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Hyun Sik Lee
- School of Biological Sciences, Seoul National University, 08826, Seoul, Republic of Korea
| | - Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Jimmy Stauffer
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Huijie Zhao
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Chiara Fiorillo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Child Neuropsychiatry, IRCCS Istituto G.Gaslini, DINOGMI University of Genova, Largo Gaslini 5, Genoa, Italy
| | - Marina Pedemonte
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria C Diana
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Simona Baldassari
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Viktoria Zakharova
- National Medical Research Center for Endocrinology, Clinical data analysis department, Moscow, Russian Federation, Russia
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Yulia Rodina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Laura Sønderberg Roos
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, København, Denmark
| | - Jolanta Wierzba
- Department of Pediatrics and Internal Medicine Nursing, Department of Rare Disorders, Medical University of Gdansk, Gdansk, Poland
| | - Artur Dobosz
- Department of Medical Genetics, Faculty of Medicine, Jagiellonian University Medical College, 30-663, Krakow, Poland
| | - Amanda Gerard
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lorraine Potocki
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Seema R Lalani
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tiana M Scott
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Daryl Scott
- Baylor Genetics Laboratories, Houston, TX, USA
| | | | | | | | | | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Pawińskiego 3C, 02-106, Warsaw, Poland
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University. College London, London, WC1N 3BG, UK
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy
| | - Marzia Ognibene
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Erin Cooney
- Division of Medical Genetics and Metabolism, Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Jenny Do
- Division of Medical Genetics and Metabolism, Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Anders Linnemann
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Suzanne Specht
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Kylie J Walters
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Hee-Jung Choi
- School of Biological Sciences, Seoul National University, 08826, Seoul, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Phillippe Youkharibache
- Cancer Science Data Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, 03080, Seoul, Republic of Korea
| | - Valeria Capra
- Child Neuropsychiatry, IRCCS Istituto G.Gaslini, DINOGMI University of Genova, Largo Gaslini 5, Genoa, Italy
| | - Sung-Gyoo Park
- Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 08826, Seoul, Republic of Korea.
| | - Christopher J Westlake
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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14
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Ramadesikan S, Colwell CM, Supinger R, Hunter J, Thomas J, Varga E, Mardis ER, Wood RJ, Koboldt DC. Novel inherited CDX2 variant segregating in a family with diverse congenital malformations of the genitourinary system. Cold Spring Harb Mol Case Stud 2023; 9:a006294. [PMID: 37816608 PMCID: PMC10815271 DOI: 10.1101/mcs.a006294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Anorectal malformations (ARMs) constitute a group of congenital defects of the gastrointestinal and urogenital systems. They affect males and females, with an estimated worldwide prevalence of 1 in 5000 live births. These malformations are clinically heterogeneous and can be part of a syndromic presentation (syndromic ARM) or as a nonsyndromic entity (nonsyndromic ARM). Despite the well-recognized heritability of nonsyndromic ARM, the genetic etiology in most patients is unknown. In this study, we describe three siblings with diverse congenital anomalies of the genitourinary system, anemia, delayed milestones, and skeletal anomalies. Genome sequencing identified a novel, paternally inherited heterozygous Caudal type Homeobox 2 (CDX2) variant (c.722A > G (p.Glu241Gly)), that was present in all three affected siblings. The variant identified in this family is absent from population databases and predicted to be damaging by most in silico pathogenicity tools. So far, only two other reports implicate variants in CDX2 with ARMs. Remarkably, the individuals described in these studies had similar clinical phenotypes and genetic alterations in CDX2 CDX2 encodes a transcription factor and is considered the master regulator of gastrointestinal development. This variant maps to the homeobox domain of the encoded protein, which is critical for interaction with DNA targets. Our finding provides a potential molecular diagnosis for this family's condition and supports the role of CDX2 in anorectal anomalies. It also highlights the clinical heterogeneity and variable penetrance of ARM predisposition variants, another well-documented phenomenon. Finally, it underscores the diagnostic utility of genomic profiling of ARMs to identify the genetic etiology of these defects.
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Affiliation(s)
- Swetha Ramadesikan
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Caitlyn M Colwell
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Rachel Supinger
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Jesse Hunter
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Jessica Thomas
- Department of Pediatric Colorectal & Pelvic Reconstructive Surgery, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Elizabeth Varga
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Elaine R Mardis
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Richard J Wood
- Department of Pediatric Colorectal & Pelvic Reconstructive Surgery, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
- Department of Surgery, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Daniel C Koboldt
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA;
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
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15
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Giovenino C, Trajkova S, Pavinato L, Cardaropoli S, Pullano V, Ferrero E, Sukarova-Angelovska E, Carestiato S, Salmin P, Rinninella A, Battaglia A, Bertoli L, Fadda A, Palermo F, Carli D, Mussa A, Dimartino P, Bruselles A, Froukh T, Mandrile G, Pasini B, De Rubeis S, Buxbaum JD, Pippucci T, Tartaglia M, Rossato M, Delledonne M, Ferrero GB, Brusco A. Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation For X-linked genes. Eur J Hum Genet 2023; 31:1228-1236. [PMID: 36879111 PMCID: PMC10620389 DOI: 10.1038/s41431-023-01324-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/24/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Despite major advances in genome technology and analysis, >50% of patients with a neurodevelopmental disorder (NDD) remain undiagnosed after extensive evaluation. A point in case is our clinically heterogeneous cohort of NDD patients that remained undiagnosed after FRAXA testing, chromosomal microarray analysis and trio exome sequencing (ES). In this study, we explored the frequency of non-random X chromosome inactivation (XCI) in the mothers of male patients and affected females, the rationale being that skewed XCI might be masking previously discarded genetic variants found on the X chromosome. A multiplex fluorescent PCR-based assay was used to analyse the pattern of XCI after digestion with HhaI methylation-sensitive restriction enzyme. In families with skewed XCI, we re-evaluated trio-based ES and identified pathogenic variants and a deletion on the X chromosome. Linkage analysis and RT-PCR were used to further study the inactive X chromosome allele, and Xdrop long-DNA technology was used to define chromosome deletion boundaries. We found skewed XCI (>90%) in 16/186 (8.6%) mothers of NDD males and in 12/90 (13.3%) NDD females, far beyond the expected rate of XCI in the normal population (3.6%, OR = 4.10; OR = 2.51). By re-analyzing ES and clinical data, we solved 7/28 cases (25%) with skewed XCI, identifying variants in KDM5C, PDZD4, PHF6, TAF1, OTUD5 and ZMYM3, and a deletion in ATRX. We conclude that XCI profiling is a simple assay that targets a subgroup of patients that can benefit from re-evaluation of X-linked variants, thus improving the diagnostic yield in NDD patients and identifying new X-linked disorders.
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Affiliation(s)
- Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Verdiana Pullano
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Pediatric Diseases, Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, 1000, Skopje, Republic of North Macedonia
| | - Silvia Carestiato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Paola Salmin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Antonina Rinninella
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124, Catania, Italy
| | - Anthony Battaglia
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Luca Bertoli
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Antonio Fadda
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Flavia Palermo
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Alessandro Bruselles
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, Orbassano, TO, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, 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
- 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
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- 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
| | - Tommaso Pippucci
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marzia Rossato
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Massimo Delledonne
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy.
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16
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Daneshi A, Garshasbi M, Farhadi M, Falavarjani KG, Vafaee-Shahi M, Almadani N, Zabihi M, Ghalavand MA, Falah M. Genetic insights into PHARC syndrome: identification of a novel frameshift mutation in ABHD12. BMC Med Genomics 2023; 16:235. [PMID: 37803361 PMCID: PMC10557151 DOI: 10.1186/s12920-023-01682-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Mutations in ABHD12 (OMIM: 613,599) are associated with polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract (PHARC) syndrome (OMIM: 612674), which is a rare autosomal recessive neurodegenerative disease. PHARC syndrome is easily misdiagnosed as other neurologic disorders, such as retinitis pigmentosa, Charcot-Marie-Tooth disease, and Refsum disease, due to phenotype variability and slow progression. This paper presents a novel mutation in ABHD12 in two affected siblings with PHARC syndrome phenotypes. In addition, we summarize genotype-phenotype information of the previously reported patients with ABHD12 mutation. METHODS Following a thorough medical evaluation, whole-exome sequencing was done on the proband to look for potential genetic causes. This was followed by confirmation of identified variant in the proband and segregation analysis in the family by Sanger sequencing. The variants were interpreted based on the American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS A novel pathogenic homozygous frameshift variant, NM_001042472.3:c.601dup, p.(Val201GlyfsTer4), was identified in exon 6 of ABHD12 (ACMG criteria: PVS1 and PM2, PM1, PM4, PP3, and PP4). Through Sanger sequencing, we showed that this variant is co-segregated with the disease in the family. Further medical evaluations confirmed the compatibility of the patients' phenotype with PHARC syndrome. CONCLUSIONS Our findings expand the spectrum of mutations in the ABHD12 and emphasize the significance of multidisciplinary diagnostic collaboration among clinicians and geneticists to solve the differential diagnosis of related disorders. Moreover, a summary based on mutations found so far in the ABHD12 gene did not suggest a clear genotype-phenotype correlation for PHARC syndrome.
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Affiliation(s)
- Ahmad Daneshi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Farhadi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Khalil Ghasemi Falavarjani
- Eye Research Centre, Five Senses Health Institute, School of Medicine, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
- Stem Cell and Regenerative Medicine Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vafaee-Shahi
- Pediatric Growth and Development Research Center, Institute of Endocrinology and metabolism, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - MohammadSina Zabihi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Ghalavand
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
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17
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de Sainte Agathe JM, Pode-Shakked B, Naudion S, Michaud V, Arveiler B, Fergelot P, Delmas J, Keren B, Poirsier C, Alkuraya FS, Tabarki B, Bend E, Davis K, Bebin M, Thompson ML, Bryant EM, Wagner M, Hannibal I, Lenberg J, Krenn M, Wigby KM, Friedman JR, Iascone M, Cereda A, Miao T, LeGuern E, Argilli E, Sherr E, Caluseriu O, Tidwell T, Bayrak-Toydemir P, Hagedorn C, Brugger M, Vill K, Morneau-Jacob FD, Chung W, Weaver KN, Owens JW, Husami A, Chaudhari BP, Stone BS, Burns K, Li R, de Lange IM, Biehler M, Ginglinger E, Gérard B, Stottmann RW, Trimouille A. ARF1-related disorder: phenotypic and molecular spectrum. J Med Genet 2023; 60:999-1005. [PMID: 37185208 PMCID: PMC10579487 DOI: 10.1136/jmg-2022-108803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
PURPOSE ARF1 was previously implicated in periventricular nodular heterotopia (PVNH) in only five individuals and systematic clinical characterisation was not available. The aim of this study is to provide a comprehensive description of the phenotypic and genotypic spectrum of ARF1-related neurodevelopmental disorder. METHODS We collected detailed phenotypes of an international cohort of individuals (n=17) with ARF1 variants assembled through the GeneMatcher platform. Missense variants were structurally modelled, and the impact of several were functionally validated. RESULTS De novo variants (10 missense, 1 frameshift, 1 splice altering resulting in 9 residues insertion) in ARF1 were identified among 17 unrelated individuals. Detailed phenotypes included intellectual disability (ID), microcephaly, seizures and PVNH. No specific facial characteristics were consistent across all cases, however microretrognathia was common. Various hearing and visual defects were recurrent, and interestingly, some inflammatory features were reported. MRI of the brain frequently showed abnormalities consistent with a neuronal migration disorder. CONCLUSION We confirm the role of ARF1 in an autosomal dominant syndrome with a phenotypic spectrum including severe ID, microcephaly, seizures and PVNH due to impaired neuronal migration.
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Affiliation(s)
| | - Ben Pode-Shakked
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sophie Naudion
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Vincent Michaud
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Benoit Arveiler
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Patricia Fergelot
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Jean Delmas
- Pediatric and Prenatal Imaging Department, Centre Hospitalier Universitaire de Bordeaux Groupe hospitalier Pellegrin, Bordeaux, France
| | - Boris Keren
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
| | | | - Fowzan S Alkuraya
- Department of Translational Genomic, Center for Genomic Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military and Medical City, Riyadh, Saudi Arabia
| | - Eric Bend
- PreventionGenetics LLC, Marshfield, Wisconsin, USA
| | - Kellie Davis
- Division of Medical Genetics, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Martina Bebin
- UAB Epilepsy Center, The University of Alabama at Birmingham Hospital, Birmingham, Alabama, USA
| | - Michelle L Thompson
- Greg Cooper's Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Emily M Bryant
- Gillette Children's Specialty Healthcare, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Matias Wagner
- Institute of Human Genetics, Technische Universitat Munchen, Munchen, Germany
- Institute of Neurogenomics, Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Umwelt und Gesundheit, Neuherberg, Germany
| | - Iris Hannibal
- Department of Pediatrics, University Hospital Munich, Munchen, Germany
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Martin Krenn
- Department of Neurology, Medizinische Universitat Wien, Wien, Austria
| | - Kristen M Wigby
- Rady Children's Hospital-San Diego, University of California, San Diego, California, USA
| | - Jennifer R Friedman
- Department of Neuroscience, Rady Children's Institute for Genomic Medicine, San Diego, California, USA
- Division of Neurology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Pediatric Department, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Térence Miao
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
- École d'ingénieurs biotechnologies Paris - SupBiotech, Sup'Biotech, Paris, France
| | - Eric LeGuern
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
- ICM, INSERM, Paris, France
| | - Emanuela Argilli
- Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Elliott Sherr
- Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta Hospital, Edmonton, Alberta, Canada
| | | | | | - Caroline Hagedorn
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munchen, Germany
| | - Katharina Vill
- Fachbereich Neuromuskuläre Erkrankungen und klinische Neurophysiologie, Dr. v. Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | | | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York City, New York, USA
| | - Kathryn N Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Joshua W Owens
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ammar Husami
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Bimal P Chaudhari
- Divisions of Neonatology, Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Brandon S Stone
- Divisions of Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Katie Burns
- Sanford Children's Specialty Clinic, Sioux Falls, South Dakota, USA
| | - Rachel Li
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - Iris M de Lange
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Margaux Biehler
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals, Strasbourg, France
| | | | - Bénédicte Gérard
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals, Strasbourg, France
| | - Rolf W Stottmann
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
- Service de Pathologie, University Hospital Centre Bordeaux Pellegrin Hospital Group, Bordeaux, France
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18
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Sheth F, Shah J, Jain D, Shah S, Patel H, Patel K, Solanki DI, Iyer AS, Menghani B, Mhatre P, Mehta S, Bajaj S, Patel V, Pandya M, Dhami D, Patel D, Sheth J, Sheth H. Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: evidence supporting whole exome sequencing as first tier test. BMC Neurol 2023; 23:292. [PMID: 37543562 PMCID: PMC10403833 DOI: 10.1186/s12883-023-03341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic architecture of ASD in India. This study aimed to identify the genetic architecture of ASD in India and to assess the use of whole exome sequencing (WES) as a first-tier test instead of chromosomal microarray (CMA) for genetic diagnosis. METHODS Between 2020 and 2022, 101 patient-parent trios of Indian origin diagnosed with ASD according to the Diagnostic and Statistical Manual, 5th edition, were recruited. All probands underwent a sequential genetic testing pathway consisting of karyotyping, Fragile-X testing (in male probands only), CMA and WES. Candidate variant validation and parental segregation analysis was performed using orthogonal methods. RESULTS Of 101 trios, no probands were identified with a gross chromosomal anomaly or Fragile-X. Three (2.9%) and 30 (29.7%) trios received a confirmed genetic diagnosis from CMA and WES, respectively. Amongst diagnosis from WES, SNVs were detected in 27 cases (90%) and CNVs in 3 cases (10%), including the 3 CNVs detected from CMA. Segregation analysis showed 66.6% (n = 3 for CNVs and n = 17 for SNVs) and 16.6% (n = 5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. MECP2 gene was the most recurrently mutated gene (n = 6; 20%) in the present cohort. Majority of the affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling. CONCLUSIONS Our study suggests de novo variants as a major cause of ASD in the Indian population, with Rett syndrome as the most commonly detected disorder. Furthermore, we provide evidence of a significant difference in the diagnostic yield between CMA (3%) and WES (30%) which supports the implementation of WES as a first-tier test for genetic diagnosis of ASD in India.
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Affiliation(s)
- Frenny Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India.
| | - Jhanvi Shah
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Siddharth Shah
- Royal Institute of Child Neurosciences, Ahmedabad, India
| | | | - Ketan Patel
- Specialty Homeopathic Clinic, Ahmedabad, India
| | | | | | - Bhargavi Menghani
- Children's Institute for Development and Advancement Centre, Vadodara, India
| | - Priti Mhatre
- Tender Kinds Centre for Child Development, Navi Mumbai, India
| | - Sanjiv Mehta
- Royal Institute of Child Neurosciences, Ahmedabad, India
| | | | - Vishal Patel
- Little Brain Pediatric Neurocare Centre, Vadodara, India
| | | | - Deepak Dhami
- Axon Child Neurology and Epilepsy Centre, Rajkot, India
| | - Darshan Patel
- Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology, Changa, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India.
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19
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Gracia-Diaz C, Zhou Y, Yang Q, Maroofian R, Espana-Bonilla P, Lee CH, Zhang S, Padilla N, Fueyo R, Waxman EA, Lei S, Otrimski G, Li D, Sheppard SE, Mark P, Harr MH, Hakonarson H, Rodan L, Jackson A, Vasudevan P, Powel C, Mohammed S, Maddirevula S, Alzaidan H, Faqeih EA, Efthymiou S, Turchetti V, Rahman F, Maqbool S, Salpietro V, Ibrahim SH, di Rosa G, Houlden H, Alharbi MN, Al-Sannaa NA, Bauer P, Zifarelli G, Estaras C, Hurst ACE, Thompson ML, Chassevent A, Smith-Hicks CL, de la Cruz X, Holtz AM, Elloumi HZ, Hajianpour MJ, Rieubland C, Braun D, Banka S, French DL, Heller EA, Saade M, Song H, Ming GL, Alkuraya FS, Agrawal PB, Reinberg D, Bhoj EJ, Martínez-Balbás MA, Akizu N. Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders. Nat Commun 2023; 14:4109. [PMID: 37433783 PMCID: PMC10336078 DOI: 10.1038/s41467-023-39645-5] [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: 07/14/2022] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Genetic variants in chromatin regulators are frequently found in neurodevelopmental disorders, but their effect in disease etiology is rarely determined. Here, we uncover and functionally define pathogenic variants in the chromatin modifier EZH1 as the cause of dominant and recessive neurodevelopmental disorders in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 methyltransferases of the PRC2 complex. Unlike the other PRC2 subunits, which are involved in cancers and developmental syndromes, the implication of EZH1 in human development and disease is largely unknown. Using cellular and biochemical studies, we demonstrate that recessive variants impair EZH1 expression causing loss of function effects, while dominant variants are missense mutations that affect evolutionarily conserved aminoacids, likely impacting EZH1 structure or function. Accordingly, we found increased methyltransferase activity leading to gain of function of two EZH1 missense variants. Furthermore, we show that EZH1 is necessary and sufficient for differentiation of neural progenitor cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell-derived neural cultures and forebrain organoids, we demonstrate that EZH1 variants perturb cortical neuron differentiation. Overall, our work reveals a critical role of EZH1 in neurogenesis regulation and provides molecular diagnosis for previously undefined neurodevelopmental disorders.
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Affiliation(s)
- Carolina Gracia-Diaz
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yijing Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qian Yang
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Paula Espana-Bonilla
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Chul-Hwan Lee
- Department of Biomedical Sciences and Pharmacology, Seoul National University, College of Medicine, Seoul, South Korea
| | - Shuo Zhang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Natàlia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Raquel Fueyo
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Elisa A Waxman
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sunyimeng Lei
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Garrett Otrimski
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul Mark
- Department of Pediatrics, Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Pradeep Vasudevan
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | - Corrina Powel
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | | | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hamad Alzaidan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Fatima Rahman
- Developmental and Behavioral Pediatrics, University of Child Health Sciences & The Children's Hospital, Lahore, Pakistan
| | - Shazia Maqbool
- Developmental and Behavioral Pediatrics, University of Child Health Sciences & The Children's Hospital, Lahore, Pakistan
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Shahnaz H Ibrahim
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Gabriella di Rosa
- Child Neuropsychiatry Unit, Department of Pediatrics, University of Messina, Messina, 98100, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Maha Nasser Alharbi
- Maternity and Children Hospital Buraidah, Qassim Health Cluster, Buraydah, Saudi Arabia
| | | | | | | | - Conchi Estaras
- Center for Translational Medicine, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA, USA
| | - Anna C E Hurst
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Anna Chassevent
- Department of Neurogenetics, Neurology and Developmental Medicine Kennedy Krieger Institute, Baltimore, MD, USA
| | - Constance L Smith-Hicks
- Department of Neurogenetics, Neurology and Developmental Medicine Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alexander M Holtz
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - M J Hajianpour
- Division of Medical Genetics and Genomics, Department of Pediatrics, Albany Medical College, Albany, NY, USA
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Deborah L French
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Murielle Saade
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, University of Miami School of Medicine and Holtz Children's Hospital, Jackson Heath System, Miami, FL, USA
| | | | - Elizabeth J Bhoj
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marian A Martínez-Balbás
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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20
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Smits DJ, Schot R, Popescu CA, Dias KR, Ades L, Briere LC, Sweetser DA, Kushima I, Aleksic B, Khan S, Karageorgou V, Ordonez N, Sleutels FJGT, van der Kaay DCM, Van Mol C, Van Esch H, Bertoli-Avella AM, Roscioli T, Mancini GMS. De novo MCM6 variants in neurodevelopmental disorders: a recognizable phenotype related to zinc binding residues. Hum Genet 2023:10.1007/s00439-023-02569-7. [PMID: 37198333 DOI: 10.1007/s00439-023-02569-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/03/2023] [Indexed: 05/19/2023]
Abstract
The minichromosome maintenance (MCM) complex acts as a DNA helicase during DNA replication, and thereby regulates cell cycle progression and proliferation. In addition, MCM-complex components localize to centrosomes and play an independent role in ciliogenesis. Pathogenic variants in genes coding for MCM components and other DNA replication factors have been linked to growth and developmental disorders as Meier-Gorlin syndrome and Seckel syndrome. Trio exome/genome sequencing identified the same de novo MCM6 missense variant p.(Cys158Tyr) in two unrelated individuals that presented with overlapping phenotypes consisting of intra-uterine growth retardation, short stature, congenital microcephaly, endocrine features, developmental delay and urogenital anomalies. The identified variant affects a zinc binding cysteine in the MCM6 zinc finger signature. This domain, and specifically cysteine residues, are essential for MCM-complex dimerization and the induction of helicase activity, suggesting a deleterious effect of this variant on DNA replication. Fibroblasts derived from the two affected individuals showed defects both in ciliogenesis and cell proliferation. We additionally traced three unrelated individuals with de novo MCM6 variants in the oligonucleotide binding (OB)-fold domain, presenting with variable (neuro)developmental features including autism spectrum disorder, developmental delay, and epilepsy. Taken together, our findings implicate de novo MCM6 variants in neurodevelopmental disorders. The clinical features and functional defects related to the zinc binding residue resemble those observed in syndromes related to other MCM components and DNA replication factors, while de novo OB-fold domain missense variants may be associated with more variable neurodevelopmental phenotypes. These data encourage consideration of MCM6 variants in the diagnostic arsenal of NDD.
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Affiliation(s)
- Daphne J Smits
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Discovery Unit, Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristiana A Popescu
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Kerith-Rae Dias
- Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, Australia
| | - Lesley Ades
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Itaru Kushima
- Medical Genomics Center, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | | | | | | | - Frank J G T Sleutels
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Daniëlle C M van der Kaay
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000, Leuven, Belgium
| | | | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
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21
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Cantarero L, García-Vargas G, Hoenicka J, Palau F. Differential effects of Mendelian GDAP1 clinical variants on mitochondria-lysosome membrane contacts sites. Biol Open 2023; 12:bio059707. [PMID: 36912213 PMCID: PMC10110396 DOI: 10.1242/bio.059707] [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: 10/24/2022] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
GDAP1 pathogenic variants cause Charcot-Marie-Tooth (CMT) disease, the most common hereditary motor and sensory neuropathy. CMT-GDAP1 can be axonal or demyelinating, with autosomal dominant or recessive inheritance, leading to phenotypic heterogeneity. Recessive GDAP1 variants cause a severe phenotype, whereas dominant variants are associated with a milder disease course. GDAP1 is an outer mitochondrial membrane protein involved in mitochondrial membrane contact sites (MCSs) with the plasmatic membrane, the endoplasmic reticulum (ER), and lysosomes. In GDAP1-deficient models, the pathophysiology includes morphological defects in mitochondrial network and ER, impaired Ca2+ homeostasis, oxidative stress, and mitochondrial MCSs defects. Nevertheless, the underlying pathophysiology of dominant variants is less understood. Here, we study the effect upon mitochondria-lysosome MCSs of two GDAP1 clinical variants located in the α-loop interaction domain of the protein. p.Thr157Pro dominant variant causes the increase in these MCSs that correlates with a hyper-fissioned mitochondrial network. In contrast, p.Arg161His recessive variant, which is predicted to significantly change the contact surface of GDAP1, causes decreased contacts with more elongated mitochondria. Given that mitochondria-lysosome MCSs regulate Ca2+ transfer from the lysosome to mitochondria, our results support that GDAP1 clinical variants have different consequences for Ca2+ handling and that could be primary insults determining differences in severity between dominant and recessive forms of the disease.
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Affiliation(s)
- Lara Cantarero
- Laboratory of Neurogenetics and Molecular Medicine – IPER, Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 08950, Barcelona, Spain
| | - Gisela García-Vargas
- Laboratory of Neurogenetics and Molecular Medicine – IPER, Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
| | - Janet Hoenicka
- Laboratory of Neurogenetics and Molecular Medicine – IPER, Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 08950, Barcelona, Spain
| | - Francesc Palau
- Laboratory of Neurogenetics and Molecular Medicine – IPER, Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 08950, Barcelona, Spain
- Department of Genetic Medicine – IPER, Hospital Sant Joan de Déu, 08950, Barcelona, Spain
- Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, 08036, Barcelona, Spain
- ERN-ITHACA
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22
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Paavo M, Lee W, Parmann R, Lima de Carvalho JR, Zernant J, Tsang SH, Allikmets R, Sparrow JR. Insights Into PROM1-Macular Disease Using Multimodal Imaging. Invest Ophthalmol Vis Sci 2023; 64:27. [PMID: 37093133 PMCID: PMC10148657 DOI: 10.1167/iovs.64.4.27] [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: 11/17/2022] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
Purpose To describe the features of genetically confirmed PROM1-macular dystrophy in multimodal images. Methods Thirty-six (36) eyes of 18 patients (5-66 years; mean age, 42.4 years) were prospectively studied by clinical examination and multimodal imaging. Short-wavelength autofluorescence (SW-AF) and quantitative fundus autofluorescence (qAF) images were acquired with a scanning laser ophthalmoscope (HRA+OCT, Heidelberg Engineering) modified by insertion of an internal autofluorescent reference. Further clinical testing included near-infrared autofluorescence (NIR-AF; HRA2, Heidelberg Engineering) with semiquantitative analysis, spectral domain-optical coherence tomography (HRA+OCT) and full-field electroretinography. All patients were genetically confirmed by exome sequencing. Results All 18 patients presented with varying degrees of maculopathy. One family with individuals affected across two generations exhibited granular fleck-like deposits across the posterior pole. Areas of granular deposition in SW-AF and NIR-AF corresponded to intermittent loss of the ellipsoid zone, whereas discrete regions of hypoautofluorescence corresponded with a loss of outer retinal layers in spectral-domain optical coherence tomography scans. For 18 of the 20 eyes, qAF levels within the macula were within the 95% confidence intervals of healthy age-matched individuals; nor was the mean NIR-AF signal increased relative to healthy eyes. Conclusions Although PROM1-macular dystrophy (Stargardt disease 4) can exhibit phenotypic overlap with recessive Stargardt disease, significantly increased SW-AF levels were not detected. As such, elevated bisretinoid lipofuscin may not be a feature of the pathophysiology of PROM1 disease. The qAF approach could serve as a method of early differential diagnosis and may help to identify appropriate disease targets as therapeutics become available to treat inherited retinal disease.
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Affiliation(s)
- Maarjaliis Paavo
- Departments of Ophthalmology, Columbia University Medical Center, New York, New York, United States
- Helsinki University Eye Hospital, Helsinki, Finland
| | - Winston Lee
- Departments of Ophthalmology, Columbia University Medical Center, New York, New York, United States
| | - Rait Parmann
- Departments of Ophthalmology, Columbia University Medical Center, New York, New York, United States
| | | | - Jana Zernant
- Departments of Ophthalmology, Columbia University Medical Center, New York, New York, United States
| | - Stephen H. Tsang
- Departments of Ophthalmology, Columbia University Medical Center, New York, New York, United States
- Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States
| | - Rando Allikmets
- Departments of Ophthalmology, Columbia University Medical Center, New York, New York, United States
- Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States
| | - Janet R. Sparrow
- Departments of Ophthalmology, Columbia University Medical Center, New York, New York, United States
- Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States
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23
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Luppe J, Sticht H, Lecoquierre F, Goldenberg A, Gorman KM, Molloy B, Agolini E, Novelli A, Briuglia S, Kuismin O, Marcelis C, Vitobello A, Denommé-Pichon AS, Julia S, Lemke JR, Abou Jamra R, Platzer K. Heterozygous and homozygous variants in STX1A cause a neurodevelopmental disorder with or without epilepsy. Eur J Hum Genet 2023; 31:345-352. [PMID: 36564538 PMCID: PMC9995539 DOI: 10.1038/s41431-022-01269-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
The neuronal SNARE complex drives synaptic vesicle exocytosis. Therefore, one of its core proteins syntaxin 1A (STX1A) has long been suspected to play a role in neurodevelopmental disorders. We assembled eight individuals harboring ultra rare variants in STX1A who present with a spectrum of intellectual disability, autism and epilepsy. Causative variants comprise a homozygous splice variant, three de novo missense variants and two inframe deletions of a single amino acid. We observed a phenotype mainly driven by epilepsy in the individuals with missense variants in contrast to intellectual disability and autistic behavior in individuals with single amino acid deletions and the splicing variant. In silico modeling of missense variants and single amino acid deletions show different impaired protein-protein interactions. We hypothesize the two phenotypic courses of affected individuals to be dependent on two different pathogenic mechanisms: (1) a weakened inhibitory STX1A-STXBP1 interaction due to missense variants results in an STX1A-related developmental epileptic encephalopathy and (2) a hampered SNARE complex formation due to inframe deletions causes an STX1A-related intellectual disability and autism phenotype. Our description of a STX1A-related neurodevelopmental disorder with or without epilepsy thus expands the group of rare diseases called SNAREopathies.
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Affiliation(s)
- Johannes Luppe
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Kathleen M Gorman
- Department of Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | | | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Silvana Briuglia
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
| | - Outi Kuismin
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Antonio Vitobello
- Inserm UMR1231 GAD, University of Burgundy-Franche Comté, Dijon, France
| | | | - Sophie Julia
- Federative Institute of Biology, CHU de Toulouse, Toulouse, France
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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24
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Mendelian inheritance revisited: dominance and recessiveness in medical genetics. Nat Rev Genet 2023:10.1038/s41576-023-00574-0. [PMID: 36806206 DOI: 10.1038/s41576-023-00574-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/22/2023]
Abstract
Understanding the consequences of genotype for phenotype (which ranges from molecule-level effects to whole-organism traits) is at the core of genetic diagnostics in medicine. Many measures of the deleteriousness of individual alleles exist, but these have limitations for predicting the clinical consequences. Various mechanisms can protect the organism from the adverse effects of functional variants, especially when the variant is paired with a wild type allele. Understanding why some alleles are harmful in the heterozygous state - representing dominant inheritance - but others only with the biallelic presence of pathogenic variants - representing recessive inheritance - is particularly important when faced with the deluge of rare genetic alterations identified by high throughput DNA sequencing. Both awareness of the specific quantitative and/or qualitative effects of individual variants and the elucidation of allelic and non-allelic interactions are essential to optimize genetic diagnosis and counselling.
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25
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Salzano E, Niceta M, Pizzi S, Radio FC, Busè M, Mercadante F, Barresi S, Ferrara A, Mancini C, Tartaglia M, Piccione M. Case report: Novel compound heterozygosity for pathogenic variants in MED23 in a syndromic patient with postnatal microcephaly. Front Neurol 2023; 14:1090082. [PMID: 36824420 PMCID: PMC9941528 DOI: 10.3389/fneur.2023.1090082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
Biallelic loss-of-function variants in MED23 cause a recessive syndromic intellectual disability condition with or without epilepsy (MRT18). Due to the small number of reported individuals, the clinical phenotype of the disorder has not been fully delineated yet, and the spectrum and frequency of neurologic features have not been fully characterized. Here, we report a 5-year-old girl with compound heterozygous for two additional MED23 variants. Besides global developmental delay, axial hypotonia and peripheral increased muscular tone, absent speech, and generalized tonic seizures, which fit well MRT18, the occurrence of postnatal progressive microcephaly has been here documented. A retrospective assessment of the previously reported clinical data for these subjects confirms the occurrence of postnatal progressive microcephaly as a previously unappreciated feature of the phenotype of MED23-related disorder.
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Affiliation(s)
- Emanuela Salzano
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy,*Correspondence: Emanuela Salzano ✉
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Martina Busè
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | | | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Arturo Ferrara
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria Piccione
- Medical Genetics Unit, AOOR Villa Sofia-Cervello Hospitals, Palermo, Italy,Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
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26
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Sheth F, Shah J, Patel K, Patel D, Jain D, Sheth J, Sheth H. A novel case of two siblings harbouring homozygous variant in the NEUROG1 gene with autism as an additional phenotype: a case report. BMC Neurol 2023; 23:20. [PMID: 36647078 PMCID: PMC9841689 DOI: 10.1186/s12883-023-03065-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION NEUROG1 gene is yet to be associated with a set of human phenotypes in the OMIM database. Three cases have previously been diagnosed with cranial dysinnervation due to biallelic variants in the NEUROG1 gene. This is the fourth and a novel report of a sibling pair harboring a homozygous variant in the NEUROG1 gene with autism as an additional phenotype. A brief review of the literature in conjunction with a genotype-phenotype correlation has been described. A potential hypothesis for the presence of the autistic phenotype in the present case has also been elucidated. CASE PRESENTATION A female aged 6 years and 9 months born to endogamous and phenotypically healthy parents was diagnosed with global developmental delay, autism spectrum disorder, hearing loss, corneal opacity and no eye blinking. Her MRI of the brain revealed mild peritrigonal white matter hyperintensity, and MRI and CT scan of the temporal bones showed abnormal cranial nerves. The proband's younger sister, aged 4-years, was similarly affected. Whole exome sequencing was performed in the proband, which revealed a novel homozygous, likely pathogenic, truncating frameshift variant, c.228_231dup (p.Thr78ProfsTer122) in exon 1 of the NEUROG1 gene (ENST00000314744.4). Segregation analysis by Sanger sequencing showed the proband and her younger sister to be homozygotes and their parents to be heterozygous carriers. CONCLUSION This is the fourth report across the globe with a variant identified in the NEUROG1 gene to be associated with cranial dysinnervation phenotype. An additional phenotype of autism in two female siblings was a novel observation. We provide a hypothetical framework which could explain the pleiotropic effect of a dysfunctional NEUROG1 protein leading to autism and posit it as a candidate for diagnosis of autism spectrum disorder with congenital cranial dysinnervation disorder.
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Affiliation(s)
- Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015, Satellite, Ahmedabad, India.
| | - Jhanvi Shah
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015, Satellite, Ahmedabad, India
| | - Ketan Patel
- Speciality Homeopathy Clinic, Ahmedabad, India
| | - Darshan Patel
- Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology, Changa, Gujarat, India
| | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015, Satellite, Ahmedabad, India
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, 380015, Satellite, Ahmedabad, India.
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27
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Chesnel F, Jullion E, Delalande O, Couturier A, Alusse A, Le Goff X, Lenglet M, Gardie B, Abadie C, Arlot-Bonnemains Y. Mutation of the proline P81 into a serine modifies the tumour suppressor function of the von Hippel-Lindau gene in the ccRCC. Br J Cancer 2022; 127:1954-1962. [PMID: 36175619 PMCID: PMC9681884 DOI: 10.1038/s41416-022-01985-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The von Hippel-Lindau disease is an autosomal dominant syndrome associated with tumour formation in various tissues, such as retina, central nervous system, kidney, and adrenal glands. VHL gene deletion or mutations support the development of various cancers. Unclassified VHL variants also referred as "of unknown significance" result from gene mutations that have an unknown or unclear effect on protein functions. The P81S mutation has been linked to low penetrance Type 1 disease but its pathogenic function was not clearly determined. METHODS We established a stable cell line expressing the pVHL213 (c.241C>T, P81S) mutant. Using biochemical and physiological approaches, we herein analysed pVHL folding, stability and function in the context of this VHL single missense mutation. RESULTS The P81S mutation mostly affects the non-canonical function of the pVHL protein. The cells expressing the pVHL213P81S acquire invasive properties in relation with modified architecture network. CONCLUSION We demonstrated the pathogenic role of this mutation in tumour development in vhl patients and confirm a medical follow up of family carrying the c.241C>T, P81S.
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Affiliation(s)
- Franck Chesnel
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Emmanuelle Jullion
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Olivier Delalande
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Anne Couturier
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Adrien Alusse
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Xavier Le Goff
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Marion Lenglet
- Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
- Nantes Université, CNRS, INSERM, l'Institut du Thorax, F-44000, Nantes, France
| | - Betty Gardie
- Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
- Nantes Université, CNRS, INSERM, l'Institut du Thorax, F-44000, Nantes, France
| | - Caroline Abadie
- Institut de Cancérologie, Boulevard Jacques Monod, 44805, Saint-Herblain, France
| | - Yannick Arlot-Bonnemains
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France.
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28
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Jain PK, Jayappa S, Sairam T, Mittal A, Paul S, Rao VJ, Chittora H, Kashyap DK, Palakodeti D, Thangaraj K, Shenthar J, Koranchery R, Rajendran R, Alireza H, Mohanan KS, Rathinavel A, Dhandapany PS. Ribosomal protein S6 kinase beta-1 gene variants cause hypertrophic cardiomyopathy. J Med Genet 2022; 59:984-992. [PMID: 34916228 DOI: 10.1136/jmedgenet-2021-107866] [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: 03/22/2021] [Accepted: 11/18/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is a genetic heart muscle disease with preserved or increased ejection fraction in the absence of secondary causes. Mutations in the sarcomeric protein-encoding genes predominantly cause HCM. However, relatively little is known about the genetic impact of signalling proteins on HCM. METHODS AND RESULTS Here, using exome and targeted sequencing methods, we analysed two independent cohorts comprising 401 Indian patients with HCM and 3521 Indian controls. We identified novel variants in ribosomal protein S6 kinase beta-1 (RPS6KB1 or S6K1) gene in two unrelated Indian families as a potential candidate gene for HCM. The two unrelated HCM families had the same heterozygous missense S6K1 variant (p.G47W). In a replication association study, we identified two S6K1 heterozygotes variants (p.Q49K and p.Y62H) in the UK Biobank cardiomyopathy cohort (n=190) compared with matched controls (n=16 479). These variants are neither detected in region-specific controls nor in the human population genome data. Additionally, we observed an S6K1 variant (p.P445S) in an Arab patient with HCM. Functional consequences were evaluated using representative S6K1 mutated proteins compared with wild type in cellular models. The mutated proteins activated the S6K1 and hyperphosphorylated the rpS6 and ERK1/2 signalling cascades, suggesting a gain-of-function effect. CONCLUSIONS Our study demonstrates for the first time that the variants in the S6K1 gene are associated with HCM, and early detection of the S6K1 variant carriers can help to identify family members at risk and subsequent preventive measures. Further screening in patients with HCM with different ethnic populations will establish the specificity and frequency of S6K1 gene variants.
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Affiliation(s)
- Pratul Kumar Jain
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
- The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, Karnataka, India
| | - Shashank Jayappa
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
| | - Thiagarajan Sairam
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
| | - Anupam Mittal
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
- Current address: Department of Translational and Regenerative Medicine, PGIMER, Chandigarh, Chandigarh, India
| | - Sayan Paul
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
| | - Vinay J Rao
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
| | - Harshil Chittora
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Deepak K Kashyap
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
- CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - Dasaradhi Palakodeti
- Integrative Chemical Biology Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
| | - Kumarasamy Thangaraj
- CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Jayaprakash Shenthar
- Department of Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bangalore, Karnataka, India
| | - Rakesh Koranchery
- Department of Cardiology, Government Medical College Calicut, Kozhikode, Kerala, India
| | - Ranjith Rajendran
- Department of Cardiology, Government Medical College Calicut, Kozhikode, Kerala, India
| | - Haghighi Alireza
- Department of Medicine, Brigham and Women's Hospital Department of Medicine, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Andiappan Rathinavel
- Department of Cardio Vascular Thoracic Surgery, Madurai Medical College, Madurai, Tamil Nadu, India
- Government Sivagangai Medical College and Hospital, Sivagangai, Tamil Nadu, India
| | - Perundurai S Dhandapany
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, India
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon, USA
- Departments of Medicine, Molecular, and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
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29
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Dixon PH, Levine AP, Cebola I, Chan MMY, Amin AS, Aich A, Mozere M, Maude H, Mitchell AL, Zhang J, Chambers J, Syngelaki A, Donnelly J, Cooley S, Geary M, Nicolaides K, Thorsell M, Hague WM, Estiu MC, Marschall HU, Gale DP, Williamson C. GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements. Nat Commun 2022; 13:4840. [PMID: 35977952 PMCID: PMC9385867 DOI: 10.1038/s41467-022-29931-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/08/2022] [Indexed: 12/15/2022] Open
Abstract
Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5-2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility.
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Affiliation(s)
- Peter H Dixon
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Adam P Levine
- Department of Renal Medicine, University College London, London, UK
- Research Department of Pathology, University College London, London, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Melanie M Y Chan
- Department of Renal Medicine, University College London, London, UK
| | - Aliya S Amin
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Anshul Aich
- Department of Renal Medicine, University College London, London, UK
| | - Monika Mozere
- Department of Renal Medicine, University College London, London, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Alice L Mitchell
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Jun Zhang
- Department of Renal Medicine, University College London, London, UK
- Division of Nephrology, Department of Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jenny Chambers
- ICP Support, 69 Mere Green Road, Sutton Coldfield, UK
- Women's Health Research Centre, Imperial College London, London, UK
| | - Argyro Syngelaki
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, UK
| | | | | | | | - Kypros Nicolaides
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, UK
| | | | - William M Hague
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Daniel P Gale
- Department of Renal Medicine, University College London, London, UK
| | - Catherine Williamson
- Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK.
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30
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Stanescu S, Bravo-Alonso I, Belanger-Quintana A, Pérez B, Medina-Diaz M, Ruiz-Sala P, Flores NP, Buenache R, Arrieta F, Rodríguez-Pombo P. Mitochondrial bioenergetic is impaired in Monocarboxylate transporter 1 deficiency: a new clinical case and review of the literature. Orphanet J Rare Dis 2022; 17:243. [PMID: 35729663 PMCID: PMC9215049 DOI: 10.1186/s13023-022-02389-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background Monocarboxylate transporter 1 (MCT1) deficiency has recently been described as a rare cause of recurrent ketosis, the result of impaired ketone utilization in extrahepatic tissues. To date, only six patients with this condition have been identified, and clinical and biochemical details remain incomplete. Results The present work reports a patient suffering from severe, recurrent episodes of metabolic acidosis and psychomotor delay, showing a pathogenic loss-of-function variation c.747_750del in homozygosity in SLC16A1 (which codes for MCT1). Persistent ketotic and lactic acidosis was accompanied by an abnormal excretion of organic acids related to redox balance disturbances. Together with an altered bioenergetic profile detected in patient-derived fibroblasts, this suggests possible mitochondrial dysfunction. Brain MRI revealed extensive, diffuse bilateral, symmetric signal alterations for the subcortical white matter and basal ganglia, together with corpus callosum agenesia. Conclusions These findings suggest that the clinical spectrum of MCT1 deficiency not only involves recurrent atacks of ketoacidosis, but may also cause lactic acidosis and neuromotor delay with a distinctive neuroimaging pattern including agenesis of corpus callosum and other brain signal alterations. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02389-4.
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Affiliation(s)
- Sinziana Stanescu
- Unidad de Enfermedades Metabólicas, Hospital Universitario Ramón y Cajal, IRYCIS, Crta de Colmenar Viejo, km 9,100, 28034, Madrid, Spain.
| | - Irene Bravo-Alonso
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CIBERER, IdiPAZ, C/Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
| | - Amaya Belanger-Quintana
- Unidad de Enfermedades Metabólicas, Hospital Universitario Ramón y Cajal, IRYCIS, Crta de Colmenar Viejo, km 9,100, 28034, Madrid, Spain
| | - Belen Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CIBERER, IdiPAZ, C/Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
| | - Montserrat Medina-Diaz
- Department of Neuroradiology, Hospital Universitario Ramón y Cajal, IRYCIS, Crta de Colmenar Viejo, km 9,100, 28034, Madrid, Spain
| | - Pedro Ruiz-Sala
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, C/Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
| | - Nathaly Paola Flores
- Paediatric Department, Hospital General La Mancha Centro, Av. Constitución, 3, 13600, Alcázar de San Juan, Ciudad Real, Spain
| | - Raquel Buenache
- Neuropediatric Department, Hospital Universitario Ramón y Cajal, IRYCIS, Crta de Colmenar Viejo, km 9,100, 28034, Madrid, Spain
| | - Francisco Arrieta
- Unidad de Enfermedades Metabólicas, Hospital Universitario Ramón y Cajal, IRYCIS, CIBER-OBN, Crta de Colmenar Viejo, km 9,100, 28034, Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CIBERER, IdiPAZ, C/Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
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31
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Paiva VDA, Gomes IDS, Monteiro CR, Mendonça MV, Martins PM, Santana CA, Gonçalves-Almeida V, Izidoro SC, Melo-Minardi RCD, Silveira SDA. Protein structural bioinformatics: An overview. Comput Biol Med 2022; 147:105695. [DOI: 10.1016/j.compbiomed.2022.105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/27/2022]
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32
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Holling T, Nampoothiri S, Tarhan B, Schneeberger PE, Vinayan KP, Yesodharan D, Roy AG, Radhakrishnan P, Alawi M, Rhodes L, Girisha KM, Kang PB, Kutsche K. Novel biallelic variants expand the SLC5A6-related phenotypic spectrum. Eur J Hum Genet 2022; 30:439-449. [PMID: 35013551 PMCID: PMC8747999 DOI: 10.1038/s41431-021-01033-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022] Open
Abstract
The sodium (Na+):multivitamin transporter (SMVT), encoded by SLC5A6, belongs to the sodium:solute symporter family and is required for the Na+-dependent uptake of biotin (vitamin B7), pantothenic acid (vitamin B5), the vitamin-like substance α-lipoic acid, and iodide. Compound heterozygous SLC5A6 variants have been reported in individuals with variable multisystemic disorder, including failure to thrive, developmental delay, seizures, cerebral palsy, brain atrophy, gastrointestinal problems, immunodeficiency, and/or osteopenia. We expand the phenotypic spectrum associated with biallelic SLC5A6 variants affecting function by reporting five individuals from three families with motor neuropathies. We identified the homozygous variant c.1285 A > G [p.(Ser429Gly)] in three affected siblings and a simplex patient and the maternally inherited c.280 C > T [p.(Arg94*)] variant and the paternally inherited c.485 A > G [p.(Tyr162Cys)] variant in the simplex patient of the third family. Both missense variants were predicted to affect function by in silico tools. 3D homology modeling of the human SMVT revealed 13 transmembrane helices (TMs) and Tyr162 and Ser429 to be located at the cytoplasmic facing region of TM4 and within TM11, respectively. The SLC5A6 missense variants p.(Tyr162Cys) and p.(Ser429Gly) did not affect plasma membrane localization of the ectopically expressed multivitamin transporter suggesting reduced but not abolished function, such as lower catalytic activity. Targeted therapeutic intervention yielded clinical improvement in four of the five patients. Early molecular diagnosis by exome sequencing is essential for timely replacement therapy in affected individuals.
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Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Bedirhan Tarhan
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Pauline E Schneeberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Amedes MVZ Wagnerstibbe für Laboratoriumsmedizin, Hämostaseologie, Humangenetik und Mikrobiologie Hannover, 30159, Hannover, Germany
| | | | - Dhanya Yesodharan
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Arun Grace Roy
- Department of Neurology, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Periyasamy Radhakrishnan
- Suma Genomics Pvt. Ltd, Manipal Universal Technology Business Incubator (MUTBI), Manipal, 576104, India
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, 576104, India
| | - Peter B Kang
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, 32610, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
- Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
- Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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Leung AWS, Leung HCM, Wong CL, Zheng ZX, Lui WW, Luk HM, Lo IFM, Luo R, Lam TW. ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell. BMC Med Genomics 2022; 15:43. [PMID: 35246132 PMCID: PMC8895767 DOI: 10.1186/s12920-022-01190-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 02/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field. Having a high sequencing error of ONT and limited throughput from a single MinION flowcell, however, limits its applicability for accurate variant detection. Medical exome sequencing (MES) targets clinically significant exon regions, allowing rapid and comprehensive screening of pathogenic variants. By applying MES with MinION sequencing, the technology can achieve a more uniform capture of the target regions, shorter turnaround time, and lower sequencing cost per sample. METHOD We introduced a cost-effective optimized workflow, ECNano, comprising a wet-lab protocol and bioinformatics analysis, for accurate variant detection at 4800 clinically important genes and regions using a single MinION flowcell. The ECNano wet-lab protocol was optimized to perform long-read target enrichment and ONT library preparation to stably generate high-quality MES data with adequate coverage. The subsequent variant-calling workflow, Clair-ensemble, adopted a fast RNN-based variant caller, Clair, and was optimized for target enrichment data. To evaluate its performance and practicality, ECNano was tested on both reference DNA samples and patient samples. RESULTS ECNano achieved deep on-target depth of coverage (DoC) at average > 100× and > 98% uniformity using one MinION flowcell. For accurate ONT variant calling, the generated reads sufficiently covered 98.9% of pathogenic positions listed in ClinVar, with 98.96% having at least 30× DoC. ECNano obtained an average read length of 1000 bp. The long reads of ECNano also covered the adjacent splice sites well, with 98.5% of positions having ≥ 30× DoC. Clair-ensemble achieved > 99% recall and accuracy for SNV calling. The whole workflow from wet-lab protocol to variant detection was completed within three days. CONCLUSION We presented ECNano, an out-of-the-box workflow comprising (1) a wet-lab protocol for ONT target enrichment sequencing and (2) a downstream variant detection workflow, Clair-ensemble. The workflow is cost-effective, with a short turnaround time for high accuracy variant calling in 4800 clinically significant genes and regions using a single MinION flowcell. The long-read exon captured data has potential for further development, promoting the application of long-read sequencing in personalized disease treatment and risk prediction.
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Affiliation(s)
- Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | | | - Chak-Lim Wong
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Zhen-Xian Zheng
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Wui-Wang Lui
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Ho-Ming Luk
- Department of Health, Clinical Genetic Service, Hong Kong, SAR, China
| | - Ivan Fai-Man Lo
- Department of Health, Clinical Genetic Service, Hong Kong, SAR, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.
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34
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Angelozzi M, Karvande A, Molin AN, Ritter AL, Leonard JMM, Savatt JM, Douglass K, Myers SM, Grippa M, Tolchin D, Zackai E, Donoghue S, Hurst ACE, Descartes M, Smith K, Velasco D, Schmanski A, Crunk A, Tokita MJ, de Lange IM, van Gassen K, Robinson H, Guegan K, Suri M, Patel C, Bournez M, Faivre L, Tran-Mau-Them F, Baker J, Fabie N, Weaver K, Shillington A, Hopkin RJ, Barge-Schaapveld DQCM, Ruivenkamp CA, Bökenkamp R, Vergano S, Seco Moro MN, Díaz de Bustamante A, Misra VK, Kennelly K, Rogers C, Friedman J, Wigby KM, Lenberg J, Graziano C, Ahrens-Nicklas RC, Lefebvre V. Consolidation of the clinical and genetic definition of a SOX4-related neurodevelopmental syndrome. J Med Genet 2022; 59:1058-1068. [PMID: 35232796 DOI: 10.1136/jmedgenet-2021-108375] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/13/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND A neurodevelopmental syndrome was recently reported in four patients with SOX4 heterozygous missense variants in the high-mobility-group (HMG) DNA-binding domain. The present study aimed to consolidate clinical and genetic knowledge of this syndrome. METHODS We newly identified 17 patients with SOX4 variants, predicted variant pathogenicity using in silico tests and in vitro functional assays and analysed the patients' phenotypes. RESULTS All variants were novel, distinct and heterozygous. Seven HMG-domain missense and five stop-gain variants were classified as pathogenic or likely pathogenic variant (L/PV) as they precluded SOX4 transcriptional activity in vitro. Five HMG-domain and non-HMG-domain missense variants were classified as of uncertain significance (VUS) due to negative results from functional tests. When known, inheritance was de novo or from a mosaic unaffected or non-mosaic affected parent for patients with L/PV, and from a non-mosaic asymptomatic or affected parent for patients with VUS. All patients had neurodevelopmental, neurological and dysmorphic features, and at least one cardiovascular, ophthalmological, musculoskeletal or other somatic anomaly. Patients with L/PV were overall more affected than patients with VUS. They resembled patients with other neurodevelopmental diseases, including the SOX11-related and Coffin-Siris (CSS) syndromes, but lacked the most specific features of CSS. CONCLUSION These findings consolidate evidence of a fairly non-specific neurodevelopmental syndrome due to SOX4 haploinsufficiency in neurogenesis and multiple other developmental processes.
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Affiliation(s)
- Marco Angelozzi
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Anirudha Karvande
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Arnaud N Molin
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Alyssa L Ritter
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacqueline M M Leonard
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Kristen Douglass
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Scott M Myers
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Mina Grippa
- U.O. Genetica Medica, Universita di Bologna, Bologna, Italy
| | - Dara Tolchin
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sarah Donoghue
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Anna C E Hurst
- Department of Genetics, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Maria Descartes
- Department of Genetics, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Kirstin Smith
- Department of Genetics, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Danita Velasco
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Andrew Schmanski
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Amy Crunk
- GeneDx Inc, Gaithersburg, Maryland, USA
| | | | - Iris M de Lange
- Department of Medical Genetics, University Medical Centre Utrecht Brain Centre, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Medical Genetics, University Medical Centre Utrecht Brain Centre, Utrecht, The Netherlands
| | - Hannah Robinson
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Katie Guegan
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Mohnish Suri
- Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Marie Bournez
- Centres de référence Anomalies du Développement et Syndrome Malformatifs, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Laurence Faivre
- Centre de Génétique, Centre Hospitalier Universitaire de Dijon Hôpital d'Enfants, Dijon, France
| | - Frédéric Tran-Mau-Them
- Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France.,Functional Unit 6254 Innovation in Genomic Diagnosis of Rare Diseases, CHU Dijon Bourgogne, Dijon, France
| | - Janice Baker
- Genomics and Genetic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Noelle Fabie
- Genomics and Genetic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - K Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Amelle Shillington
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Robert J Hopkin
- Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Claudia Al Ruivenkamp
- Laboratory for Diagnostic Genome Analyses, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Regina Bökenkamp
- Department of Pediatric Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Samantha Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia, USA
| | | | | | - Vinod K Misra
- Department of Pediatrics, Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan, USA.,Discipline of Pediatrics, Central Michigan University, Mount Pleasant, Michigan, USA
| | - Kelly Kennelly
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Caleb Rogers
- Department of Molecular and Medical Genetics, Oregon Health & Science University School of Medicine, Portland, Oregon, USA
| | - Jennifer Friedman
- Department of Pediatrics, University of California San Diego, San Diego, California, USA.,Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA.,Department of Neurosciences, University of California San Diego, San Diego, California, USA.,Division of Neurology, Rady Children's Hospital, San Diego, California, USA
| | - Kristen M Wigby
- Department of Pediatrics, University of California San Diego, San Diego, California, USA.,Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Jerica Lenberg
- Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Claudio Graziano
- Department of Pediatrics, University of California San Diego, San Diego, California, USA .,Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA.,Department of Neurosciences, University of California San Diego, San Diego, California, USA.,Division of Neurology, Rady Children's Hospital, San Diego, California, USA.,U.O. Genetica Medica, AUSL della Romagna Rimini, Cesena, Italy
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Veronique Lefebvre
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
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Novel phenotype and genotype spectrum of WDR62 in two patients with associated primary autosomal recessive microcephaly. Ir J Med Sci 2022; 191:2733-2741. [PMID: 35031939 DOI: 10.1007/s11845-021-02890-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Microcephaly is a prominent feature of patients with primary autosomal recessive microcephaly 2 (MCPH2) caused by mutations in the WD Repeat Domain 62 (WDR62; OMIM: 613,583). AIM The study aimed to identify the underlying genetic factor(s) causing microcephaly in two patients in a consanguineous Iranian family. METHODS Two male patients (11 and 27 years old) were noticed due to microcephaly, neurodevelopmental delay, and occasional seizures. The younger patient (the proband) was subjected to paired-end whole-exome sequencing followed by Sanger sequencing to detect any underlying genetic factor. RESULTS Upon examination, both patients showed microcephaly as a prominent manifestation; they were under-weighted as well. The patients had a moderate gross motor impairment, severe cognitive disability and speech delay, increased deep tendon reflexes, flexible joint contractures, sensorineural hearing loss, and vertical nystagmus as a new ocular finding. The proband had more severe neurodevelopmental delay symptoms. The brain magnetic resonance imaging series revealed severe structural and cortical brain abnormalities in addition to hemiatrophy. Using Whole-exome Sequencing, a novel homozygous missense variant-NM_001083961.2; c.1598A > G: p.(His533Arg)-was identified in the WDR62. Subsequently, in silico analyses determined the possible impacts of the novel variant on the structure and function of WDR62 protein. CONCLUSIONS Herein, we identified a novel homozygous missense variant in the WDR62 in two patients with MCPH2. Vertical nystagmus and sensorineural hearing loss were detected as novel neurological findings. The present study expands the phenotype and genotype spectrum of MCPH2.
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Lai CY, Tsai IJ, Chiu PC, Ascher DB, Chien YH, Huang YH, Lin YL, Hwu WL, Lee NC. A novel deep intronic variant strongly associates with Alkaptonuria. NPJ Genom Med 2021; 6:89. [PMID: 34686677 PMCID: PMC8536767 DOI: 10.1038/s41525-021-00252-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022] Open
Abstract
Alkaptonuria is a rare autosomal recessive inherited disorder of tyrosine metabolism, which causes ochronosis, arthropathy, cardiac valvular calcification, and urolithiasis. The epidemiology of alkaptonuria in East Asia is not clear. In this study, patients diagnosed with alkaptonuria from January 2010 to June 2020 were reviewed. Their clinical and molecular features were further compared with those of patients from other countries. Three patients were found to have alkaptonuria. Mutation analyses of the homogentisate 1,2-dioxygenase gene (HGD) showed four novel variants c.16-2063 A > C, p.(Thr196Ile), p.(Gly344AspfsTer25), and p.(Gly362Arg) in six mutated alleles (83.3%). RNA sequencing revealed that c.16-2063 A > C activates a cryptic exon, causing protein truncation p.(Tyr5_Ile6insValTer17). A literature search identified another 6 patients with alkaptonuria in East Asia; including our cases, 13 of the 18 mutated alleles have not been reported elsewhere in the world. Alkaptonuria is rare in Taiwan and East Asia, with HGD variants being mostly novel and private.
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Affiliation(s)
- Chien-Yi Lai
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - I-Jung Tsai
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
| | - Pao-Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry, Bio21 Institute, University of Cambridge, Cambridge, UK
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
| | - Yu-Hsuan Huang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan.
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Ciolfi A, Foroutan A, Capuano A, Pedace L, Travaglini L, Pizzi S, Andreani M, Miele E, Invernizzi F, Reale C, Panteghini C, Iascone M, Niceta M, Gavrilova RH, Schultz-Rogers L, Agolini E, Bedeschi MF, Prontera P, Garibaldi M, Galosi S, Leuzzi V, Soliveri P, Olson RJ, Zorzi GS, Garavaglia BM, Tartaglia M, Sadikovic B. Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile. Clin Epigenetics 2021; 13:157. [PMID: 34380541 PMCID: PMC8359374 DOI: 10.1186/s13148-021-01145-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
Background Dystonia is a clinically and genetically heterogeneous movement disorder characterized by sustained or intermittent muscle contractions causing abnormal, often repetitive, movements and/or postures. Heterozygous variants in lysine methyltransferase 2B (KMT2B), encoding a histone H3 methyltransferase, have been associated with a childhood-onset, progressive and complex form of dystonia (dystonia 28, DYT28). Since 2016, more than one hundred rare KMT2B variants have been reported, including frameshift, nonsense, splice site, missense and other in-frame changes, many having an uncertain clinical impact. Results We characterize the genome-wide peripheral blood DNA methylation profiles of a cohort of 18 patients with pathogenic and unclassified KMT2B variants. We resolve the “episignature” associated with KMT2B haploinsufficiency, proving that this approach is robust in diagnosing clinically unsolved cases, properly classifying them with respect to other partially overlapping dystonic phenotypes, other rare neurodevelopmental disorders and healthy controls. Notably, defective KMT2B function in DYT28 causes a non-random DNA hypermethylation across the genome, selectively involving promoters and other regulatory regions positively controlling gene expression. Conclusions We demonstrate a distinctive DNA hypermethylation pattern associated with DYT28, provide an epigenetic signature for this disorder enabling accurate diagnosis and reclassification of ambiguous genetic findings and suggest potential therapeutic approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01145-y.
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Affiliation(s)
- Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Alessandro Capuano
- Department of Neuroscience, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Lorena Travaglini
- 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
| | - Marco Andreani
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Federica Invernizzi
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Chiara Reale
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Celeste Panteghini
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Maria Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | | | - Emanuele Agolini
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Paolo Prontera
- Maternal-Infantile Department, University Hospital of Perugia, Perugia, Italy
| | - Matteo Garibaldi
- Department of Neuroscience, NESMOS, Sapienza University, Sant'Andrea Hospital, Rome, Italy
| | - Serena Galosi
- Department of Human Neuroscience, Child Neurology and Psychiatry, Sapienza University, Rome, Italy
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Child Neurology and Psychiatry, Sapienza University, Rome, Italy
| | - Paola Soliveri
- Department of Neurology, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Rory J Olson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Giovanna S Zorzi
- Department of Child Neurology, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Barbara M Garavaglia
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Marco Tartaglia
- 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, ON, N6A 3K7, Canada. .,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada. .,Molecular Diagnostics Division, London Health Sciences Centre, London, Canada.
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Broadening INPP5E phenotypic spectrum: detection of rare variants in syndromic and non-syndromic IRD. NPJ Genom Med 2021; 6:53. [PMID: 34188062 PMCID: PMC8242099 DOI: 10.1038/s41525-021-00214-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Pathogenic variants in INPP5E cause Joubert syndrome (JBTS), a ciliopathy with retinal involvement. However, despite sporadic cases in large cohort sequencing studies, a clear association with non-syndromic inherited retinal degenerations (IRDs) has not been made. We validate this association by reporting 16 non-syndromic IRD patients from ten families with bi-allelic mutations in INPP5E. Additional two patients showed early onset IRD with limited JBTS features. Detailed phenotypic description for all probands is presented. We report 14 rare INPP5E variants, 12 of which have not been reported in previous studies. We present tertiary protein modeling and analyze all INPP5E variants for deleteriousness and phenotypic correlation. We observe that the combined impact of INPP5E variants in JBTS and non-syndromic IRD patients does not reveal a clear genotype-phenotype correlation, suggesting the involvement of genetic modifiers. Our study cements the wide phenotypic spectrum of INPP5E disease, adding proof that sequence defects in this gene can lead to early-onset non-syndromic IRD.
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39
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Variants in GCNA, X-linked germ-cell genome integrity gene, identified in men with primary spermatogenic failure. Hum Genet 2021; 140:1169-1182. [PMID: 33963445 DOI: 10.1007/s00439-021-02287-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/23/2021] [Indexed: 01/25/2023]
Abstract
Male infertility impacts millions of couples yet, the etiology of primary infertility remains largely unknown. A critical element of successful spermatogenesis is maintenance of genome integrity. Here, we present a genomic study of spermatogenic failure (SPGF). Our initial analysis (n = 176) did not reveal known gene-candidates but identified a potentially significant single-nucleotide variant (SNV) in X-linked germ-cell nuclear antigen (GCNA). Together with a larger follow-up study (n = 2049), 7 likely clinically relevant GCNA variants were identified. GCNA is critical for genome integrity in male meiosis and knockout models exhibit impaired spermatogenesis and infertility. Single-cell RNA-seq and immunohistochemistry confirm human GCNA expression from spermatogonia to elongated spermatids. Five identified SNVs were located in key functional regions, including N-terminal SUMO-interacting motif and C-terminal Spartan-like protease domain. Notably, variant p.Ala115ProfsTer7 results in an early frameshift, while Spartan-like domain missense variants p.Ser659Trp and p.Arg664Cys change conserved residues, likely affecting 3D structure. For variants within GCNA's intrinsically disordered region, we performed computational modeling for consensus motifs. Two SNVs were predicted to impact the structure of these consensus motifs. All identified variants have an extremely low minor allele frequency in the general population and 6 of 7 were not detected in > 5000 biological fathers. Considering evidence from animal models, germ-cell-specific expression, 3D modeling, and computational predictions for SNVs, we propose that identified GCNA variants disrupt structure and function of the respective protein domains, ultimately arresting germ-cell division. To our knowledge, this is the first study implicating GCNA, a key genome integrity factor, in human male infertility.
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40
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Gillentine MA, Wang T, Hoekzema K, Rosenfeld J, Liu P, Guo H, Kim CN, De Vries BBA, Vissers LELM, Nordenskjold M, Kvarnung M, Lindstrand A, Nordgren A, Gecz J, Iascone M, Cereda A, Scatigno A, Maitz S, Zanni G, Bertini E, Zweier C, Schuhmann S, Wiesener A, Pepper M, Panjwani H, Torti E, Abid F, Anselm I, Srivastava S, Atwal P, Bacino CA, Bhat G, Cobian K, Bird LM, Friedman J, Wright MS, Callewaert B, Petit F, Mathieu S, Afenjar A, Christensen CK, White KM, Elpeleg O, Berger I, Espineli EJ, Fagerberg C, Brasch-Andersen C, Hansen LK, Feyma T, Hughes S, Thiffault I, Sullivan B, Yan S, Keller K, Keren B, Mignot C, Kooy F, Meuwissen M, Basinger A, Kukolich M, Philips M, Ortega L, Drummond-Borg M, Lauridsen M, Sorensen K, Lehman A, Lopez-Rangel E, Levy P, Lessel D, Lotze T, Madan-Khetarpal S, Sebastian J, Vento J, Vats D, Benman LM, Mckee S, Mirzaa GM, Muss C, Pappas J, Peeters H, Romano C, Elia M, Galesi O, Simon MEH, van Gassen KLI, Simpson K, Stratton R, Syed S, Thevenon J, Palafoll IV, Vitobello A, Bournez M, Faivre L, Xia K, Earl RK, Nowakowski T, Bernier RA, Eichler EE. Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders. Genome Med 2021; 13:63. [PMID: 33874999 PMCID: PMC8056596 DOI: 10.1186/s13073-021-00870-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND With the increasing number of genomic sequencing studies, hundreds of genes have been implicated in neurodevelopmental disorders (NDDs). The rate of gene discovery far outpaces our understanding of genotype-phenotype correlations, with clinical characterization remaining a bottleneck for understanding NDDs. Most disease-associated Mendelian genes are members of gene families, and we hypothesize that those with related molecular function share clinical presentations. METHODS We tested our hypothesis by considering gene families that have multiple members with an enrichment of de novo variants among NDDs, as determined by previous meta-analyses. One of these gene families is the heterogeneous nuclear ribonucleoproteins (hnRNPs), which has 33 members, five of which have been recently identified as NDD genes (HNRNPK, HNRNPU, HNRNPH1, HNRNPH2, and HNRNPR) and two of which have significant enrichment in our previous meta-analysis of probands with NDDs (HNRNPU and SYNCRIP). Utilizing protein homology, mutation analyses, gene expression analyses, and phenotypic characterization, we provide evidence for variation in 12 HNRNP genes as candidates for NDDs. Seven are potentially novel while the remaining genes in the family likely do not significantly contribute to NDD risk. RESULTS We report 119 new NDD cases (64 de novo variants) through sequencing and international collaborations and combined with published clinical case reports. We consider 235 cases with gene-disruptive single-nucleotide variants or indels and 15 cases with small copy number variants. Three hnRNP-encoding genes reach nominal or exome-wide significance for de novo variant enrichment, while nine are candidates for pathogenic mutations. Comparison of HNRNP gene expression shows a pattern consistent with a role in cerebral cortical development with enriched expression among radial glial progenitors. Clinical assessment of probands (n = 188-221) expands the phenotypes associated with HNRNP rare variants, and phenotypes associated with variation in the HNRNP genes distinguishes them as a subgroup of NDDs. CONCLUSIONS Overall, our novel approach of exploiting gene families in NDDs identifies new HNRNP-related disorders, expands the phenotypes of known HNRNP-related disorders, strongly implicates disruption of the hnRNPs as a whole in NDDs, and supports that NDD subtypes likely have shared molecular pathogenesis. To date, this is the first study to identify novel genetic disorders based on the presence of disorders in related genes. We also perform the first phenotypic analyses focusing on related genes. Finally, we show that radial glial expression of these genes is likely critical during neurodevelopment. This is important for diagnostics, as well as developing strategies to best study these genes for the development of therapeutics.
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Affiliation(s)
- Madelyn A Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Jill Rosenfeld
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Hui Guo
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Bert B A De Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Magnus Nordenskjold
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jozef Gecz
- School of Medicine and the Robinson Research Institute, the University of Adelaide at the Women's and Children's Hospital, Adelaide, South Australia, Australia.,Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Agnese Scatigno
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Maitz
- Genetic Unit, Department of Pediatrics, Fondazione MBBM S. Gerardo Hospital, Monza, Italy
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sarah Schuhmann
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Micah Pepper
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | - Heena Panjwani
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | | | - Farida Abid
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Irina Anselm
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paldeep Atwal
- The Atwal Clinic: Genomic & Personalized Medicine, Jacksonville, FL, USA
| | - Carlos A Bacino
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gifty Bhat
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Katherine Cobian
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA, USA
| | - Jennifer Friedman
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Meredith S Wright
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bert Callewaert
- Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Florence Petit
- Clinique de Génétique, Hôpital Jeanne de Flandre, Bâtiment Modulaire, CHU, 59037, Lille Cedex, France
| | - Sophie Mathieu
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Alexandra Afenjar
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Celenie K Christensen
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kerry M White
- Department of Medical and Molecular Genetics, IU Health, Indianapolis, IN, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Itai Berger
- Pediatric Neurology, Assuta-Ashdod University Hospital, Ashdod, Israel.,Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Edward J Espineli
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Timothy Feyma
- Gillette Children's Specialty Healthcare, Saint Paul, MN, USA
| | - Susan Hughes
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA.,The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
| | - Isabelle Thiffault
- The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA.,Children's Mercy Kansas City, Center for Pediatric Genomic Medicine, Kansas City, MO, USA
| | - Bonnie Sullivan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Shuang Yan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kory Keller
- Oregon Health & Science University, Corvallis, OR, USA
| | - Boris Keren
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Cyril Mignot
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Alice Basinger
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Mary Kukolich
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Meredith Philips
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Lucia Ortega
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | | | - Mathilde Lauridsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kristina Sorensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital and BC Women's Hospital, Vancouver, BC, Canada
| | | | - Elena Lopez-Rangel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Division of Developmental Pediatrics, Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada.,Sunny Hill Health Centre for Children, Vancouver, BC, Canada
| | - Paul Levy
- Department of Pediatrics, The Children's Hospital at Montefiore, Bronx, NY, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Lotze
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Suneeta Madan-Khetarpal
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.,UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jodie Vento
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Divya Vats
- Kaiser Permanente Southern California, Los Angeles, CA, USA
| | | | - Shane Mckee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Candace Muss
- Al Dupont Hospital for Children, Wilmington, DE, USA
| | - John Pappas
- NYU Grossman School of Medicine, Department of Pediatrics, Clinical Genetic Services, New York, NY, USA
| | - Hilde Peeters
- Center for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | | | | | | | - Marleen E H Simon
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Kara Simpson
- Rare Disease Institute, Children's National Health System, Washington, DC, USA
| | - Robert Stratton
- Department of Genetics, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Sabeen Syed
- Department of Pediatric Gastroenterology, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Julien Thevenon
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebrón, Barcelona, Spain
| | | | - Antonio Vitobello
- UF Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne and INSERM UMR1231 GAD, Université de Bourgogne Franche-Comté, F-21000, Dijon, France.,INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France
| | - Marie Bournez
- Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Rachel K Earl
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Tomasz Nowakowski
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Raphael A Bernier
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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41
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Li D, March ME, Fortugno P, Cox LL, Matsuoka LS, Monetta R, Seiler C, Pyle LC, Bedoukian EC, Sánchez-Soler MJ, Caluseriu O, Grand K, Tam A, Aycinena ARP, Camerota L, Guo Y, Sleiman P, Callewaert B, Kumps C, Dheedene A, Buckley M, Kirk EP, Turner A, Kamien B, Patel C, Wilson M, Roscioli T, Christodoulou J, Cox TC, Zackai EH, Brancati F, Hakonarson H, Bhoj EJ. Pathogenic variants in CDH11 impair cell adhesion and cause Teebi hypertelorism syndrome. Hum Genet 2021; 140:1061-1076. [PMID: 33811546 DOI: 10.1007/s00439-021-02274-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Teebi hypertelorism syndrome (THS; OMIM 145420) is a rare craniofacial disorder characterized by hypertelorism, prominent forehead, short nose with broad or depressed nasal root. Some cases of THS have been attributed to SPECC1L variants. Homozygous variants in CDH11 truncating the transmembrane and intracellular domains have been implicated in Elsahy-Waters syndrome (EWS; OMIM 211380) with hypertelorism. We report THS due to CDH11 heterozygous missense variants on 19 subjects from 9 families. All affected residues in the extracellular region of Cadherin-11 (CHD11) are highly conserved across vertebrate species and classical cadherins. Six of the variants that cluster around the EC2-EC3 and EC3-EC4 linker regions are predicted to affect Ca2+ binding that is required for cadherin stability. Two of the additional variants [c.164G > C, p.(Trp55Ser) and c.418G > A, p.(Glu140Lys)] are also notable as they are predicted to directly affect trans-homodimer formation. Immunohistochemical study demonstrates that CDH11 is strongly expressed in human facial mesenchyme. Using multiple functional assays, we show that five variants from the EC1, EC2-EC3 linker, and EC3 regions significantly reduced the cell-substrate trans adhesion activity and one variant from EC3-EC4 linker results in changes in cell morphology, focal adhesion, and migration, suggesting dominant negative effect. Characteristic features in this cohort included depressed nasal root, cardiac and umbilical defects. These features distinguished this phenotype from that seen in SPECC1L-related hypertelorism syndrome and CDH11-related EWS. Our results demonstrate heterozygous variants in CDH11, which decrease cell-cell adhesion and increase cell migratory behavior, cause a form of THS, as termed CDH11-related THS.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Michael E March
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paola Fortugno
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Rome, Italy.,Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Liza L Cox
- Departments of Oral and Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City School of Dentistry, Kansas City, MO, 64108, USA
| | - Leticia S Matsuoka
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rosanna Monetta
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Rome, Italy.,Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Christoph Seiler
- Zebrafish Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Louise C Pyle
- Individualized Medical Genetics Center, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Emma C Bedoukian
- Individualized Medical Genetics Center, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - María José Sánchez-Soler
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, España
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada.,The Stollery Pediatric Hospital, Edmonton, AB, T6G 2H7, Canada
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Allison Tam
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Alicia R P Aycinena
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Letizia Camerota
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Yiran Guo
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patrick Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Michael Buckley
- NSW Health Pathology Genomics Laboratory, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Edwin P Kirk
- NSW Health Pathology Genomics Laboratory, Prince of Wales Hospital, Randwick, NSW, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Anne Turner
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Tony Roscioli
- NSW Health Pathology Genomics Laboratory, Prince of Wales Hospital, Randwick, NSW, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.,Neuroscience Research Australia and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Timothy C Cox
- Departments of Oral and Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City School of Dentistry, Kansas City, MO, 64108, USA
| | - Elaine H Zackai
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy.,Institute of Translational Pharmacology, National Research Council, Rome, Italy.,IRCCS San Raffaele Pisana, Rome, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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Heron SE, Regan BM, Harris RV, Gardner AE, Coleman MJ, Bennett MF, Grinton BE, Helbig KL, Sperling MR, Haut S, Geller EB, Widdess-Walsh P, Pelekanos JT, Bahlo M, Petrovski S, Heinzen EL, Hildebrand MS, Corbett MA, Scheffer IE, Gécz J, Berkovic SF. Association of SLC32A1 Missense Variants With Genetic Epilepsy With Febrile Seizures Plus. Neurology 2021; 96:e2251-e2260. [PMID: 34038384 DOI: 10.1212/wnl.0000000000011855] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/05/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To identify the causative gene in a large unsolved family with genetic epilepsy with febrile seizures plus (GEFS+), we sequenced the genomes of family members, and then determined the contribution of the identified gene to the pathogenicity of epilepsies by examining sequencing data from 2,772 additional patients. METHODS We performed whole genome sequencing of 3 members of a GEFS+ family. Subsequently, whole exome sequencing data from 1,165 patients with epilepsy from the Epi4K dataset and 1,329 Australian patients with epilepsy from the Epi25 dataset were interrogated. Targeted resequencing was performed on 278 patients with febrile seizures or GEFS+ phenotypes. Variants were validated and familial segregation examined by Sanger sequencing. RESULTS Eight previously unreported missense variants were identified in SLC32A1, coding for the vesicular inhibitory amino acid cotransporter VGAT. Two variants cosegregated with the phenotype in 2 large GEFS+ families containing 8 and 10 affected individuals, respectively. Six further variants were identified in smaller families with GEFS+ or idiopathic generalized epilepsy (IGE). CONCLUSION Missense variants in SLC32A1 cause GEFS+ and IGE. These variants are predicted to alter γ-aminobutyric acid (GABA) transport into synaptic vesicles, leading to altered neuronal inhibition. Examination of further epilepsy cohorts will determine the full genotype-phenotype spectrum associated with SLC32A1 variants.
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Affiliation(s)
- Sarah E Heron
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Brigid M Regan
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Rebekah V Harris
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Alison E Gardner
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Matthew J Coleman
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Mark F Bennett
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Bronwyn E Grinton
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Katherine L Helbig
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Michael R Sperling
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Sheryl Haut
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Eric B Geller
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Peter Widdess-Walsh
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - James T Pelekanos
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Melanie Bahlo
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Slavé Petrovski
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Erin L Heinzen
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Michael S Hildebrand
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Mark A Corbett
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Ingrid E Scheffer
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Jozef Gécz
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia.
| | - Samuel F Berkovic
- From the Adelaide Medical School, Faculty of Health and Medical Sciences (S.E.H., A.E.G., M.A.C., J.G.), and Robinson Research Institute (J.G.), The University of Adelaide; Epilepsy Research Centre, Department of Medicine (B.M.R., R.V.H., M.C., B.E.G., M.F.B., S.P., M.S.H., I.E.S., S.F.B.), Austin Health, University of Melbourne, Heidelberg; Population Health and Immunity Division (M.F.B., M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.F.B., M.B.), University of Melbourne, Parkville, Australia; Division of Neurology (K.L.H.), Children's Hospital of Philadelphia; Department of Neurology (M.R.S.), Thomas Jefferson University, Philadelphia, PA; Department of Neurology (S.H.), Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY; Institute of Neurology and Neurosurgery at Saint Barnabas (E.B.G.), Livingston, NJ; Department of Neurology (P.W.-W.), Beaumont Hospital, Dublin, Ireland; Royal Brisbane and Women's Hospital (J.T.P.), Brisbane, Australia; Centre for Genomics Research (S.P.), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Institute for Genomic Medicine (E.L.H.), Columbia University Medical Center, New York, NY; Murdoch Children's Research Institute (M.S.H., I.E.S.), Parkville; Department of Paediatrics (I.E.S.), Royal Children's Hospital, University of Melbourne; Florey Institute of Neuroscience and Mental Health (I.E.S.), Melbourne; and Healthy Mothers, Babies and Children (J.G.), South Australian Health and Medical Research Institute, Adelaide, Australia
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Burlet B, Ramla S, Fournier C, Abrey-Recalde MJ, Sauter C, Chrétien ML, Rossi C, Duffourd Y, Ragot S, Buriller C, Tournier B, Chapusot C, Nadal N, Racine J, Guy J, Bailly F, Martin L, Casasnovas O, Bastie JN, Caillot D, Albuisson J, Broccardo C, Thieblemont C, Delva L, Maynadié M, Aucagne R, Callanan MB. Identification of novel, clonally stable, somatic mutations targeting transcription factors PAX5 and NKX2-3, the epigenetic regulator LRIF1, and BRAF in a case of atypical B-cell chronic lymphocytic leukemia harboring a t(14;18)(q32;q21). Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005934. [PMID: 33608382 PMCID: PMC7903887 DOI: 10.1101/mcs.a005934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/06/2021] [Indexed: 12/15/2022] Open
Abstract
Diagnosis of B-cell chronic lymphocytic leukemia (B-CLL) is usually straightforward, involving clinical, immunophenotypic (Matutes score), and (immuno)genetic analyses (to refine patient prognosis for treatment). CLL cases with atypical presentation (e.g., Matutes ≤ 3) are also encountered, and for these diseases, biology and prognostic impact are less clear. Here we report the genomic characterization of a case of atypical B-CLL in a 70-yr-old male patient; B-CLL cells showed a Matutes score of 3, chromosomal translocation t(14;18)(q32;q21) (BCL2/IGH), mutated IGHV, deletion 17p, and mutations in BCL2, NOTCH1 (subclonal), and TP53 (subclonal). Quite strikingly, a novel PAX5 mutation that was predicted to be loss of function was also seen. Exome sequencing identified, in addition, a potentially actionable BRAF mutation, together with novel somatic mutations affecting the homeobox transcription factor NKX2-3, known to control B-lymphocyte development and homing, and the epigenetic regulator LRIF1, which is implicated in chromatin compaction and gene silencing. Neither NKX2-3 nor LRIF1 mutations, predicted to be loss of function, have previously been reported in B-CLL. Sequencing confirmed the presence of these mutations together with BCL2, NOTCH1, and BRAF mutations, with the t(14;18)(q32;q21) translocation, in the initial diagnostic sample obtained 12 yr prior. This is suggestive of a role for these novel mutations in B-CLL initiation and stable clonal evolution, including upon treatment withdrawal. This case extends the spectrum of atypical B-CLL with t(14;18)(q32;q21) and highlights the value of more global precision genomics for patient follow-up and treatment in these patients.
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Affiliation(s)
- Bénédicte Burlet
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Selim Ramla
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Cyril Fournier
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Maria Jimena Abrey-Recalde
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Camille Sauter
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Marie-Lorraine Chrétien
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Cédric Rossi
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Yannis Duffourd
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Sylviane Ragot
- Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Céline Buriller
- Genetics Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Benjamin Tournier
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Caroline Chapusot
- Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Nathalie Nadal
- Genetics Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Jessica Racine
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Julien Guy
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - François Bailly
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Laurent Martin
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Olivier Casasnovas
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Jean-Noël Bastie
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Denis Caillot
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Juliette Albuisson
- Oncogenetics laboratory, Centre George François Leclerc, 21079 Dijon, France
| | - Cyril Broccardo
- Centre de Recherches en Cancérologie de Toulouse, Inserm UMR1037, Université de Toulouse III - Paul Sabatier, 31037 Toulouse, France
| | - Catherine Thieblemont
- Department of Hemato-oncology, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.,Université de Paris, NF-kappaB, Différenciation et Cancer, 75006 Paris, France
| | - Laurent Delva
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Marc Maynadié
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France.,Registre des hémopathies malignes de Côte d'Or, University of Burgundy, Faculty of Medicine, 21079 Dijon, France
| | - Romain Aucagne
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Mary B Callanan
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
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Wang X, Tang N, Shen N, Zhu Y, Lu Y, Gao L. Normal activated partial thromboplastin time in Chinese patients with mild hemophilia B. ACTA ACUST UNITED AC 2021; 25:484-488. [PMID: 33295842 DOI: 10.1080/16078454.2020.1853403] [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: 10/22/2022]
Abstract
OBJECTIVES Hemophilia B (HB, OMIM: 300746) is one of the most common bleeding disorders with an X-linked recessive inheritance pattern, caused by the deficiency of coagulation factor IX (FIX). FIX is encoded by the F9 gene located on Xq27.1. Diagnosis of HB is primarily suspected by prolonged activated partial thromboplastin time (APTT), decreased FIX activity (FIX:C) or genetic test of the F9 gene. We herein described a Chinese family with patients of mild HB. METHODS Sanger sequencing of the F9 gene was applied to identify mutation. Coagulation tests were performed. RESULTS The proband was a 5-year-old boy. He suffered prolonged bleeding after tonsillectomy recently and circumcision last year as well. His grandfather experienced prolonged bleeding after gastric surgery. Both patients showed normal APTT, though they had significantly decreased FIX:C. Sanger sequencing of the F9 gene revealed a novel hemizygous F9 c.639C > A (p.Asn213Lys) missense mutation in both patients. The proband's mother carried heterozygous mutation. This mutation was located in the activation peptide domain of FIX. CONCLUSION In conclusion, we confirmed that APTT could be normal in mild HB patients. Highly sensitive APTT for mild HB and molecular genetic test could confirm the diagnosis of mild HB.
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Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ning Tang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yaowu Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Linna Gao
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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Markus F, Kannengießer A, Näder P, Atigbire P, Scholten A, Vössing C, Bültmann E, Korenke GC, Owczarek-Lipska M, Neidhardt J. A novel missense variant in the EML1 gene associated with bilateral ribbon-like subcortical heterotopia leads to ciliary defects. J Hum Genet 2021; 66:1159-1167. [PMID: 34211111 PMCID: PMC8612930 DOI: 10.1038/s10038-021-00947-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023]
Abstract
Heterotopia is a brain malformation caused by a failed migration of cortical neurons during development. Clinical symptoms of heterotopia vary in severity of intellectual disability and may be associated with epileptic disorders. Abnormal neuronal migration is known to be associated with mutations in the doublecortin gene (DCX), the platelet-activating factor acetylhydrolase gene (PAFAH1B1), or tubulin alpha-1A gene (TUBA1A). Recently, a new gene encoding echinoderm microtubule-associated protein-like 1 (EML1) was reported to cause a particular form of subcortical heterotopia, the ribbon-like subcortical heterotopia (RSH). EML1 mutations are inherited in an autosomal recessive manner. Only six unrelated EML1-associated heterotopia-affected families were reported so far. The EML1 protein is a member of the microtubule-associated proteins family, playing an important role in microtubule assembly and stabilization as well as in mitotic spindle formation in interphase. Herein, we present a novel homozygous missense variant in EML1 (NM_004434.2: c.692G>A, NP_004425.2: p.Gly231Asp) identified in a male RSH-affected patient. Our clinical and molecular findings confirm the genotype-phenotype associations of EML1 mutations and RSH. Analyses of patient-derived fibroblasts showed the significantly reduced length of primary cilia. In addition, our results presented, that the mutated EML1 protein did not change binding capacities with tubulin. The data described herein will expand the mutation spectrum of the EML1 gene and provide further insight into molecular and cellular bases of the pathogenic mechanisms underlying RSH.
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Affiliation(s)
- Fenja Markus
- grid.5560.60000 0001 1009 3608Junior Research Group, Genetics of Childhood Brain Malformations, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany ,grid.5560.60000 0001 1009 3608Human Genetics, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Annika Kannengießer
- grid.5560.60000 0001 1009 3608Junior Research Group, Genetics of Childhood Brain Malformations, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany ,grid.5560.60000 0001 1009 3608Human Genetics, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Patricia Näder
- grid.5560.60000 0001 1009 3608Human Genetics, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Paul Atigbire
- grid.5560.60000 0001 1009 3608Human Genetics, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Alexander Scholten
- grid.5560.60000 0001 1009 3608Division of Biochemistry, Biochemistry of signal transduction/neurosensory processes, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Christine Vössing
- grid.5560.60000 0001 1009 3608Human Genetics, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Eva Bültmann
- grid.10423.340000 0000 9529 9877Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - G. Christoph Korenke
- grid.419838.f0000 0000 9806 6518Department of Neuropediatrics, University Children’s Hospital, Klinikum Oldenburg, Oldenburg, Germany
| | - Marta Owczarek-Lipska
- grid.5560.60000 0001 1009 3608Junior Research Group, Genetics of Childhood Brain Malformations, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany ,grid.5560.60000 0001 1009 3608Human Genetics, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany ,grid.5560.60000 0001 1009 3608Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
| | - John Neidhardt
- grid.5560.60000 0001 1009 3608Human Genetics, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany ,grid.5560.60000 0001 1009 3608Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
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MobiDetails: online DNA variants interpretation. Eur J Hum Genet 2020; 29:356-360. [PMID: 33161418 DOI: 10.1038/s41431-020-00755-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/22/2020] [Indexed: 11/08/2022] Open
Abstract
MobiDetails is an expert tool, online application which gathers useful data for the interpretation of DNA variants in the context of molecular diagnosis. It brings together in a single tool many sources of data, such as population genetics, various kinds of predictors, Human Genome Variation Society (HGVS) nomenclatures, curated databases, and access to various annotations. Accurate interpretation of DNA variants is crucial and can impact the patient care or have familial outcomes (prenatal diagnosis). Its importance will increase in the coming years with the expansion of the personalized medicine. MobiDetails is specifically designed to help with this task. Exonic or intronic substitutions and small insertions/deletions related to more than 18,000 human genes are easily submitted and annotated in real-time. It is a responsive website that can be accessed using mobiles or tablets during medical staff meetings. MobiDetails is based on publicly available resources, does not include any specific data on patients or phenotypes, and is freely available for academic use at https://mobidetails.iurc.montp.inserm.fr/MD/ .
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Wang X, Tang N, Shen N, Lu Y, Li D. Congenital fibrinogen disorder caused by digenic mutations of the FGA and FGB genes. Hematology 2020; 25:145-148. [PMID: 32228225 DOI: 10.1080/16078454.2020.1746109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Ning Tang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Dengju Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
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De novo CLTC variants are associated with a variable phenotype from mild to severe intellectual disability, microcephaly, hypoplasia of the corpus callosum, and epilepsy. Genet Med 2019; 22:797-802. [PMID: 31776469 DOI: 10.1038/s41436-019-0703-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/14/2019] [Accepted: 11/06/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To delineate the genotype-phenotype correlation in individuals with likely pathogenic variants in the CLTC gene. METHODS We describe 13 individuals with de novo CLTC variants. Causality of variants was determined by using the tolerance landscape of CLTC and computer-assisted molecular modeling where applicable. Phenotypic abnormalities observed in the individuals identified with missense and in-frame variants were compared with those with nonsense or frameshift variants in CLTC. RESULTS All de novo variants were judged to be causal. Combining our data with that of 14 previously reported affected individuals (n = 27), all had intellectual disability (ID), ranging from mild to moderate/severe, with or without additional neurologic, behavioral, craniofacial, ophthalmologic, and gastrointestinal features. Microcephaly, hypoplasia of the corpus callosum, and epilepsy were more frequently observed in individuals with missense and in-frame variants than in those with nonsense and frameshift variants. However, this difference was not significant. CONCLUSIONS The wide phenotypic variability associated with likely pathogenic CLTC variants seems to be associated with allelic heterogeneity. The detailed clinical characterization of a larger cohort of individuals with pathogenic CLTC variants is warranted to support the hypothesis that missense and in-frame variants exert a dominant-negative effect, whereas the nonsense and frameshift variants would result in haploinsufficiency.
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