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Kagermeier T, Hauser S, Sarieva K, Laugwitz L, Groeschel S, Janzarik WG, Yentür Z, Becker K, Schöls L, Krägeloh-Mann I, Mayer S. Human organoid model of pontocerebellar hypoplasia 2a recapitulates brain region-specific size differences. Dis Model Mech 2024; 17:dmm050740. [PMID: 39034883 DOI: 10.1242/dmm.050740] [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: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 07/23/2024] Open
Abstract
Pontocerebellar hypoplasia type 2a (PCH2a) is an ultra-rare, autosomal recessive pediatric disorder with limited treatment options. Its anatomical hallmark is hypoplasia of the cerebellum and pons accompanied by progressive microcephaly. A homozygous founder variant in TSEN54, which encodes a tRNA splicing endonuclease (TSEN) complex subunit, is causal. The pathological mechanism of PCH2a remains unknown due to the lack of a model system. Therefore, we developed human models of PCH2a using regionalized neural organoids. We generated induced pluripotent stem cell (iPSC) lines from three males with genetically confirmed PCH2a and subsequently differentiated cerebellar and neocortical organoids. Mirroring clinical neuroimaging findings, PCH2a cerebellar organoids were reduced in size compared to controls starting early in differentiation. Neocortical PCH2a organoids demonstrated milder growth deficits. Although PCH2a cerebellar organoids did not upregulate apoptosis, their stem cell zones showed altered proliferation kinetics, with increased proliferation at day 30 and reduced proliferation at day 50 compared to controls. In summary, we generated a human model of PCH2a, providing the foundation for deciphering brain region-specific disease mechanisms. Our first analyses suggest a neurodevelopmental aspect of PCH2a.
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Affiliation(s)
- Theresa Kagermeier
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- Graduate Training Centre of Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Hauser
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
| | - Kseniia Sarieva
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- Graduate Training Centre of Neuroscience, University of Tübingen, 72076 Tübingen, Germany
- International Max Planck Research School, Graduate Training Centre of Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Lucia Laugwitz
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, 72076 Tübingen, Germany
| | - Samuel Groeschel
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, 72076 Tübingen, Germany
| | - Wibke G Janzarik
- Department of Neuropediatrics and Muscle Disorders, Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Zeynep Yentür
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- Graduate Training Centre of Neuroscience, University of Tübingen, 72076 Tübingen, Germany
- International Max Planck Research School, Graduate Training Centre of Neuroscience, University of Tübingen, 72076 Tübingen, Germany
- Heidelberger Akademie der Wissenschaften, 69117 Heidelberg, Germany
| | - Katharina Becker
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Ludger Schöls
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
| | - Ingeborg Krägeloh-Mann
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, 72076 Tübingen, Germany
| | - Simone Mayer
- Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
- Heidelberger Akademie der Wissenschaften, 69117 Heidelberg, Germany
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2
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Zakaria RBM, Malta M, Pelletier F, Addour-Boudrahem N, Pinchefsky E, Martin CS, Srour M. Classic "PCH" Genes are a Rare Cause of Radiologic Pontocerebellar Hypoplasia. CEREBELLUM (LONDON, ENGLAND) 2024; 23:418-430. [PMID: 36971923 DOI: 10.1007/s12311-023-01544-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/08/2023] [Indexed: 03/29/2023]
Abstract
The term Pontocerebellar Hypoplasia (PCH) was initially used to designate a heterogeneous group of fetal-onset genetic neurodegenerative disorders. As a descriptive term, PCH refers to pons and cerebellum of reduced volume. In addition to the classic PCH types described in OMIM, many other disorders can result in a similar imaging appearance. This study aims to review imaging, clinical and genetic features and underlying etiologies of a cohort of children with PCH on imaging. We systematically reviewed brain images and clinical charts of 38 patients with radiologic evidence of PCH. Our cohort included 21 males and 17 females, with ages ranging between 8 days to 15 years. All individuals had pons and cerebellar vermis hypoplasia, and 63% had cerebellar hemisphere hypoplasia. Supratentorial anomalies were found in 71%. An underlying etiology was identified in 68% and included chromosomal (21%), monogenic (34%) and acquired (13%) causes. Only one patient had pathogenic variants in an OMIM listed PCH gene. Outcomes were poor regardless of etiology, though no one had regression. Approximately one third of patients deceased at a median age of 8 months. All individuals had global developmental delay, 50% were non-verbal, 64% were non-ambulatory and 45% required gastrostomy feeding. This cohort demonstrates that radiologic PCH has heterogenous etiologies and the "classic" OMIM-listed PCH genes underlie only a minority of cases. Broad genetic testing, including chromosomal microarray and exome or multigene panels, is recommended in individuals with PCH-like imaging appearance. Our results strongly suggest that the term PCH should be used to designate radiologic findings, and not to imply neurogenerative disorders.
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Affiliation(s)
| | - Maisa Malta
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Child Neurology, Department of Neurology and Neurosurgery, Federal University of São Paulo, São Paulo, Brazil
| | - Felixe Pelletier
- Division of Pediatric Neurology, Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | | | - Elana Pinchefsky
- Division of Pediatric Neurology, Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | | | - Myriam Srour
- Division of Pediatric Neurology, Department of Pediatrics, McGill University, Montreal, Quebec, Canada.
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
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3
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Seo Y, Joo K, Lee J, Diaz A, Jang S, Cherry TJ, Bujakowska KM, Han J, Woo SJ, Small KW. Two novel non-coding single nucleotide variants in the DNase1 hypersensitivity site of PRDM13 causing North Carolina macular dystrophy in Korea. Mol Vis 2024; 30:58-66. [PMID: 38601016 PMCID: PMC11006008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 02/17/2024] [Indexed: 04/12/2024] Open
Abstract
Purpose Pathogenic variants in North Carolina macular dystrophy (NCMD) have rarely been reported in the East Asian population. Herein, we reported novel variants of NCMD in 2 Korean families. Methods The regions associated with NCMD were analyzed with genome sequencing, and variants were filtered based on the minor allele frequency (0.5%) and heterozygosity. Non-coding variants were functionally annotated using multiple computational tools. Results We identified two rare novel variants, chr6:g.99,598,914T>C (hg38; V17) and chr6:g.99,598,926G>A (hg38; V18) upstream of PRDM13 in families A and B, respectively. In Family 1, Grade 2 NCMD and a best-corrected visual acuity of 20/25 and 20/200 in the right and left eyes, respectively, were observed. In Family B, all affected individuals had Grade 1 NCMD with characteristic confluent drusen at the fovea and a best-corrected visual acuity of 20/20 in both eyes. These two variants are 10-22 bp downstream of the reported V10 variant within the DNase1 hypersensitivity site. This site is associated with progressive bifocal chorioretinal atrophy and congenital posterior polar chorioretinal hypertrophy and lies in the putative enhancer site of PRDM13. Conclusion We identified two novel NCMD variants in the Korean population and further validated the regulatory role of the DNase1 hypersensitivity site upstream of PRDM13.
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Affiliation(s)
- Yuri Seo
- Institute of Vision Research, Department of Ophthalmology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Gyeonggi-do, South Korea
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Junwon Lee
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Amber Diaz
- Macula and Retina Institute, Glendale and Los Angeles, CA
- Molecular Insight Research Foundation, Glendale and Los Angeles, CA
| | | | - Timothy J. Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
- Brotman Baty Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Kinga M. Bujakowska
- Ocular Genomic Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Ocular Genomic Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Kent W. Small
- Macula and Retina Institute, Glendale and Los Angeles, CA
- Molecular Insight Research Foundation, Glendale and Los Angeles, CA
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4
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Ghasemi MR, Tehrani Fateh S, Moeinafshar A, Sadeghi H, Karimzadeh P, Mirfakhraie R, Rezaei M, Hashemi-Gorji F, Rezvani Kashani M, Fazeli Bavandpour F, Bagheri S, Moghimi P, Rostami M, Madannejad R, Roudgari H, Miryounesi M. Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review. BMC Med Genomics 2024; 17:51. [PMID: 38347586 PMCID: PMC10863249 DOI: 10.1186/s12920-024-01810-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Pontocerebellar hypoplasia is an umbrella term describing a heterogeneous group of prenatal neurodegenerative disorders mostly affecting the pons and cerebellum, with 17 types associated with 25 genes. However, some types of PCH lack sufficient information, which highlights the importance of investigating and introducing more cases to further elucidate the clinical, radiological, and biochemical features of these disorders. The aim of this study is to provide an in-depth review of PCH and to identify disease genes and their inheritance patterns in 12 distinct Iranian families with clinically confirmed PCH. METHODS Cases included in this study were selected based on their phenotypic and genetic information available at the Center for Comprehensive Genetic Services. Whole-exome sequencing (WES) was used to discover the underlying genetic etiology of participants' problems, and Sanger sequencing was utilized to confirm any suspected alterations. We also conducted a comprehensive molecular literature review to outline the genetic features of the various subtypes of PCH. RESULTS This study classified and described the underlying etiology of PCH into three categories based on the genes involved. Twelve patients also were included, eleven of whom were from consanguineous parents. Ten different variations in 8 genes were found, all of which related to different types of PCH. Six novel variations were reported, including SEPSECS, TSEN2, TSEN54, AMPD2, TOE1, and CLP1. Almost all patients presented with developmental delay, hypotonia, seizure, and microcephaly being common features. Strabismus and elevation in lactate levels in MR spectroscopy were novel phenotypes for the first time in PCH types 7 and 9. CONCLUSIONS This study merges previously documented phenotypes and genotypes with unique novel ones. Due to the diversity in PCH, we provided guidance for detecting and diagnosing these heterogeneous groups of disorders. Moreover, since certain critical conditions, such as spinal muscular atrophy, can be a differential diagnosis, providing cases with novel variations and clinical findings could further expand the genetic and clinical spectrum of these diseases and help in better diagnosis. Therefore, six novel genetic variants and novel clinical and paraclinical findings have been reported for the first time. Further studies are needed to elucidate the underlying mechanisms and potential therapeutic targets for PCH.
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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
| | | | - Aysan Moeinafshar
- School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Hossein Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
| | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, 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
| | - Mitra Rezaei
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Morteza Rezvani Kashani
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Saman Bagheri
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Parinaz Moghimi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Masoumeh Rostami
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rasoul Madannejad
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Roudgari
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - 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.
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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5
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Schilling K. Revisiting the development of cerebellar inhibitory interneurons in the light of single-cell genetic analyses. Histochem Cell Biol 2024; 161:5-27. [PMID: 37940705 PMCID: PMC10794478 DOI: 10.1007/s00418-023-02251-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
The present review aims to provide a short update of our understanding of the inhibitory interneurons of the cerebellum. While these cells constitute but a minority of all cerebellar neurons, their functional significance is increasingly being recognized. For one, inhibitory interneurons of the cerebellar cortex are now known to constitute a clearly more diverse group than their traditional grouping as stellate, basket, and Golgi cells suggests, and this diversity is now substantiated by single-cell genetic data. The past decade or so has also provided important information about interneurons in cerebellar nuclei. Significantly, developmental studies have revealed that the specification and formation of cerebellar inhibitory interneurons fundamentally differ from, say, the cortical interneurons, and define a mode of diversification critically dependent on spatiotemporally patterned external signals. Last, but not least, in the past years, dysfunction of cerebellar inhibitory interneurons could also be linked with clinically defined deficits. I hope that this review, however fragmentary, may stimulate interest and help focus research towards understanding the cerebellum.
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Affiliation(s)
- Karl Schilling
- Anatomisches Institut - Anatomie und Zellbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Nussallee 10, 53115, Bonn, Germany.
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6
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Jaillard A, Valence S, Vande Perre S, Dhombres F, Héron D, Billette de Villemeur T, Keren B, Afenjar A, Qebibo L, Harion M, Quenum-Miraillet G, Rodriguez D, Jouannic JM, Burglen L, Garel C. Prenatal diagnosis of pontocerebellar hypoplasia with postnatal follow-up. Prenat Diagn 2024; 44:35-48. [PMID: 38165124 DOI: 10.1002/pd.6495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/25/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE To describe the MR features enabling prenatal diagnosis of pontocerebellar hypoplasia (PCH). METHOD This was a retrospective single monocentre study. The inclusion criteria were decreased cerebellar biometry on dedicated neurosonography and available fetal Magnetic Resonance Imaging (MRI) with PCH diagnosis later confirmed either genetically or clinically on post-natal MRI or by autopsy. The exclusion criteria were non-available MRI and sonographic features suggestive of a known genetic or other pathologic diagnosis. The collected data were biometric or morphological imaging parameters, clinical outcome, termination of pregnancy (TOP), pathological findings and genetic analysis (karyotyping, chromosomal microarray, DNA sequencing targeted or exome). PCH was classified as classic, non-classic, chromosomal, or unknown type. RESULTS Forty-two fetuses were diagnosed with PCH, of which 27 were referred for decreased transverse cerebellar diameter at screening ultrasound. Neurosonography and fetal MRI were performed at a mean gestational age of 29 + 4 and 31 + 0 weeks, respectively. Termination of pregnancy occurred. Pregnancy was terminated in 24 cases. Neuropathological examination confirmed the diagnosis in 24 cases and genetic testing identified abnormalities in 29 cases (28 families, 14 chromosomal anomaly). Classic PCH is associated with pontine atrophy and small MR measurements decreasing with advancing gestation. CONCLUSION This is the first large series of prenatally diagnosed PCHs. Our study shows the essential contribution of fetal MRI to the prenatal diagnosis of PCH. Classic PCHs are particularly severe and are associated with certain MR features.
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Affiliation(s)
- Alienor Jaillard
- Department of Radiology, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Stéphanie Valence
- Department of Pediatric Neurology, Reference Center for Rare Diseases and Intellectual Deficiencies of Rare Causes, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Saskia Vande Perre
- Department of Radiology, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Ferdinand Dhombres
- Fetal Medicine Department, Armand-Trousseau Hospital, APHP, Sorbonne University, GRC-26, Paris, France
| | - Delphine Héron
- Department of Genetics, Division of Medical Genetics, Reference Center for Rare Diseases and Intellectual Deficiencies of Rare Causes, La Pitié-Salpêtrière Hospital, APHP, Sorbonne University, Paris, France
| | - Thierry Billette de Villemeur
- Department of Pediatric Neurology, Reference Center for Rare Diseases and Intellectual Deficiencies of Rare Causes, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Boris Keren
- Department of Genetics, APHP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France
| | - Alexandra Afenjar
- Clinical Genetics Unit, Reference Center for Cerebellar Malformations and Congenital Diseases, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Leila Qebibo
- Department of Genetics, Pediatric Neurogenetics Laboratory, Reference Center for Cerebellar Malformations and Congenital Diseases, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Madeleine Harion
- Department of Pediatric Neurology, Reference Center for Rare Diseases and Intellectual Deficiencies of Rare Causes, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | | | - Diana Rodriguez
- Department of Pediatric Neurology, Reference Center for Rare Diseases and Intellectual Deficiencies of Rare Causes, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Jean-Marie Jouannic
- Fetal Medicine Department, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
| | - Lydie Burglen
- Department of Genetics, Pediatric Neurogenetics Laboratory, Reference Center for Cerebellar Malformations and Congenital Diseases, Armand-Trousseau Hospital, APHP, Sorbonne University, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, Paris, France
| | - Catherine Garel
- Department of Radiology, Reference Center for Cerebellar Malformations and Congenital Diseases, Armand-Trousseau Hospital, APHP, Sorbonne University, INSERM UMR 1163, Paris, France
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7
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Guo H, Deng Z, Xu Q, Wang Z, Zeng X, Hong X, Wang Q, Sun Y, Yuan H. Genetic and prenatal diagnosis of a Chinese pedigree with pathogenic TOE1 variants causing pontocerebellar hypoplasia type 7. J Matern Fetal Neonatal Med 2023; 36:2250895. [PMID: 37635087 DOI: 10.1080/14767058.2023.2250895] [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: 01/13/2023] [Revised: 07/24/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
Objective: Biallelic pathogenic variants in TOE1 cause pontocerebellar hypoplasia type 7 (PCH7), a rare neurological condition characterized by psychomotor retardation, spastic paraplegia, seizures, gonadal abnormalities and brain anomalies. Currently, only 14 postnatally diagnosed PCH7 patients have been described. However, the prenatal clinical profile of PCH7 has not yet been reported.Method: Whole-exome sequencing (WES) was performed to screen for causal variants.Results: We report the pedigree of a Chinese woman with two eventful pregnancies with fetuses that showed brain anomalies, including microcephaly, cerebral anomalies, enlarged ventricles, corpus callosum thinning, abnormal lateral fissure, underdeveloped insula and pons and brainstem hypoplasia. Interestingly, corpus callosum thinning was observed in fetus 1 but not in fetus 2. An abnormal lateral fissure and an underdeveloped insula were shown in fetus 2 but not fetus 1. Biallelic variants c.716T > C (p.Phe239Ser) and c.955C > T (p.His319Tyr) in TOE1 were identified in both fetuses.Conclusion: We first describe the prenatal features of a Chinese pedigree with PCH7 caused by biallelic pathogenic variants in TOE1, with phenotypic variability observed even within the same family. Novel phenotypes, an abnormal lateral fissure and an underdeveloped insula were observed in the fetus in our study. These findings will enrich our knowledge of the clinical characteristics, management and genetic counseling of PCH7.
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Affiliation(s)
- Hongmei Guo
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Zhengxi Deng
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Qiuhong Xu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Zhong Wang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Xiumei Zeng
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Xiaochun Hong
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Qingming Wang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
- Department of Medical Genetics, Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Yan Sun
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
| | - Haiming Yuan
- Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
- Department of Medical Genetics, Dongguan Maternal and Child Health Care Hospital, Dongguan, P.R. China
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8
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Nicolle R, Altin N, Siquier-Pernet K, Salignac S, Blanc P, Munnich A, Bole-Feysot C, Malan V, Caron B, Nitschké P, Desguerre I, Boddaert N, Rio M, Rausell A, Cantagrel V. A non-coding variant in the Kozak sequence of RARS2 strongly decreases protein levels and causes pontocerebellar hypoplasia. BMC Med Genomics 2023; 16:143. [PMID: 37344844 DOI: 10.1186/s12920-023-01582-z] [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: 10/21/2022] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Bi-allelic variants in the mitochondrial arginyl-transfer RNA synthetase (RARS2) gene have been involved in early-onset encephalopathies classified as pontocerebellar hypoplasia (PCH) type 6 and in epileptic encephalopathy. A variant (NM_020320.3:c.-2A > G) in the promoter and 5'UTR of the RARS2 gene has been previously identified in a family with PCH. Only a mild impact of this variant on the mRNA level has been detected. As RARS2 is non-dosage-sensitive, this observation is not conclusive in regard of the pathogenicity of the variant.We report and describe here a new patient with the same variant in the RARS2 gene, at the homozygous state. This patient presents with a clinical phenotype consistent with PCH6 although in the absence of lactic acidosis. In agreement with the previous study, we measured RARS2 mRNA levels in patient's fibroblasts and detected a partially preserved gene expression compared to control. Importantly, this variant is located in the Kozak sequence that controls translation initiation. Therefore, we investigated the impact on protein translation using a bioinformatic approach and western blotting. We show here that this variant, additionally to its effect on the transcription, also disrupts the consensus Kozak sequence, and has a major impact on RARS2 protein translation. Through the identification of this additional case and the characterization of the molecular consequences, we clarified the involvement of this Kozak variant in PCH and on protein synthesis. This work also points to the current limitation in the pathogenicity prediction of variants located in the translation initiation region.
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Affiliation(s)
- Romain Nicolle
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France
- Clinical Bioinformatics Laboratory, Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, 75015, France
| | - Nami Altin
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France
| | - Karine Siquier-Pernet
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France
| | - Sherlina Salignac
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France
| | - Pierre Blanc
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, AP-HP, Necker Hospital for Sick Children, Paris, 75015, France
| | - Arnold Munnich
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, AP-HP, Necker Hospital for Sick Children, Paris, 75015, France
| | - Christine Bole-Feysot
- Genomics Platform, Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, 75015, France
| | - Valérie Malan
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, AP-HP, Necker Hospital for Sick Children, Paris, 75015, France
| | - Barthélémy Caron
- Clinical Bioinformatics Laboratory, Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, 75015, France
| | - Patrick Nitschké
- Bioinformatics Core Facility, Université Paris Cité, INSERM UMR 1163, Imagine Institute, 75015, Paris, France
| | - Isabelle Desguerre
- Département de Neurologie Pédiatrique, AP-HP, Necker Hospital for Sick Children, 75015, Paris, France
| | - Nathalie Boddaert
- Département de Radiologie Pédiatrique, AP-HP, Necker Hospital for Sick Children and Université Paris Cité, INSERM UMR 1163 and INSERM U1299, Imagine Institute, Paris, 75015, France
| | - Marlène Rio
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, AP-HP, Necker Hospital for Sick Children, Paris, 75015, France
| | - Antonio Rausell
- Clinical Bioinformatics Laboratory, Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, 75015, France
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, AP-HP, Necker Hospital for Sick Children, Paris, 75015, France
| | - Vincent Cantagrel
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, 75015, Paris, France.
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The diagnostic yield, candidate genes, and pitfalls for a genetic study of intellectual disability in 118 middle eastern families. Sci Rep 2022; 12:18862. [PMID: 36344539 PMCID: PMC9640568 DOI: 10.1038/s41598-022-22036-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
Global Developmental Delay/Intellectual disability (ID) is the term used to describe various disorders caused by abnormal brain development and characterized by impairments in cognition, communication, behavior, or motor skills. In the past few years, whole-exome sequencing (WES) has been proven to be a powerful, robust, and scalable approach for candidate gene discoveries in consanguineous populations. In this study, we recruited 215 patients affected with ID from 118 Middle Eastern families. Whole-exome sequencing was completed for 188 individuals. The average age at which WES was completed was 8.5 years. Pathogenic or likely pathogenic variants were detected in 32/118 families (27%). Variants of uncertain significance were seen in 33/118 families (28%). The candidate genes with a possible association with ID were detected in 32/118 (27%) with a total number of 64 affected individuals. These genes are novel, were previously reported in a single family, or cause strikingly different phenotypes with a different mode of inheritance. These genes included: AATK, AP1G2, CAMSAP1, CCDC9B, CNTROB, DNAH14, DNAJB4, DRG1, DTNBP1, EDRF1, EEF1D, EXOC8, EXOSC4, FARSB, FBXO22, FILIP1, INPP4A, P2RX7, PRDM13, PTRHD1, SCN10A, SCYL2, SMG8, SUPV3L1, TACC2, THUMPD1, XPR1, ZFYVE28. During the 5 years of the study and through gene matching databases, several of these genes have now been confirmed as causative of ID. In conclusion, understanding the causes of ID will help understand biological mechanisms, provide precise counseling for affected families, and aid in primary prevention.
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Van de Sompele S, Small KW, Cicekdal MB, Soriano VL, D'haene E, Shaya FS, Agemy S, Van der Snickt T, Rey AD, Rosseel T, Van Heetvelde M, Vergult S, Balikova I, Bergen AA, Boon CJF, De Zaeytijd J, Inglehearn CF, Kousal B, Leroy BP, Rivolta C, Vaclavik V, van den Ende J, van Schooneveld MJ, Gómez-Skarmeta JL, Tena JJ, Martinez-Morales JR, Liskova P, Vleminckx K, De Baere E. Multi-omics approach dissects cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy. Am J Hum Genet 2022; 109:2029-2048. [PMID: 36243009 PMCID: PMC9674966 DOI: 10.1016/j.ajhg.2022.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/28/2022] [Indexed: 01/26/2023] Open
Abstract
North Carolina macular dystrophy (NCMD) is a rare autosomal-dominant disease affecting macular development. The disease is caused by non-coding single-nucleotide variants (SNVs) in two hotspot regions near PRDM13 and by duplications in two distinct chromosomal loci, overlapping DNase I hypersensitive sites near either PRDM13 or IRX1. To unravel the mechanisms by which these variants cause disease, we first established a genome-wide multi-omics retinal database, RegRet. Integration of UMI-4C profiles we generated on adult human retina then allowed fine-mapping of the interactions of the PRDM13 and IRX1 promoters and the identification of eighteen candidate cis-regulatory elements (cCREs), the activity of which was investigated by luciferase and Xenopus enhancer assays. Next, luciferase assays showed that the non-coding SNVs located in the two hotspot regions of PRDM13 affect cCRE activity, including two NCMD-associated non-coding SNVs that we identified herein. Interestingly, the cCRE containing one of these SNVs was shown to interact with the PRDM13 promoter, demonstrated in vivo activity in Xenopus, and is active at the developmental stage when progenitor cells of the central retina exit mitosis, suggesting that this region is a PRDM13 enhancer. Finally, mining of single-cell transcriptional data of embryonic and adult retina revealed the highest expression of PRDM13 and IRX1 when amacrine cells start to synapse with retinal ganglion cells, supporting the hypothesis that altered PRDM13 or IRX1 expression impairs interactions between these cells during retinogenesis. Overall, this study provides insight into the cis-regulatory mechanisms of NCMD and supports that this condition is a retinal enhanceropathy.
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Affiliation(s)
- Stijn Van de Sompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kent W Small
- Macula and Retina Institute, Los Angeles and Glendale, California, USA
| | - Munevver Burcu Cicekdal
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Víctor López Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Eva D'haene
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Fadi S Shaya
- Macula and Retina Institute, Los Angeles and Glendale, California, USA
| | - Steven Agemy
- Department of Ophthalmology, SUNY Downstate Medical Center University, Brooklyn, New York, USA
| | - Thijs Van der Snickt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Mattias Van Heetvelde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Irina Balikova
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | - Arthur A Bergen
- Department of Human Genetics, Amsterdam UMC, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; Queen Emma Centre of Precision Medicine, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Chris F Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Bohdan Kousal
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium; Department of Head & Skin, Ghent University, Ghent, Belgium; Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Veronika Vaclavik
- University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland
| | | | - Mary J van Schooneveld
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Bartiméus, Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Juan R Martinez-Morales
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Petra Liskova
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Kris Vleminckx
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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