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Nadler MJS, Chang W, Ozkaynak E, Huo Y, Nong Y, Boillot M, Johnson M, Moreno A, Matthew P Anderson. Hominoid SVA-lncRNA AK057321 targets human-specific SVA retrotransposons in SCN8A and CDK5RAP2 to initiate neuronal maturation. Commun Biol 2023; 6:347. [PMID: 36997626 PMCID: PMC10063665 DOI: 10.1038/s42003-023-04683-8] [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: 06/09/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons arose and expanded in the genome of hominoid primates concurrent with the slowing of brain maturation. We report genes with intronic SVA transposons are enriched for neurodevelopmental disease and transcribed into long non-coding SVA-lncRNAs. Human-specific SVAs in microcephaly CDK5RAP2 and epilepsy SCN8A gene introns repress their expression via transcription factor ZNF91 to delay neuronal maturation. Deleting the SVA in CDK5RAP2 initiates multi-dimensional and in SCN8A selective sodium current neuronal maturation by upregulating these genes. SVA-lncRNA AK057321 forms RNA:DNA heteroduplexes with the genomic SVAs and upregulates these genes to initiate neuronal maturation. SVA-lncRNA AK057321 also promotes species-specific cortex and cerebellum-enriched expression upregulating human genes with intronic SVAs (e.g., HTT, CHAF1B and KCNJ6) but not mouse orthologs. The diversity of neuronal genes with intronic SVAs suggest this hominoid-specific SVA transposon-based gene regulatory mechanism may act at multiple steps to specialize and achieve neoteny of the human brain.
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Affiliation(s)
- Monica J S Nadler
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Weipang Chang
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Ekim Ozkaynak
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Yuda Huo
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Neuroscience Therapeutic Focus Area, Regeneron, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Yi Nong
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Neuroscience Therapeutic Focus Area, Regeneron, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Morgane Boillot
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Mark Johnson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Antonio Moreno
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Matthew P Anderson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA.
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA.
- Boston Children's Hospital Intellectual and Developmental Disabilities Research Center, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Program in Neuroscience, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Neuroscience Therapeutic Focus Area, Regeneron, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
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Asif M, Abdullah U, Nürnberg P, Tinschert S, Hussain MS. Congenital Microcephaly: A Debate on Diagnostic Challenges and Etiological Paradigm of the Shift from Isolated/Non-Syndromic to Syndromic Microcephaly. Cells 2023; 12:cells12040642. [PMID: 36831309 PMCID: PMC9954724 DOI: 10.3390/cells12040642] [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: 01/08/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Congenital microcephaly (CM) exhibits broad clinical and genetic heterogeneity and is thus categorized into several subtypes. However, the recent bloom of disease-gene discoveries has revealed more overlaps than differences in the underlying genetic architecture for these clinical sub-categories, complicating the differential diagnosis. Moreover, the mechanism of the paradigm shift from a brain-restricted to a multi-organ phenotype is only vaguely understood. This review article highlights the critical factors considered while defining CM subtypes. It also presents possible arguments on long-standing questions of the brain-specific nature of CM caused by a dysfunction of the ubiquitously expressed proteins. We argue that brain-specific splicing events and organ-restricted protein expression may contribute in part to disparate clinical manifestations. We also highlight the role of genetic modifiers and de novo variants in the multi-organ phenotype of CM and emphasize their consideration in molecular characterization. This review thus attempts to expand our understanding of the phenotypic and etiological variability in CM and invites the development of more comprehensive guidelines.
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Affiliation(s)
- Maria Asif
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University, Rawalpindi, Rawalpindi 46300, Pakistan
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sigrid Tinschert
- Zentrum Medizinische Genetik, Medizinische Universität, 6020 Innsbruck, Austria
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence:
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Chen H, Jin X, Li T, Ye Z. Brain organoids: Establishment and application. Front Cell Dev Biol 2022; 10:1029873. [PMID: 36506083 PMCID: PMC9726712 DOI: 10.3389/fcell.2022.1029873] [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: 08/28/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022] Open
Abstract
Brain organoids are produced by the differentiation of pluripotent stem cells under three-dimensional culture conditions by adding neurodevelopment-related regulatory signals. They are similar to the cell composition and anatomical structure of the brain, and can reflect the developmental process of the brain, as well as their physiology, pathology, and pharmacology. Brain organoids are good models to study human brain development and brain-related diseases in vitro. Here, we mainly focus on the construction of brain organoids and review the application of brain organoids in disease modelingand drug screening.
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Affiliation(s)
- Hao Chen
- Department of Neurovascular Surgery, First Hospital, Jilin University, Changchun, China
| | - Xin Jin
- Department of Oncology and Hematology, Second Hospital, Jilin University, Changchun, China
| | - Tie Li
- Department of Rheumatology, First Hospital, Jilin University, Changchun, China
| | - Zhuang Ye
- Department of Rheumatology, First Hospital, Jilin University, Changchun, China,*Correspondence: Zhuang Ye,
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Makhdoom EUH, Anwar H, Baig SM, Hussain G. Whole exome sequencing identifies a novel mutation in ASPM and ultra-rare mutation in CDK5RAP2 causing Primary microcephaly in consanguineous Pakistani families. Pak J Med Sci 2022; 38:84-89. [PMID: 35035405 PMCID: PMC8713189 DOI: 10.12669/pjms.38.1.4464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/29/2021] [Accepted: 10/29/2021] [Indexed: 12/04/2022] Open
Abstract
Background & Objectives: Primary Microcephaly (MCPH) is a rare neurogenetic disease, manifesting congenitally reduced head circumference and non-progressive intellectual disability (ID). To date, twenty-eight genes with biallelic mutations have been reported for this disorder. The study aimed for molecular genetic characterization of Pakistani families segregating MCPH. Methods: We studied two unrelated consanguineous families (family A and B) presenting >2 patients with diagnostic symptoms of MCPH, born to asymptomatic parents. We employed whole-exome sequencing (WES) of probands to find putative causal mutations. The candidate variants were further confirmed and analyzed for co-segregation by Sanger sequencing of all available members of each family. This study was conducted at Government College University, Faisalabad, Pakistan, and Cologne Center for Genomics (CCG), University of Cologne, Germany; during 2017-2020. Results: We identified a novel homozygous variant c.10097_10098delGA, p.(Gly3366Glufs*19) in exon 26 of ASPM gene in family A which presents with moderate intellectual disability, speech impairment, visual abnormalities, seizures, and ptyalism. Family B was found to segregate nonsense, homozygous variant c.448C>T p.(Arg150*) in CDK5RAP2. The patients also exhibited mild to severe seizures without ptyalism that has not been previously reported in patients with mutations in the CDK5RAP2 gene. Conclusion: We report a novel mutation in ASPM and ultra-rare mutation in the CDK5RAP2 gene, both causing primary microcephaly. The study expands the mutational spectrum of the ASPM gene to 212, and also adds to the clinical spectrum of CDK5RAP2 mutations. It also demonstrated the utility of WES in the investigation and genetic diagnosis of genetically heterogeneous disorders like MCPH. These findings would aid in diagnostic and preventive strategies including carrier screening, cascade testing, and genetic counselling.
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Affiliation(s)
- Ehtisham Ul Haq Makhdoom
- Ehtisham ul Haq Makhdoom (MPhil), Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, 38000, Faisalabad, Pakistan. Human Molecular Genetics Laboratory, Health Biotechnology Division, NIBGE College, PIEAS, 38000, Faisalabad, Pakistan
| | - Haseeb Anwar
- Haseeb Anwar (PhD), Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, 38000, Faisalabad, Pakistan
| | - Shahid Mahmood Baig
- Shahid Mahmood Baig (PhD), Department of Biological and Biomedical Sciences, The Aga Khan University, 74000, Karachi, Pakistan. Pakistan Science Foundation, Constitution Avenue, 44000, Islamabad, Pakistan. Human Molecular Genetics Laboratory, Health Biotechnology Division, NIBGE College, PIEAS, 38000, Faisalabad, Pakistan
| | - Ghulam Hussain
- Ghulam Hussain (PhD), Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, 38000, Faisalabad, Pakistan
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Centrosome dysfunction in human diseases. Semin Cell Dev Biol 2021; 110:113-122. [DOI: 10.1016/j.semcdb.2020.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
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Cep215 is essential for morphological differentiation of astrocytes. Sci Rep 2020; 10:17000. [PMID: 33046744 PMCID: PMC7550586 DOI: 10.1038/s41598-020-72728-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 08/31/2020] [Indexed: 11/08/2022] Open
Abstract
Cep215 (also known as Cdk5rap2) is a centrosome protein which is involved in microtubule organization. Cep215 is also placed at specific subcellular locations and organizes microtubules outside the centrosome. Here, we report that Cep215 is involved in morphological differentiation of astrocytes. Cep215 was specifically localized at the glial processes as well as centrosomes in developing astrocytes. Morphological differentiation of astrocytes was suppressed in the Cep215-deleted P19 cells and in the Cep215-depleted embryonic hippocampal culture. We confirm that the microtubule organizing function of Cep215 is critical for the glial process formation. However, Cep215 is not involved in the regulation of cell proliferation nor cell specification. Based on the results, we propose that Cep215 organizes microtubules for glial process formation during astrocyte differentiation.
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Nasser H, Vera L, Elmaleh-Bergès M, Steindl K, Letard P, Teissier N, Ernault A, Guimiot F, Afenjar A, Moutard ML, Héron D, Alembik Y, Momtchilova M, Milani P, Kubis N, Pouvreau N, Zollino M, Guilmin Crepon S, Kaguelidou F, Gressens P, Verloes A, Rauch A, El Ghouzzi V, Drunat S, Passemard S. CDK5RAP2 primary microcephaly is associated with hypothalamic, retinal and cochlear developmental defects. J Med Genet 2020; 57:389-399. [PMID: 32015000 DOI: 10.1136/jmedgenet-2019-106474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/22/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Primary hereditary microcephaly (MCPH) comprises a large group of autosomal recessive disorders mainly affecting cortical development and resulting in a congenital impairment of brain growth. Despite the identification of >25 causal genes so far, it remains a challenge to distinguish between different MCPH forms at the clinical level. METHODS 7 patients with newly identified mutations in CDK5RAP2 (MCPH3) were investigated by performing prospective, extensive and systematic clinical, MRI, psychomotor, neurosensory and cognitive examinations under similar conditions. RESULTS All patients displayed neurosensory defects in addition to microcephaly. Small cochlea with incomplete partition type II was found in all cases and was associated with progressive deafness in 4 of them. Furthermore, the CDK5RAP2 protein was specifically identified in the developing cochlea from human fetal tissues. Microphthalmia was also present in all patients along with retinal pigmentation changes and lipofuscin deposits. Finally, hypothalamic anomalies consisting of interhypothalamic adhesions, a congenital midline defect usually associated with holoprosencephaly, was detected in 5 cases. CONCLUSION This is the first report indicating that CDK5RAP2 not only governs brain size but also plays a role in ocular and cochlear development and is necessary for hypothalamic nuclear separation at the midline. Our data indicate that CDK5RAP2 should be considered as a potential gene associated with deafness and forme fruste of holoprosencephaly. These children should be given neurosensory follow-up to prevent additional comorbidities and allow them reaching their full educational potential. TRIAL REGISTRATION NUMBER NCT01565005.
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Affiliation(s)
- Hala Nasser
- Département de Génétique, APHP, Hopital Robert Debré, 75019 Paris, France.,Service des Explorations Fonctionnelles, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Liza Vera
- Service d'Ophtalmologie, APHP, Hopital Robert Debré, 75019 Paris, France
| | | | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Pascaline Letard
- Département de Génétique, APHP, Hopital Robert Debré, 75019 Paris, France.,Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,Service d'Anatomopathologie, Hopital Jean Verdier, APHP, Bondy, France.,Université Paris 13, 93140 Bondy, France
| | - Natacha Teissier
- Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,Service d'ORL, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Anais Ernault
- Département de Génétique, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Fabien Guimiot
- Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,Service de Foetopathologie, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Alexandra Afenjar
- CRMR déficiences intellectuelles de causes rares, Département de génétique, Sorbonne Université, APHP, Hôpital Trousseau, 75012 Paris, France
| | | | - Delphine Héron
- Département de Génétique, APHP, Hopital La Pitié-Salpetriere, 75013 Paris, France
| | - Yves Alembik
- Service de Génétique Médicale, CHU de Strasbourg, Hopital de Hautepierre, 67200 Strasbourg, France
| | | | - Paolo Milani
- Service des Explorations Fonctionnelles, APHP, Hopital Lariboisière, 75010 Paris, France
| | - Nathalie Kubis
- Service des Explorations Fonctionnelles, APHP, Hopital Lariboisière, 75010 Paris, France
| | - Nathalie Pouvreau
- Département de Génétique, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Marcella Zollino
- Universita Cattolica Sacro Cuore Istituto di Medicina Genomica, Roma, Italy.,Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | | | - Florentia Kaguelidou
- Université de Paris, Centre d'Investigation Clinique, CIC 1426, INSERM, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Pierre Gressens
- Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,Center for Developing Brain, King's College, St. Thomas' Campus, London, United Kingdom
| | - Alain Verloes
- Département de Génétique, APHP, Hopital Robert Debré, 75019 Paris, France.,Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,European Reference Network ERN ITHACA, 75019 Paris, France
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | | | - Severine Drunat
- Département de Génétique, APHP, Hopital Robert Debré, 75019 Paris, France.,Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,European Reference Network ERN ITHACA, 75019 Paris, France
| | - Sandrine Passemard
- Département de Génétique, APHP, Hopital Robert Debré, 75019 Paris, France .,Université de Paris, NeuroDiderot, Inserm, F-75019 Paris, France.,European Reference Network ERN ITHACA, 75019 Paris, France.,Service de Neuropédiatrie, APHP, Hopital Robert Debré, 75019 Paris, France
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Mir YR, Kuchay RAH. Advances in identification of genes involved in autosomal recessive intellectual disability: a brief review. J Med Genet 2019; 56:567-573. [PMID: 30842223 DOI: 10.1136/jmedgenet-2018-105821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/28/2022]
Abstract
Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1%-3% of the general population. The number of ID-causing genes is high. Many X-linked genes have been implicated in ID. Autosomal dominant genes have recently been the focus of several large-scale studies. The total number of autosomal recessive ID (ARID) genes is estimated to be very high, and most are still unknown. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause ARID has lagged behind, predominantly due to non-availability of sizeable families. A commonly used approach to identify genetic loci for recessive disorders in consanguineous families is autozygosity mapping and whole-exome sequencing. Combination of these two approaches has recently led to identification of many genes involved in ID. These genes have diverse function and control various biological processes. In this review, we will present an update regarding genes that have been recently implicated in ID with focus on ARID.
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Affiliation(s)
- Yaser Rafiq Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Raja Amir Hassan Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
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