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Dalal S, Ramirez-Gomez J, Sharma B, Devara D, Kumar S. MicroRNAs and Synapse Turnover in Alzheimer's Disease. Ageing Res Rev 2024; 99:102377. [PMID: 38871301 DOI: 10.1016/j.arr.2024.102377] [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: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Alzheimer's Disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of amyloid-beta plaques and neurofibrillary tangles in the brain, leading to synaptic dysfunction and cognitive decline. Healthy synapses are the crucial for normal brain function, memory restoration and other neurophysiological function. Synapse loss and synaptic dysfunction are two primary events that occur during AD initiation. Synapse lifecycle and/or synapse turnover is divided into five key stages and several sub-stages such as synapse formation, synapse assembly, synapse maturation, synapse transmission and synapse termination. In normal state, the synapse turnover is regulated by various biological and molecular factors for a healthy neurotransmission. In AD, the different stages of synapse turnover are affected by AD-related toxic proteins. MicroRNAs (miRNAs) have emerged as critical regulators of gene expression and have been implicated in various neurological diseases, including AD. Deregulation of miRNAs modulate the synaptic proteins and affect the synapse turnover at different stages. In this review, we discussed the key milestones of synapse turnover and how they are affected in AD. Further, we discussed the involvement of miRNAs in synaptic turnover, focusing specifically on their role in AD pathogenesis. We also emphasized the regulatory mechanisms by which miRNAs modulate the synaptic turnover stages in AD. Current studies will help to understand the synaptic life-cycle and role of miRNAs in each stage that is deregulated in AD, further allowing for a better understanding of the pathogenesis of devastating disease.
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Affiliation(s)
- Sarthak Dalal
- Center of Emphasis in Neuroscience, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Jaime Ramirez-Gomez
- Center of Emphasis in Neuroscience, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Bhupender Sharma
- Center of Emphasis in Neuroscience, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Davin Devara
- Center of Emphasis in Neuroscience, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Subodh Kumar
- Center of Emphasis in Neuroscience, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA; L. Frederick Francis Graduate School of Biomedicael Sciences, Texas Tech University Health Sciences Center, El Paso, Texas, USA.
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2
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Cesari E, Farini D, Medici V, Ehrmann I, Guerra M, Testa E, Naro C, Geloso MC, Pagliarini V, La Barbera L, D’Amelio M, Orsini T, Vecchioli SF, Tamagnone L, Fort P, Viscomi MT, Elliott DJ, Sette C. Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development. Nucleic Acids Res 2024; 52:4167-4184. [PMID: 38324473 PMCID: PMC11077083 DOI: 10.1093/nar/gkae071] [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: 04/18/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Sam68 and SLM2 are paralog RNA binding proteins (RBPs) expressed in the cerebral cortex and display similar splicing activities. However, their relative functions during cortical development are unknown. We found that these RBPs exhibit an opposite expression pattern during development. Sam68 expression declines postnatally while SLM2 increases after birth, and this developmental pattern is reinforced by hierarchical control of Sam68 expression by SLM2. Analysis of Sam68:Slm2 double knockout (Sam68:Slm2dko) mice revealed hundreds of exons that respond to joint depletion of these proteins. Moreover, parallel analysis of single and double knockout cortices indicated that exons regulated mainly by SLM2 are characterized by a dynamic splicing pattern during development, whereas Sam68-dependent exons are spliced at relatively constant rates. Dynamic splicing of SLM2-sensitive exons is completely suppressed in the Sam68:Slm2dko developing cortex. Sam68:Slm2dko mice die perinatally with defects in neurogenesis and in neuronal differentiation, and develop a hydrocephalus, consistent with splicing alterations in genes related to these biological processes. Thus, our study reveals that developmental control of separate Sam68 and Slm2 paralog genes encoding homologous RBPs enables the orchestration of a dynamic splicing program needed for brain development and viability, while ensuring a robust redundant mechanism that supports proper cortical development.
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Affiliation(s)
- Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Vanessa Medici
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Ingrid Ehrmann
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle NE1 3BZ, UK
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Erika Testa
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Maria Concetta Geloso
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Livia La Barbera
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Marcello D’Amelio
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
- Università Campus Bio-Medico di Roma, Via Álvaro del Portillo, 21, 00128 Rome, Italy
| | - Tiziana Orsini
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC/CNR), Monterotondo, 00015 Rome, Italy
| | - Stefano Farioli Vecchioli
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC/CNR), Monterotondo, 00015 Rome, Italy
| | - Luca Tamagnone
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - Philippe Fort
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 05, France
| | - Maria Teresa Viscomi
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - David J Elliott
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle NE1 3BZ, UK
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
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3
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Liu X, Qin H, Liu Y, Ma J, Li Y, He Y, Zhu H, Mao L. The biological functions and pathological mechanisms of CASK in various diseases. Heliyon 2024; 10:e28863. [PMID: 38638974 PMCID: PMC11024568 DOI: 10.1016/j.heliyon.2024.e28863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
Background As a scaffold protein, calcium/calmodulin-dependent serine protein kinase (CASK) has been extensively studied in a variety of tissues throughout the body. The Cask gene is ubiquitous in several tissues, such as the neurons, islets, heart, kidneys and sperm, and is mostly localised in the cytoplasm adjacent to the basement membrane. CASK binds to a variety of proteins through its domains to exerting its biological activity. Scope of review Here, we discuss the role of CASK in multiple tissues throughout the body. The role of different CASK domains in regulating neuronal development, neurotransmitter release and synaptic vesicle secretion was emphasised; the regulatory mechanism of CASK on the function of pancreatic islet β cells was analysed; the role of CASK in cardiac physiology, kidney and sperm development was discussed; and the role of CASK in different tumours was compared. Finally, we clarify the importance of the Cask gene in the body, and how deletion or mutation of the Cask gene can have adverse consequences. Major conclusions CASK is a conserved gene with similar roles in various tissues. The function of the Cask gene in the nervous system is mainly involved in the development of the nervous system and the release of neurotransmitters. In the endocrine system, an involvement of CASK has been reported in the process of insulin vesicle transport. CASK is also involved in cardiomyocyte ion channel regulation, kidney and sperm development, and tumour proliferation. CASK is an indispensable gene for the whole body, and CASK mutations can cause foetal malformations or death at birth. In this review, we summarise the biological functions and pathological mechanisms of CASK in various systems, thereby providing a basis for further in-depth studies of CASK functions.
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Affiliation(s)
- Xingjing Liu
- Department of Endocrinology, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
| | - Haonan Qin
- Department of Orthopedics, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
| | - Yuanyuan Liu
- Department of Endocrinology, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
| | - Jingjing Ma
- Department of Endocrinology, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
| | - Yiming Li
- Department of Endocrinology, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
| | - Yu He
- Department of Endocrinology, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
| | - Huimin Zhu
- Department of Electrophysiology, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
| | - Li Mao
- Department of Endocrinology, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu Province, China
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4
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Yahia A, Li D, Lejerkrans S, Rajagopalan S, Kalnak N, Tammimies K. Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder. Hum Genet 2024; 143:169-183. [PMID: 38300321 PMCID: PMC10881898 DOI: 10.1007/s00439-023-02636-z] [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: 09/20/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Developmental language disorder (DLD) overlaps clinically, genetically, and pathologically with other neurodevelopmental disorders (NDD), corroborating the concept of the NDD continuum. There is a lack of studies to understand the whole genetic spectrum in individuals with DLD. Previously, we recruited 61 probands with severe DLD from 59 families and examined 59 of them and their families using microarray genotyping with a 6.8% diagnostic yield. Herein, we investigated 53 of those probands using whole exome sequencing (WES). Additionally, we used polygenic risk scores (PRS) to understand the within family enrichment of neurodevelopmental difficulties and examine the associations between the results of language-related tests in the probands and language-related PRS. We identified clinically significant variants in four probands, resulting in a 7.5% (4/53) molecular diagnostic yield. Those variants were in PAK2, MED13, PLCB4, and TNRC6B. We also prioritized additional variants for future studies for their role in DLD, including high-impact variants in PARD3 and DIP2C. PRS did not explain the aggregation of neurodevelopmental difficulties in these families. We did not detect significant associations between the language-related tests and language-related PRS. Our results support using WES as the first-tier genetic test for DLD as it can identify monogenic DLD forms. Large-scale sequencing studies for DLD are needed to identify new genes and investigate the polygenic contribution to the condition.
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Affiliation(s)
- Ashraf Yahia
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Shyam Rajagopalan
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Nelli Kalnak
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
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5
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Mastropasqua F, Oksanen M, Soldini C, Alatar S, Arora A, Ballarino R, Molinari M, Agostini F, Poulet A, Watts M, Rabkina I, Becker M, Li D, Anderlid BM, Isaksson J, Lundin Remnelius K, Moslem M, Jacob Y, Falk A, Crosetto N, Bienko M, Santini E, Borgkvist A, Bölte S, Tammimies K. Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis. Biol Open 2023; 12:bio060113. [PMID: 37815090 PMCID: PMC10581386 DOI: 10.1242/bio.060113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 10/11/2023] Open
Abstract
Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.
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Affiliation(s)
- Francesca Mastropasqua
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Marika Oksanen
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Cristina Soldini
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Shemim Alatar
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Abishek Arora
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Roberto Ballarino
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Maya Molinari
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Federico Agostini
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Michelle Watts
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Ielyzaveta Rabkina
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Martin Becker
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Johan Isaksson
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Department of Medical Sciences, Child and Adolescent Psychiatry Unit, Uppsala University, 75309 Uppsala, Sweden
| | - Karl Lundin Remnelius
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
| | - Mohsen Moslem
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
- Lund Stem Cell Center, Lund University, 22100 Lund, Sweden
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17164 Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Emanuela Santini
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Anders Borgkvist
- Department of Neuroscience, Karolinska Institutet, 17176 Solna, Sweden
| | - Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
- Curtin Autism Research Group, Curtin School of Allied Health, Curtin University, 6845 Perth, Western Australia
- Child and Adolescent Psychiatry, Stockholm Health Care Services, Region Stockholm, 10431 Stockholm, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden
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Tello JA, Jiang L, Zohar Y, Restifo LL. Drosophila CASK regulates brain size and neuronal morphogenesis, providing a genetic model of postnatal microcephaly suitable for drug discovery. Neural Dev 2023; 18:6. [PMID: 37805506 PMCID: PMC10559581 DOI: 10.1186/s13064-023-00174-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND CASK-related neurodevelopmental disorders are untreatable. Affected children show variable severity, with microcephaly, intellectual disability (ID), and short stature as common features. X-linked human CASK shows dosage sensitivity with haploinsufficiency in females. CASK protein has multiple domains, binding partners, and proposed functions at synapses and in the nucleus. Human and Drosophila CASK show high amino-acid-sequence similarity in all functional domains. Flies homozygous for a hypomorphic CASK mutation (∆18) have motor and cognitive deficits. A Drosophila genetic model of CASK-related disorders could have great scientific and translational value. METHODS We assessed the effects of CASK loss of function on morphological phenotypes in Drosophila using established genetic, histological, and primary neuronal culture approaches. NeuronMetrics software was used to quantify neurite-arbor morphology. Standard nonparametric statistics methods were supplemented by linear mixed effects modeling in some cases. Microfluidic devices of varied dimensions were fabricated and numerous fluid-flow parameters were used to induce oscillatory stress fields on CNS tissue. Dissociation into viable neurons and neurite outgrowth in vitro were assessed. RESULTS We demonstrated that ∆18 homozygous flies have small brains, small heads, and short bodies. When neurons from developing CASK-mutant CNS were cultured in vitro, they grew small neurite arbors with a distinctive, quantifiable "bushy" morphology that was significantly rescued by transgenic CASK+. As in humans, the bushy phenotype showed dosage-sensitive severity. To overcome the limitations of manual tissue trituration for neuronal culture, we optimized the design and operation of a microfluidic system for standardized, automated dissociation of CNS tissue into individual viable neurons. Neurons from CASK-mutant CNS dissociated in the microfluidic system recapitulate the bushy morphology. Moreover, for any given genotype, device-dissociated neurons grew larger arbors than did manually dissociated neurons. This automated dissociation method is also effective for rodent CNS. CONCLUSIONS These biological and engineering advances set the stage for drug discovery using the Drosophila model of CASK-related disorders. The bushy phenotype provides a cell-based assay for compound screening. Nearly a dozen genes encoding CASK-binding proteins or transcriptional targets also have brain-development mutant phenotypes, including ID. Hence, drugs that improve CASK phenotypes might also benefit children with disorders due to mutant CASK partners.
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Affiliation(s)
- Judith A Tello
- Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, 85721, USA
- Department of Neurology, University of Arizona Health Sciences, 1501 N. Campbell Ave, Tucson, AZ, 85724-5023, USA
- Present address: Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, 10010, USA
| | - Linan Jiang
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Yitshak Zohar
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721, USA
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, 85721, USA
- BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Linda L Restifo
- Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Neurology, University of Arizona Health Sciences, 1501 N. Campbell Ave, Tucson, AZ, 85724-5023, USA.
- BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Cellular & Molecular Medicine, University of Arizona Health Sciences, Tucson, AZ, 85724, USA.
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7
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Mori T, Zhou M, Tabuchi K. Diverse Clinical Phenotypes of CASK-Related Disorders and Multiple Functional Domains of CASK Protein. Genes (Basel) 2023; 14:1656. [PMID: 37628707 PMCID: PMC10454856 DOI: 10.3390/genes14081656] [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: 08/07/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
CASK-related disorders are a form of rare X-linked neurological diseases and most of the patients are females. They are characterized by several symptoms, including microcephaly with pontine and cerebellar hypoplasia (MICPCH), epilepsy, congenital nystagmus, and neurodevelopmental disorders. Whole-genome sequencing has identified various mutations, including nonsense and missense mutations, from patients with CASK-related disorders, revealing correlations between specific mutations and clinical phenotypes. Notably, missense mutations associated with epilepsy and intellectual disability were found throughout the whole region of the CASK protein, while missense mutations related to microcephaly and MICPCH were restricted in certain domains. To investigate the pathophysiology of CASK-related disorders, research groups have employed diverse methods, including the generation of CASK knockout mice and the supplementation of CASK to rescue the phenotypes. These approaches have yielded valuable insights into the identification of functional domains of the CASK protein associated with a specific phenotype. Additionally, recent advancements in the AI-based prediction of protein structure, such as AlphaFold2, and the application of genome-editing techniques to generate CASK mutant mice carrying missense mutations from patients with CASK-related disorders, allow us to understand the pathophysiology of CASK-related disorders in more depth and to develop novel therapeutic methods for the fundamental treatment of CASK-related disorders.
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Affiliation(s)
- Takuma Mori
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Mengyun Zhou
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Katsuhiko Tabuchi
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
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8
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Arora A, Becker M, Marques C, Oksanen M, Li D, Mastropasqua F, Watts ME, Arora M, Falk A, Daub CO, Lanekoff I, Tammimies K. Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics. Sci Rep 2023; 13:10519. [PMID: 37386098 PMCID: PMC10310850 DOI: 10.1038/s41598-023-37488-0] [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: 02/03/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023] Open
Abstract
Research continues to identify genetic variation, environmental exposures, and their mixtures underlying different diseases and conditions. There is a need for screening methods to understand the molecular outcomes of such factors. Here, we investigate a highly efficient and multiplexable, fractional factorial experimental design (FFED) to study six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine hydrochloride and zinc deficiency) and four human induced pluripotent stem cell line derived differentiating human neural progenitors. We showcase the FFED coupled with RNA-sequencing to identify the effects of low-grade exposures to these environmental factors and analyse the results in the context of autism spectrum disorder (ASD). We performed this after 5-day exposures on differentiating human neural progenitors accompanied by a layered analytical approach and detected several convergent and divergent, gene and pathway level responses. We revealed significant upregulation of pathways related to synaptic function and lipid metabolism following lead and fluoxetine exposure, respectively. Moreover, fluoxetine exposure elevated several fatty acids when validated using mass spectrometry-based metabolomics. Our study demonstrates that the FFED can be used for multiplexed transcriptomic analyses to detect relevant pathway-level changes in human neural development caused by low-grade environmental risk factors. Future studies will require multiple cell lines with different genetic backgrounds for characterising the effects of environmental exposures in ASD.
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Affiliation(s)
- Abishek Arora
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Martin Becker
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Cátia Marques
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Marika Oksanen
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Francesca Mastropasqua
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Michelle Evelyn Watts
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Lund Stem Cell Center, Division of Neurobiology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Carsten Oliver Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Ingela Lanekoff
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
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9
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Wang W, Bo T, Zhang G, Li J, Ma J, Ma L, Hu G, Tong H, Lv Q, Araujo DJ, Luo D, Chen Y, Wang M, Wang Z, Wang GZ. Noncoding transcripts are linked to brain resting-state activity in non-human primates. Cell Rep 2023; 42:112652. [PMID: 37335775 DOI: 10.1016/j.celrep.2023.112652] [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: 09/21/2022] [Revised: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
Brain-derived transcriptomes are known to correlate with resting-state brain activity in humans. Whether this association holds in nonhuman primates remains uncertain. Here, we search for such molecular correlates by integrating 757 transcriptomes derived from 100 macaque cortical regions with resting-state activity in separate conspecifics. We observe that 150 noncoding genes explain variations in resting-state activity at a comparable level with protein-coding genes. In-depth analysis of these noncoding genes reveals that they are connected to the function of nonneuronal cells such as oligodendrocytes. Co-expression network analysis finds that the modules of noncoding genes are linked to both autism and schizophrenia risk genes. Moreover, genes associated with resting-state noncoding genes are highly enriched in human resting-state functional genes and memory-effect genes, and their links with resting-state functional magnetic resonance imaging (fMRI) signals are altered in the brains of patients with autism. Our results highlight the potential for noncoding RNAs to explain resting-state activity in the nonhuman primate brain.
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Affiliation(s)
- Wei Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tingting Bo
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Clinical Neuroscience Center, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ge Zhang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China
| | - Jie Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liangxiao Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Lv
- School of Psychological and Cognitive Sciences, Beijing Key Laboratory of Behavior and Mental Health, IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Daniel J Araujo
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Dong Luo
- School of Biomedical Engineering, Hainan University, Haikou, Hainan, China
| | - Yuejun Chen
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Meiyun Wang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China
| | - Zheng Wang
- School of Psychological and Cognitive Sciences, Beijing Key Laboratory of Behavior and Mental Health, IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; School of Biomedical Engineering, Hainan University, Haikou, Hainan, China.
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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10
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Watts ME, Oksanen M, Lejerkrans S, Mastropasqua F, Gorospe M, Tammimies K. Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein. BMC Biol 2023; 21:127. [PMID: 37237280 DOI: 10.1186/s12915-023-01627-w] [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: 10/27/2022] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Circular RNA (circRNA) molecules, generated through non-canonical back-splicing of exon-exon junctions, have recently been implicated in diverse biological functions including transcriptional regulation and modulation of protein interactions. CircRNAs are emerging as a key component of the complex neural transcriptome implicated in brain development. However, the specific expression patterns and functions of circRNAs in human neuronal differentiation have not been explored. RESULTS Using total RNA sequencing analysis, we identified expressed circRNAs during the differentiation of human neuroepithelial stem (NES) cells into developing neurons and discovered that many circRNAs originated from host genes associated with synaptic function. Interestingly, when assessing population data, exons giving rise to circRNAs in our dataset had a higher frequency of genetic variants. Additionally, screening for RNA-binding protein sites identified enrichment of Splicing Factor Proline and Glutamine Rich (SFPQ) motifs in increased circRNAs, several of which were reduced by SFPQ knockdown and enriched in SFPQ ribonucleoprotein complexes. CONCLUSIONS Our study provides an in-depth characterisation of circRNAs in a human neuronal differentiation model and highlights SFPQ as both a regulator and binding partner of circRNAs elevated during neuronal maturation.
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Affiliation(s)
- Michelle E Watts
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Marika Oksanen
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD, USA
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Francesca Mastropasqua
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD, USA
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
- Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Sweden.
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11
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Coschiera A, Watts ME, Kere J, Tammimies K, Swoboda P. Human LUHMES and NES cells as models for studying primary cilia in neurons. Methods Cell Biol 2023; 176:27-41. [PMID: 37164541 DOI: 10.1016/bs.mcb.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Primary cilia are antenna-like organelles emanating from the cell surface. They are involved in cell-to-cell communication and bidirectional signal transduction to/from the extracellular environment. During brain formation, cilia critically aid in neurogenesis and maturation of neuronal structures such as axons, dendrites and synapses. Aberrations in cilia function can induce neuron differentiation defects and pathological consequences of varying severity, resulting in ciliopathies and likely a number of neurodevelopmental disorders. Despite the documented relevance of cilia for proper brain development, human neuronal models to recognize and study cilia biology are still scarce. We have established two types of cell models, Lund Human Mesencephalic (LUHMES) cells and neuroepithelial stem (NES) cells derived from induced pluripotent stem cells (iPSC), to investigate cilia biology in both proliferating neuronal progenitors/precursors and during the entire neuron differentiation and maturation process. We employ improved immunocytochemistry assays able to specifically detect cilia by confocal and super-resolution microscopy. We provide straightforward and robust methods to easily maintain cells in culture, for immunostaining and characterization of cilia orientation, anatomy and shape in human neurons across all stages of differentiation.
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Affiliation(s)
- Andrea Coschiera
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Michelle Evelyn Watts
- Karolinska Institute, Department of Women's and Children's Health and Center for Psychiatry Research, Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Juha Kere
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden; University of Helsinki, Stem Cells and Metabolism Research Program and Folkhälsan Research Center, Helsinki, Finland
| | - Kristiina Tammimies
- Karolinska Institute, Department of Women's and Children's Health and Center for Psychiatry Research, Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden.
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12
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Waqas A, Liaqat R, Shaheen S, Khan AZ, Habib AH, Binothman N, Aljadani M, Zehri Z, Shaheen S, Alkathiri A, Naz R, Umair M, Abbas S. A novel homozygous truncating variant in PPFIBP1 further delineates PPFIBP1-associated neurodevelopmental disorder. Int J Dev Neurosci 2022; 83:191-200. [PMID: 36527195 DOI: 10.1002/jdn.10247] [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: 08/24/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are classified as a group of disorders affecting function and development of the brain and having wide clinical variability. Herein, we describe two affected individuals segregating a recessive NDD. The affected individuals exhibited phenotypes such as global developmental delay (GDD), intellectual disability (ID), microcephaly and speech delay. Whole-exome sequencing (WES) followed by bidirectional Sanger sequencing techniques identified a homozygous nonsense variant (c.466C > T; p.Gln156*) in the PPFIBP1 gene (NM_003622.4) that segregated with the disease phenotype. Further, to elucidate the effect of the variant on protein structure, 3D protein modelling was performed for the mutant and normal protein that suggested substantial reduction of the mutant protein. Our data support the evidence that PPFIBP1 has a pivotal role in neurodevelopment in humans, and loss-of-function variants cause clinically variable neurodevelopmental phenotypes.
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Affiliation(s)
- Ahmed Waqas
- Department Zoology, Division of Science and Technology, University of Education, Lahore, Punjab, Pakistan
| | - Romana Liaqat
- Institute of Chemical Science, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sidrah Shaheen
- Department of Higher Education, Government Girls degree College No. 1, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Ali Zaman Khan
- Department of Surgery, Surgical Ward 'A', Khyber Teaching Hospital, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Majidah Aljadani
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Zamrud Zehri
- Shaheed Nawab Ghous Bakhsh Raisani Memorial Hospital, Mastung, Balochistan, Pakistan
| | - Shabnam Shaheen
- Department of Higher Education, Government Girls Degree College, Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
| | - Afnan Alkathiri
- Medical Genetics, Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Rubina Naz
- Institute of Chemical Science, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, USA
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13
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Yang K, Lin L, Yuan F, Li X, Liu Z, Lan X, Wang Y, Ren Y, Li J, Chen Y. Two heterozygous mutations in the calcium/calmodulin-dependent serine protein kinase gene (CASK) in cases with developmental disorders. Mol Genet Genomic Med 2022; 10:e2065. [PMID: 36168867 PMCID: PMC9651610 DOI: 10.1002/mgg3.2065] [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: 05/16/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The calcium/calmodulin-dependent serine protein kinase gene (CASK) is an essential gene in mammals, critical for neurodevelopment. The purpose of this study is to expand the understanding of the diagnosis of CASK-linked disorders. MATERIALS/METHODS From clinical and genetic mutational analyses, relevant data in 2 Han Chinese patients were collected and analyzed. Real-time quantitative PCR (RT-qPCR) was performed to investigate the CASK expression levels in the patients. The X-chromosome inactivation (XCI) patterns of the patients and their nuclear families were tested by quantitation of methylation of the polymorphic human androgen receptor (HUMARA) locus. RESULTS Two Han Chinese patients both presented with intellectual disability (ID), microcephaly with pontine and cerebellar hypoplasia (MICPCH). Two de novo mutations of c.82C>T (p.Arg28*) and c.846C>G (p.Tyr282*) in CASK have been investigated and predicted to be deleterious, which have produced truncated proteins. The functional protein association network of STRING (http://string-db.org) generated three-dimensional (3D) atomic models based on protein sequences in CASK and two Arg28 and Tyr282 residues were marked. RT-qPCR showed lower copy numbers of CASK expression in the patients than in their parents, as well as the sex- and age- matched control groups. Patient 1 showed a skewed XCI pattern, while no related changes noted in patient 2. CONCLUSIONS Patients carrying different nonsense variants may have different degrees of different clinical phenotypes. This study expands the spectrum of genotype and phenotype correlations of CASK-linked disorders in the Han Chinese ethnicity and provides new insights into the molecular mechanism.
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Affiliation(s)
- Kunfang Yang
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Longlong Lin
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Fang Yuan
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xiaoguang Li
- Department of EmergencyShanghai United Family HospitalShanghaiChina
| | - Zhiping Liu
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xiaoping Lan
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Yilin Wang
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Yun Ren
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Jiaoyan Li
- Department of PediatricsShanghai United Family HospitalShanghaiChina
| | - Yucai Chen
- Department of Neurology, Shanghai Children's Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
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14
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McSweeney D, Gabriel R, Jin K, Pang ZP, Aronow B, Pak C. CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons. iScience 2022; 25:105187. [PMID: 36262316 PMCID: PMC9574418 DOI: 10.1016/j.isci.2022.105187] [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: 03/17/2022] [Revised: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022] Open
Abstract
Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models to study the dynamic roles of this molecule during neuronal maturation and synapse development. Here, we investigate cell-autonomous functions of CASK in cortical excitatory induced neurons (iNs) generated from CASK knockout (KO) isogenic human embryonic stem cells (hESCs) using gene expression, morphometrics, and electrophysiology. While immature CASK KO iNs show robust neuronal outgrowth, mature CASK KO iNs display severe defects in synaptic transmission and synchronized network activity without compromising neuronal morphology and synapse numbers. In the developing human cortical excitatory neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients.
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Affiliation(s)
- Danny McSweeney
- Graduate Program in Molecular and Cellular Biology, UMass Amherst, Amherst, MA 01003, USA,Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Rafael Gabriel
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Kang Jin
- Departments of Biomedical Informatics, Pediatrics, University of Cincinnati, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Zhiping P. Pang
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Bruce Aronow
- Departments of Biomedical Informatics, Pediatrics, University of Cincinnati, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA,Corresponding author
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15
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Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy, and periventricular calcifications. Am J Hum Genet 2022; 109:1421-1435. [PMID: 35830857 PMCID: PMC9388382 DOI: 10.1016/j.ajhg.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
PPFIBP1 encodes for the liprin-β1 protein, which has been shown to play a role in neuronal outgrowth and synapse formation in Drosophila melanogaster. By exome and genome sequencing, we detected nine ultra-rare homozygous loss-of-function variants in 16 individuals from 12 unrelated families. The individuals presented with moderate to profound developmental delay, often refractory early-onset epilepsy, and progressive microcephaly. Further common clinical findings included muscular hyper- and hypotonia, spasticity, failure to thrive and short stature, feeding difficulties, impaired vision, and congenital heart defects. Neuroimaging revealed abnormalities of brain morphology with leukoencephalopathy, ventriculomegaly, cortical abnormalities, and intracranial periventricular calcifications as major features. In a fetus with intracranial calcifications, we identified a rare homozygous missense variant that by structural analysis was predicted to disturb the topology of the SAM domain region that is essential for protein-protein interaction. For further insight into the effects of PPFIBP1 loss of function, we performed automated behavioral phenotyping of a Caenorhabditis elegans PPFIBP1/hlb-1 knockout model, which revealed defects in spontaneous and light-induced behavior and confirmed resistance to the acetylcholinesterase inhibitor aldicarb, suggesting a defect in the neuronal presynaptic zone. In conclusion, we establish bi-allelic loss-of-function variants in PPFIBP1 as a cause of an autosomal recessive severe neurodevelopmental disorder with early-onset epilepsy, microcephaly, and periventricular calcifications.
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16
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Wu S, Jiang C, Li J, Zhang G, Shen Y, Wang J. A novel missense variant in the CASK gene causes intellectual developmental disorder and microcephaly with pontine and cerebellar hypoplasia. BMC Med Genomics 2022; 15:127. [PMID: 35668446 PMCID: PMC9169347 DOI: 10.1186/s12920-022-01275-z] [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: 09/03/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variants in the CASK gene result in a wide range of observed phenotypes in humans, such as FG Syndrome 4 and intellectual disabilities. Intellectual developmental disorder with microcephaly and pontine and cerebellar hypoplasia (MICPCH) is an X-linked disorder that affects females and is characterized by severely impaired intellectual development and variable degrees of pontocerebellar hypoplasia. Variants in CASK are the main genetic cause of MICPCH. Variants in CASK can explain most patients with MICPCH, but there are still some patients whose disease aetiology cannot be explained. CASE PRESENTATION An 11-month-old female diagnosed with MICPCH exhibited general developmental delays, microcephaly, and cerebellar hypoplasia. Whole-exome sequencing (WES) was used to find a novel heterozygous missense variant (NM_003688.3: c.638T>G) of CASK in this patient. Strikingly, this variant reduced the expression of CASK at the protein level but not at the mRNA level. By using protein structure prediction analysis, this study found that the amino acid change caused by the variant resulted in further changes in the stability of the protein structure, and these changes caused the downregulation of protein expression and loss of protein function. CONCLUSION In this study, we first reported a novel heterozygous pathogenic variant and a causative mechanism of MICPCH. The amino acid change cause by this variant led to changes in the protein structure and a decrease in its stability, which caused a loss of protein function. This study could be helpful to the genetic diagnosis of this disease.
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Affiliation(s)
- Sixian Wu
- Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.,West China School of Pharmacy, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Chuan Jiang
- Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiaman Li
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Guohui Zhang
- Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Ying Shen
- Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Jing Wang
- Department of Obstetrics and Gynaecology, West China Second University Hospital of Sichuan University and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, People's Republic of China.
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17
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The Non-Linear Path from Gene Dysfunction to Genetic Disease: Lessons from the MICPCH Mouse Model. Cells 2022; 11:cells11071131. [PMID: 35406695 PMCID: PMC8997851 DOI: 10.3390/cells11071131] [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: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Most human disease manifests as a result of tissue pathology, due to an underlying disease process (pathogenesis), rather than the acute loss of specific molecular function(s). Successful therapeutic strategies thus may either target the correction of a specific molecular function or halt the disease process. For the vast majority of brain diseases, clear etiologic and pathogenic mechanisms are still elusive, impeding the discovery or design of effective disease-modifying drugs. The development of valid animal models and their proper characterization is thus critical for uncovering the molecular basis of the underlying pathobiological processes of brain disorders. MICPCH (microcephaly and pontocerebellar hypoplasia) is a monogenic condition that results from variants of an X-linked gene, CASK (calcium/calmodulin-dependent serine protein kinase). CASK variants are associated with a wide range of clinical presentations, from lethality and epileptic encephalopathies to intellectual disabilities, microcephaly, and autistic traits. We have examined CASK loss-of-function mutations in model organisms to simultaneously understand the pathogenesis of MICPCH and the molecular function/s of CASK. Our studies point to a highly complex relationship between the potential molecular function/s of CASK and the phenotypes observed in model organisms and humans. Here we discuss the implications of our observations from the pathogenesis of MICPCH as a cautionary narrative against oversimplifying molecular interpretations of data obtained from genetically modified animal models of human diseases.
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18
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Following Excitation/Inhibition Ratio Homeostasis from Synapse to EEG in Monogenetic Neurodevelopmental Disorders. Genes (Basel) 2022; 13:genes13020390. [PMID: 35205434 PMCID: PMC8872324 DOI: 10.3390/genes13020390] [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: 12/28/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 12/26/2022] Open
Abstract
Pharmacological options for neurodevelopmental disorders are limited to symptom suppressing agents that do not target underlying pathophysiological mechanisms. Studies on specific genetic disorders causing neurodevelopmental disorders have elucidated pathophysiological mechanisms to develop more rational treatments. Here, we present our concerted multi-level strategy ‘BRAINMODEL’, focusing on excitation/inhibition ratio homeostasis across different levels of neuroscientific interrogation. The aim is to develop personalized treatment strategies by linking iPSC-based models and novel EEG measurements to patient report outcome measures in individual patients. We focus our strategy on chromatin- and SNAREopathies as examples of severe genetic neurodevelopmental disorders with an unmet need for rational interventions.
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19
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St George-Hyslop F, Kivisild T, Livesey FJ. The role of contactin-associated protein-like 2 in neurodevelopmental disease and human cerebral cortex evolution. Front Mol Neurosci 2022; 15:1017144. [PMID: 36340692 PMCID: PMC9630569 DOI: 10.3389/fnmol.2022.1017144] [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: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022] Open
Abstract
The contactin-associated protein-like 2 (CNTNAP2) gene is associated with multiple neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), and specific language impairment (SLI). Experimental work has shown that CNTNAP2 is important for neuronal development and synapse formation. There is also accumulating evidence for the differential use of CNTNAP2 in the human cerebral cortex compared with other primates. Here, we review the current literature on CNTNAP2, including what is known about its expression, disease associations, and molecular/cellular functions. We also review the evidence for its role in human brain evolution, such as the presence of eight human accelerated regions (HARs) within the introns of the gene. While progress has been made in understanding the function(s) of CNTNAP2, more work is needed to clarify the precise mechanisms through which CNTNAP2 acts. Such information will be crucial for developing effective treatments for CNTNAP2 patients. It may also shed light on the longstanding question of what makes us human.
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Affiliation(s)
- Frances St George-Hyslop
- Zayed Centre for Research Into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Frederick J Livesey
- Zayed Centre for Research Into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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20
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Leifsdottir K, Jost K, Siljehav V, Thelin EP, Lassarén P, Nilsson P, Haraldsson Á, Eksborg S, Herlenius E. The cerebrospinal fluid proteome of preterm infants predicts neurodevelopmental outcome. Front Pediatr 2022; 10:921444. [PMID: 35928685 PMCID: PMC9343678 DOI: 10.3389/fped.2022.921444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Survival rate increases for preterm infants, but long-term neurodevelopmental outcome predictors are lacking. Our primary aim was to determine whether a specific proteomic profile in cerebrospinal fluid (CSF) of preterm infants differs from that of term infants and to identify novel biomarkers of neurodevelopmental outcome in preterm infants. METHODS Twenty-seven preterm infants with median gestational age 27 w + 4 d and ten full-term infants were enrolled prospectively. Protein profiling of CSF were performed utilizing an antibody suspension bead array. The relative levels of 178 unique brain derived proteins and inflammatory mediators, selected from the Human Protein Atlas, were measured. RESULTS The CSF protein profile of preterm infants differed from that of term infants. Increased levels of brain specific proteins that are associated with neurodevelopment and neuroinflammatory pathways made up a distinct protein profile in the preterm infants. The most significant differences were seen in proteins involved in neurodevelopmental regulation and synaptic plasticity, as well as components of the innate immune system. Several proteins correlated with favorable outcome in preterm infants at 18-24 months corrected age. Among the proteins that provided strong predictors of outcome were vascular endothelial growth factor C, Neurocan core protein and seizure protein 6, all highly important in normal brain development. CONCLUSION Our data suggest a vulnerability of the preterm brain to postnatal events and that alterations in protein levels may contribute to unfavorable neurodevelopmental outcome.
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Affiliation(s)
- Kristin Leifsdottir
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,The Children's Hospital of Iceland, Reykjavik, Iceland
| | - Kerstin Jost
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Veronica Siljehav
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Eric P Thelin
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Philipp Lassarén
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Peter Nilsson
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | | | - Staffan Eksborg
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Eric Herlenius
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
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21
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Russ N, Schröder M, Berger BT, Mandel S, Aydogan Y, Mauer S, Pohl C, Drewry DH, Chaikuad A, Müller S, Knapp S. Design and Development of a Chemical Probe for Pseudokinase Ca 2+/calmodulin-Dependent Ser/Thr Kinase. J Med Chem 2021; 64:14358-14376. [PMID: 34543009 DOI: 10.1021/acs.jmedchem.1c00845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CASK (Ca2+/calmodulin-dependent Ser/Thr kinase) is a member of the MAGUK (membrane-associated guanylate kinase) family that functions as neurexin kinases with roles implicated in neuronal synapses and trafficking. The lack of a canonical DFG motif, which is altered to GFG in CASK, led to the classification as a pseudokinase. However, functional studies revealed that CASK can still phosphorylate substrates in the absence of divalent metals. CASK dysfunction has been linked to many diseases, including colorectal cancer, Parkinson's disease, and X-linked mental retardation, suggesting CASK as a potential drug target. Here, we exploited structure-based design for the development of highly potent and selective CASK inhibitors based on 2,4-diaminopyrimidine-5-carboxamides targeting an unusual pocket created by the GFG motif. The presented inhibitor design offers a more general strategy for the development of pseudokinase ligands that harbor unusual sequence motifs. It also provides a first chemical probe for studying the biological roles of CASK.
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Affiliation(s)
- Nadine Russ
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Martin Schröder
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Sebastian Mandel
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Yagmur Aydogan
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Sandy Mauer
- Buchman Institute for Molecular Life Science and Institute of Biochemistry II, Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Christian Pohl
- Buchman Institute for Molecular Life Science and Institute of Biochemistry II, Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,UNC Lineberger Comprehensive Cancer Center, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Apirat Chaikuad
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Susanne Müller
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany.,German Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
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22
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van Husen LS, Katsori AM, Meineke B, Tjernberg LO, Schedin-Weiss S, Elsässer SJ. Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids. Chembiochem 2021; 22:3208-3213. [PMID: 34431592 PMCID: PMC9290828 DOI: 10.1002/cbic.202100399] [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: 08/06/2021] [Revised: 08/24/2021] [Indexed: 11/07/2022]
Abstract
Human induced pluripotent stem cell (hiPSC) technology has revolutionized studies on human biology. A wide range of cell types and tissue models can be derived from hiPSCs to study complex human diseases. Here, we use PiggyBac-mediated transgenesis to engineer hiPSCs with an expanded genetic code. We demonstrate that genomic integration of expression cassettes for a pyrrolysyl-tRNA synthetase (PylRS), pyrrolysyl-tRNA (PylT) and the target protein of interest enables site-specific incorporation of a non-canonical amino acid (ncAA) in response to an amber stop codon. Neural stem cells, neurons and brain organoids derived from the engineered hiPSCs continue to express the amber suppression machinery and produce ncAA-bearing reporter. The incorporated ncAA can serve as a minimal bioorthogonal handle for further modifications by labeling with fluorescent dyes. Site-directed ncAA mutagenesis will open a wide range of applications to probe and manipulate proteins in brain organoids and other hiPSC-derived cell types and complex tissue models.
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Affiliation(s)
- Lea S van Husen
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden.,Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Anna-Maria Katsori
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden
| | - Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden
| | - Lars O Tjernberg
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Sophia Schedin-Weiss
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden
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23
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Crosstalk among Calcium ATPases: PMCA, SERCA and SPCA in Mental Diseases. Int J Mol Sci 2021; 22:ijms22062785. [PMID: 33801794 PMCID: PMC8000800 DOI: 10.3390/ijms22062785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Calcium in mammalian neurons is essential for developmental processes, neurotransmitter release, apoptosis, and signal transduction. Incorrectly processed Ca2+ signal is well-known to trigger a cascade of events leading to altered response to variety of stimuli and persistent accumulation of pathological changes at the molecular level. To counterbalance potentially detrimental consequences of Ca2+, neurons are equipped with sophisticated mechanisms that function to keep its concentration in a tightly regulated range. Calcium pumps belonging to the P-type family of ATPases: plasma membrane Ca2+-ATPase (PMCA), sarco/endoplasmic Ca2+-ATPase (SERCA) and secretory pathway Ca2+-ATPase (SPCA) are considered efficient line of defense against abnormal Ca2+ rises. However, their role is not limited only to Ca2+ transport, as they present tissue-specific functionality and unique sensitive to the regulation by the main calcium signal decoding protein—calmodulin (CaM). Based on the available literature, in this review we analyze the contribution of these three types of Ca2+-ATPases to neuropathology, with a special emphasis on mental diseases.
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