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Munezane H, Imamura K, Fujimoto N, Hotta A, Yukitake H, Inoue H. Elimination of the extra chromosome of Dup15q syndrome iPSCs for cellular and molecular investigation. Eur J Cell Biol 2024; 103:151446. [PMID: 39059105 DOI: 10.1016/j.ejcb.2024.151446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/23/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Chromosome 15q11.2-13.1 duplication (Dup15q) syndrome is one of the most common autism spectrum disorders (ASDs) associated with copy number variants (CNVs). For the analysis of CNV-relevant pathological cellular phenotypes, a CNV-corrected isogenic cell line is useful for excluding the influence of genetic background. Here, we devised a strategy to remove the isodicentric chromosome 15 by inserting a puro-ΔTK selection cassette into the extra chromosome using the CRISPR-Cas9 system, followed by a subsequent two-step drug selection. A series of assays, including qPCR-based copy number analysis and karyotype analysis, confirmed the elimination of the extra chromosome. Furthermore, cerebral organoids were generated from the parental Dup15q iPSCs and their isogenic iPSCs. scRNA-seq analysis revealed the alteration of expression levels in ion-channel-related genes and synapse-related genes in glutamatergic and GABAergic neurons in Dup15q organoids, respectively. The established isogenic cell line is a valuable resource for unraveling cellular and molecular alterations associated with Dup15q syndrome.
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Affiliation(s)
- Haruka Munezane
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA (T-CiRA) Joint Program, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Japan
| | - Keiko Imamura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA (T-CiRA) Joint Program, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Japan; iPSC-based Drug discovery and Development Team, RIKEN BioResource Research Center, 1-7 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; Medical-Risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naoko Fujimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA (T-CiRA) Joint Program, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA (T-CiRA) Joint Program, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Japan
| | - Hiroshi Yukitake
- Takeda-CiRA (T-CiRA) Joint Program, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Japan; Global Advanced Platform, Takeda Pharmaceutical Company Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Japan
| | - Haruhisa Inoue
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA (T-CiRA) Joint Program, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Japan; iPSC-based Drug discovery and Development Team, RIKEN BioResource Research Center, 1-7 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; Medical-Risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
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Dias C, Mo A, Cai C, Sun L, Cabral K, Brownstein CA, Rockowitz S, Walsh CA. Cell-type-specific effects of autism-associated 15q duplication syndrome in the human brain. Am J Hum Genet 2024; 111:1544-1558. [PMID: 39079538 PMCID: PMC11339625 DOI: 10.1016/j.ajhg.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 08/11/2024] Open
Abstract
Recurrent copy-number variation represents one of the most well-established genetic drivers in neurodevelopmental disorders, including autism spectrum disorder. Duplication of 15q11-q13 (dup15q) is a well-described neurodevelopmental syndrome that increases the risk of autism more than 40-fold. However, the effects of this duplication on gene expression and chromatin accessibility in specific cell types in the human brain remain unknown. To identify the cell-type-specific transcriptional and epigenetic effects of dup15q in the human frontal cortex, we conducted single-nucleus RNA sequencing and multi-omic sequencing on dup15q-affected individuals (n = 6) as well as individuals with non-dup15q autism (n = 7) and neurotypical control individuals (n = 7). Cell-type-specific differential expression analysis identified significantly regulated genes, critical biological pathways, and differentially accessible genomic regions. Although there was overall increased gene expression across the duplicated genomic region, cellular identity represented an important factor mediating gene-expression changes. As compared to other cell types, neuronal subtypes showed greater upregulation of gene expression across a critical region within the duplication. Genes that fell within the duplicated region and had high baseline expression in control individuals showed only modest changes in dup15q, regardless of cell type. Of note, dup15q and autism had largely distinct signatures of chromatin accessibility but shared the majority of transcriptional regulatory motifs, suggesting convergent biological pathways. However, the transcriptional binding-factor motifs implicated in each condition implicated distinct biological mechanisms: neuronal JUN and FOS networks in autism vs. an inflammatory transcriptional network in dup15q microglia. This work provides a cell-type-specific analysis of how dup15q changes gene expression and chromatin accessibility in the human brain, and it finds evidence of marked cell-type-specific effects of this genetic driver. These findings have implications for guiding therapeutic development in dup15q syndrome, as well as understanding the functional effects of copy-number variants more broadly in neurodevelopmental disorders.
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Affiliation(s)
- Caroline Dias
- Division of Developmental Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Alisa Mo
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chunhui Cai
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kristen Cabral
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Shira Rockowitz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
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Saravanapandian V, Madani M, Nichols I, Vincent S, Dover M, Dikeman D, Philpot BD, Takumi T, Colwell CS, Jeste S, Paul KN, Golshani P. Sleep EEG signatures in mouse models of 15q11.2-13.1 duplication (Dup15q) syndrome. J Neurodev Disord 2024; 16:39. [PMID: 39014349 PMCID: PMC11251350 DOI: 10.1186/s11689-024-09556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Sleep disturbances are a prevalent and complex comorbidity in neurodevelopmental disorders (NDDs). Dup15q syndrome (duplications of 15q11.2-13.1) is a genetic disorder highly penetrant for NDDs such as autism and intellectual disability and it is frequently accompanied by significant disruptions in sleep patterns. The 15q critical region harbors genes crucial for brain development, notably UBE3A and a cluster of gamma-aminobutyric acid type A receptor (GABAAR) genes. We previously described an electrophysiological biomarker of the syndrome, marked by heightened beta oscillations (12-30 Hz) in individuals with Dup15q syndrome, akin to electroencephalogram (EEG) alterations induced by allosteric modulation of GABAARs. Those with Dup15q syndrome exhibited increased beta oscillations during the awake resting state and during sleep, and they showed profoundly abnormal NREM sleep. This study aims to assess the translational validity of these EEG signatures and to delve into their neurobiological underpinnings by quantifying sleep physiology in chromosome-engineered mice with maternal (matDp/ + mice) or paternal (patDp/ + mice) inheritance of the full 15q11.2-13.1-equivalent duplication, and mice with duplication of just the UBE3A gene (Ube3a overexpression mice; Ube3a OE mice) and comparing the sleep metrics with their respective wildtype (WT) littermate controls. METHODS We collected 48-h EEG/EMG recordings from 35 (23 male, 12 female) 12-24-week-old matDp/ + , patDp/ + , Ube3a OE mice, and their WT littermate controls. We quantified baseline sleep, sleep fragmentation, spectral power dynamics during sleep states, and recovery following sleep deprivation. Within each group, distinctions between Dup15q mutant mice and WT littermate controls were evaluated using analysis of variance (ANOVA) and student's t-test. The impact of genotype and time was discerned through repeated measures ANOVA, and significance was established at p < 0.05. RESULTS Our study revealed that across brain states, matDp/ + mice mirrored the elevated beta oscillation phenotype observed in clinical EEGs from individuals with Dup15q syndrome. Time to sleep onset after light onset was significantly reduced in matDp/ + and Ube3a OE mice. However, NREM sleep between Dup15q mutant and WT littermate mice remained unaltered, suggesting a divergence from the clinical presentation in humans. Additionally, while increased beta oscillations persisted in matDp/ + mice after 6-h of sleep deprivation, recovery NREM sleep remained unaltered in all groups, thus suggesting that these mice exhibit resilience in the fundamental processes governing sleep-wake regulation. CONCLUSIONS Quantification of mechanistic and translatable EEG biomarkers is essential for advancing our understanding of NDDs and their underlying pathophysiology. Our study of sleep physiology in the Dup15q mice underscores that the beta EEG biomarker has strong translational validity, thus opening the door for pre-clinical studies of putative drug targets, using the biomarker as a translational measure of drug-target engagement. The unaltered NREM sleep may be due to inherent differences in neurobiology between mice and humans. These nuanced distinctions highlight the complexity of sleep disruptions in Dup15q syndrome and emphasize the need for a comprehensive understanding that encompasses both shared and distinct features between murine models and clinical populations.
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Affiliation(s)
- Vidya Saravanapandian
- Department of Neurology and Semel Institute for Neuroscience, David Geffen School of Medicine, 710 Westwood Plaza, Los Angeles, CA, 90095, USA.
| | - Melika Madani
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - India Nichols
- Department of Biology, Spelman College, 350 Spelman Lane, Atlanta, GA, 30314, USA
| | - Scott Vincent
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Mary Dover
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Dante Dikeman
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Benjamin D Philpot
- Neuroscience Center, Department of Cell Biology and Physiology, and the Carolina Institute for Developmental Disabilities, UNC-Chapel Hill, NC, 27599, USA
| | - Toru Takumi
- Kobe University School of Medicine, Chuo, Kobe, 650-0017, Japan
| | - Christopher S Colwell
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Shafali Jeste
- Children's Hospital Los Angeles, 4650 Sunset Blvd, MS 82, Los Angeles, CA, 90027, USA
| | - Ketema N Paul
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Peyman Golshani
- Department of Neurology and Semel Institute for Neuroscience, David Geffen School of Medicine, 710 Westwood Plaza, Los Angeles, CA, 90095, USA
- West Los Angeles VA Medical Center, 11301 Wilshire Blvd, Los Angeles, CA, 90073, USA
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Montani C, Balasco L, Pagani M, Alvino FG, Barsotti N, de Guzman AE, Galbusera A, de Felice A, Nickl-Jockschat TK, Migliarini S, Casarosa S, Lau P, Mattioni L, Pasqualetti M, Provenzano G, Bozzi Y, Lombardo MV, Gozzi A. Sex-biasing influence of autism-associated Ube3a gene overdosage at connectomic, behavioral, and transcriptomic levels. SCIENCE ADVANCES 2024; 10:eadg1421. [PMID: 38996019 PMCID: PMC11244557 DOI: 10.1126/sciadv.adg1421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
Genomic mechanisms enhancing risk in males may contribute to sex bias in autism. The ubiquitin protein ligase E3A gene (Ube3a) affects cellular homeostasis via control of protein turnover and by acting as transcriptional coactivator with steroid hormone receptors. Overdosage of Ube3a via duplication or triplication of chromosomal region 15q11-13 causes 1 to 2% of autistic cases. Here, we test the hypothesis that increased dosage of Ube3a may influence autism-relevant phenotypes in a sex-biased manner. We show that mice with extra copies of Ube3a exhibit sex-biasing effects on brain connectomics and autism-relevant behaviors. These effects are associated with transcriptional dysregulation of autism-associated genes, as well as genes differentially expressed in 15q duplication and in autistic people. Increased Ube3a dosage also affects expression of genes on the X chromosome, genes influenced by sex steroid hormone, and genes sex-differentially regulated by transcription factors. These results suggest that Ube3a overdosage can contribute to sex bias in neurodevelopmental conditions via influence on sex-differential mechanisms.
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Affiliation(s)
- Caterina Montani
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Luigi Balasco
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Marco Pagani
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
- Autism Center, Child Mind Institute, New York, NY, USA
- IMT School for Advanced Studies, Lucca, Italy
| | - Filomena Grazia Alvino
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Noemi Barsotti
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy
| | - A. Elizabeth de Guzman
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Alberto Galbusera
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Alessia de Felice
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Thomas K. Nickl-Jockschat
- Department of Psychiatry and Psychotherapy, Otto-von-Guericke University, Magdeburg, Germany
- German Center for Mental Health (DZPG), partner site Halle-Jena-Magdeburg, Germany
- Center for Intervention and Research on adaptive and maladaptive brain Circuits underlying mental health (C-I-R-C), Halle-Jena-Magdeburg, Germany
| | - Sara Migliarini
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy
| | - Simona Casarosa
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | - Pierre Lau
- Istituto Italiano di Tecnologia, Center for Human Technologies, Genova, Italy
| | - Lorenzo Mattioni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Massimo Pasqualetti
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy
| | - Giovanni Provenzano
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yuri Bozzi
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Rovereto, Italy
- CNR Neuroscience Institute, Pisa, Italy
| | - Michael V. Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Alessandro Gozzi
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
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Dias C, Mo A, Cai C, Sun L, Cabral K, Brownstein CA, Rockowitz S, Walsh CA. Cell-type-specific effects of autism-associated chromosome 15q11.2-13.1 duplications in human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595175. [PMID: 38826276 PMCID: PMC11142199 DOI: 10.1101/2024.05.22.595175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Recurrent copy number variation represents one of the most well-established genetic drivers in neurodevelopmental disorders, including autism spectrum disorder (ASD). Duplication of 15q11.2-13.1 (dup15q) is a well-described neurodevelopmental syndrome that increases the risk of ASD by over 40-fold. However, the effects of this duplication on gene expression and chromatin accessibility in specific cell types in the human brain remain unknown. To identify the cell-type-specific transcriptional and epigenetic effects of dup15q in the human frontal cortex we conducted single-nucleus RNA-sequencing and multi-omic sequencing on dup15q cases (n=6) as well as non-dup15q ASD (n=7) and neurotypical controls (n=7). Cell-type-specific differential expression analysis identified significantly regulated genes, critical biological pathways, and differentially accessible genomic regions. Although there was overall increased gene expression across the duplicated genomic region, cellular identity represented an important factor mediating gene expression changes. Neuronal subtypes, showed greater upregulation of gene expression across a critical region within the duplication as compared to other cell types. Genes within the duplicated region that had high baseline expression in control individuals showed only modest changes in dup15q, regardless of cell type. Of note, dup15q and ASD had largely distinct signatures of chromatin accessibility, but shared the majority of transcriptional regulatory motifs, suggesting convergent biological pathways. However, the transcriptional binding factor motifs implicated in each condition implicated distinct biological mechanisms; neuronal JUN/FOS networks in ASD vs. an inflammatory transcriptional network in dup15q microglia. This work provides a cell-type-specific analysis of how dup15q changes gene expression and chromatin accessibility in the human brain and finds evidence of marked cell-type-specific effects of this genetic driver. These findings have implications for guiding therapeutic development in dup15q syndrome, as well as understanding the functional effects CNVs more broadly in neurodevelopmental disorders.
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Affiliation(s)
- Caroline Dias
- Current Address: Department of Pediatrics, Section of Developmental Pediatrics, Section of Genetics and Metabolism, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- Division of Developmental Medicine, Boston Children's Hospital, Boston, MA 02115
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Alisa Mo
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
| | - Chunhui Cai
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115
| | - Kristen Cabral
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Shira Rockowitz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115
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Rogers-Hammond R, Howell C. An integrated action plan to fund and support drug development for Dup15q syndrome: a patient organization perspective. THERAPEUTIC ADVANCES IN RARE DISEASE 2024; 5:26330040241234932. [PMID: 38450288 PMCID: PMC10916487 DOI: 10.1177/26330040241234932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Maternal 15q11.2-13.1 duplication syndrome, or Dup15q syndrome (Dup15q), is a rare neurodevelopmental disorder affecting as many as 1 in 5000 to 1 in 20,000 children worldwide. Autism and seizures are two of the most commonly observed phenotypes in Dup15q, with intellectual disability, hypotonia, gastrointestinal distress, and substantial fine and gross motor deficits also commonly reported. The community that is now known as the Dup15q Alliance started in 1994 as a small group of families raising children with chromosome 15q duplications. Originally named IsoDicentric 15 Exchange, Advocacy and Support (IDEAS), the group received official nonprofit organization status 10 years later and rebranded to its current name, Dup15q Alliance, shortly thereafter. Today, there are over 2200 families affiliated with Dup15q Alliance, with an average intake of 10 new families each month. Historically, Dup15q Alliance has provided the community with access to family and caregiver resources in addition to serving as a repository for basic educational information about Dup15q and research developments. The recent installation of a dedicated director of scientific and clinical initiatives alongside other infrastructural changes has now primed the Dup15q Alliance to expand its scientific footprint by funding cutting-edge research, supporting clinical sites and trials, and investing in novel therapeutics that have the potential to change the reality of a Dup15q syndrome diagnosis. To do this, we have developed the LEARN. TREAT. CURE. program to align initiatives, fast-track progress, and bring hope and reality into coexistence. Briefly, we seek to learn as much as we can about the syndrome through cutting-edge research, natural history studies, and patient registry utilization, identify and develop methods to treat the symptoms of our patient community, with the ultimate goal of developing a cure for the disease-causing symptoms of the syndrome.
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Roy B, Amemasor E, Hussain S, Castro K. UBE3A: The Role in Autism Spectrum Disorders (ASDs) and a Potential Candidate for Biomarker Studies and Designing Therapeutic Strategies. Diseases 2023; 12:7. [PMID: 38248358 PMCID: PMC10814747 DOI: 10.3390/diseases12010007] [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: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Published reports from the CDC's Autism and Development Disabilities Monitoring Networks have shown that an average of 1 in every 44 (2.3%) 8-year-old children were estimated to have ASD in 2018. Many of the ASDs exhibiting varying degrees of autism-like phenotypes have chromosomal anomalies in the Chr15q11-q13 region. Numerous potential candidate genes linked with ASD reside in this chromosomal segment. However, several clinical, in vivo, and in vitro studies selected one gene more frequently than others randomly and unbiasedly. This gene codes for UBE3A or Ubiquitin protein ligase E3A [also known as E6AP ubiquitin-protein ligase (E6AP)], an enzyme involved in the cellular degradation of proteins. This gene has been listed as one of the several genes with a high potential of causing ASD in the Autism Database. The gain of function mutations, triplication, or duplication in the UBE3A gene is also associated with ASDs like Angelman Syndrome (AS) and Dup15q Syndrome. The genetic imprinting of UBE3A in the brain and a preference for neuronal maternal-specific expression are the key features of various ASDs. Since the UBE3A gene is involved in two main important diseases associated with autism-like symptoms, there has been widespread research going on in understanding the link between this gene and autism. Additionally, since no universal methodology or mechanism exists for identifying UBE3A-mediated ASD, it continues to be challenging for neurobiologists, neuroscientists, and clinicians to design therapies or diagnostic tools. In this review, we focus on the structure and functional aspects of the UBE3A protein, discuss the primary relevance of the 15q11-q13 region in the cause of ASDs, and highlight the link between UBE3A and ASD. We try to broaden the knowledge of our readers by elaborating on the possible mechanisms underlying UBE3A-mediated ASDs, emphasizing the usage of UBE3A as a prospective biomarker in the preclinical diagnosis of ASDs and discuss the positive outcomes, advanced developments, and the hurdles in the field of therapeutic strategies against UBE3A-mediated ASDs. This review is novel as it lays a very detailed and comprehensive platform for one of the most important genes associated with diseases showing autistic-like symptoms. Additionally, this review also attempts to lay optimistic feedback on the possible steps for the diagnosis, prevention, and therapy of these UBE3A-mediated ASDs in the upcoming years.
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Affiliation(s)
- Bidisha Roy
- Life Science Centre, Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA; (E.A.); (S.H.); (K.C.)
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Gilmore RB, Gorka D, Stoddard CE, Cotney JL, Chamberlain SJ. Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555563. [PMID: 37693591 PMCID: PMC10491257 DOI: 10.1101/2023.08.30.555563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Angelman Syndrome (AS) and Prader-Willi Syndrome (PWS), two distinct neurodevelopmental disorders, result from loss of expression from imprinted genes in the chromosome 15q11-13 locus most commonly caused by a megabase-scale deletion on either the maternal or paternal allele, respectively. Each occurs at an approximate incidence of 1/15,000 to 1/30,000 live births and has a range of debilitating phenotypes. Patient-derived induced pluripotent stem cells (iPSCs) have been valuable tools to understand human-relevant gene regulation at this locus and have contributed to the development of therapeutic approaches for AS. Nonetheless, gaps remain in our understanding of how these deletions contribute to dysregulation and phenotypes of AS and PWS. Variability across cell lines due to donor differences, reprogramming methods, and genetic background make it challenging to fill these gaps in knowledge without substantially increasing the number of cell lines used in the analyses. Isogenic cell lines that differ only by the genetic mutation causing the disease can ease this burden without requiring such a large number of cell lines. Here, we describe the development of isogenic human embryonic stem cell (hESC) lines modeling the most common genetic subtypes of AS and PWS. These lines allow for a facile interrogation of allele-specific gene regulation at the chromosome 15q11-q13 locus. Additionally, these lines are an important resource to identify and test targeted therapeutic approaches for patients with AS and PWS.
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Affiliation(s)
- Rachel B Gilmore
- Department of Genetics and Genome Sciences, UConn Health; Farmington, CT, USA
| | - Dea Gorka
- Department of Genetics and Genome Sciences, UConn Health; Farmington, CT, USA
| | | | - Justin L Cotney
- Department of Genetics and Genome Sciences, UConn Health; Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, UConn Health; Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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9
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Elamin M, Dumarchey A, Stoddard C, Robinson TM, Cowie C, Gorka D, Chamberlain SJ, Levine ES. The role of UBE3A in the autism and epilepsy-related Dup15q syndrome using patient-derived, CRISPR-corrected neurons. Stem Cell Reports 2023; 18:884-898. [PMID: 36898382 PMCID: PMC10147551 DOI: 10.1016/j.stemcr.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Chromosome 15q11-q13 duplication syndrome (Dup15q) is a neurodevelopmental disorder caused by maternal duplications of this region. Autism and epilepsy are key features of Dup15q. UBE3A, which encodes an E3 ubiquitin ligase, is likely a major driver of Dup15q because UBE3A is the only imprinted gene expressed solely from the maternal allele. Nevertheless, the exact role of UBE3A has not been determined. To establish whether UBE3A overexpression is required for Dup15q neuronal deficits, we generated an isogenic control line for a Dup15q patient-derived induced pluripotent stem cell line. Dup15q neurons exhibited hyperexcitability compared with control neurons, and this phenotype was generally prevented by normalizing UBE3A levels using antisense oligonucleotides. Overexpression of UBE3A resulted in a profile similar to that of Dup15q neurons except for synaptic phenotypes. These results indicate that UBE3A overexpression is necessary for most Dup15q cellular phenotypes but also suggest a role for other genes in the duplicated region.
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Affiliation(s)
- Marwa Elamin
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Aurelie Dumarchey
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Christopher Stoddard
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Tiwanna M Robinson
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Christopher Cowie
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Dea Gorka
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Eric S Levine
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA.
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10
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O'Geen H, Beitnere U, Garcia MS, Adhikari A, Cameron DL, Fenton TA, Copping NA, Deng P, Lock S, Halmai JANM, Villegas IJ, Liu J, Wang D, Fink KD, Silverman JL, Segal DJ. Transcriptional reprogramming restores UBE3A brain-wide and rescues behavioral phenotypes in an Angelman syndrome mouse model. Mol Ther 2023; 31:1088-1105. [PMID: 36641623 PMCID: PMC10124086 DOI: 10.1016/j.ymthe.2023.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Angelman syndrome (AS) is a neurogenetic disorder caused by the loss of ubiquitin ligase E3A (UBE3A) gene expression in the brain. The UBE3A gene is paternally imprinted in brain neurons. Clinical features of AS are primarily due to the loss of maternally expressed UBE3A in the brain. A healthy copy of paternal UBE3A is present in the brain but is silenced by a long non-coding antisense transcript (UBE3A-ATS). Here, we demonstrate that an artificial transcription factor (ATF-S1K) can silence Ube3a-ATS in an adult mouse model of Angelman syndrome (AS) and restore endogenous physiological expression of paternal Ube3a. A single injection of adeno-associated virus (AAV) expressing ATF-S1K (AAV-S1K) into the tail vein enabled whole-brain transduction and restored UBE3A protein in neurons to ∼25% of wild-type protein. The ATF-S1K treatment was highly specific to the target site with no detectable inflammatory response 5 weeks after AAV-S1K administration. AAV-S1K treatment of AS mice showed behavioral rescue in exploratory locomotion, a task involving gross and fine motor abilities, similar to low ambulation and velocity in AS patients. The specificity and tolerability of a single injection of AAV-S1K therapy for AS demonstrate the use of ATFs as a promising translational approach for AS.
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Affiliation(s)
| | | | | | - Anna Adhikari
- MIND Institute, UC Davis Health System, Sacramento, CA, USA; Department of Psychiatry and Behavioral Sciences, UC Davis Health System, Sacramento, CA, USA
| | - David L Cameron
- Neurology Department, Stem Cell Program and Gene Therapy Center, UC Davis Health System, Sacramento, CA, USA; MIND Institute, UC Davis Health System, Sacramento, CA, USA
| | - Timothy A Fenton
- MIND Institute, UC Davis Health System, Sacramento, CA, USA; Department of Psychiatry and Behavioral Sciences, UC Davis Health System, Sacramento, CA, USA
| | - Nycole A Copping
- MIND Institute, UC Davis Health System, Sacramento, CA, USA; Department of Psychiatry and Behavioral Sciences, UC Davis Health System, Sacramento, CA, USA
| | - Peter Deng
- Neurology Department, Stem Cell Program and Gene Therapy Center, UC Davis Health System, Sacramento, CA, USA; MIND Institute, UC Davis Health System, Sacramento, CA, USA
| | - Samantha Lock
- Neurology Department, Stem Cell Program and Gene Therapy Center, UC Davis Health System, Sacramento, CA, USA; MIND Institute, UC Davis Health System, Sacramento, CA, USA
| | - Julian A N M Halmai
- Neurology Department, Stem Cell Program and Gene Therapy Center, UC Davis Health System, Sacramento, CA, USA; MIND Institute, UC Davis Health System, Sacramento, CA, USA
| | - Isaac J Villegas
- Neurology Department, Stem Cell Program and Gene Therapy Center, UC Davis Health System, Sacramento, CA, USA; MIND Institute, UC Davis Health System, Sacramento, CA, USA
| | - Jiajian Liu
- Genome Editing and Novel Modalities (GENM), MilliporeSigma, St. Louis, MO, USA
| | - Danhui Wang
- Genome Editing and Novel Modalities (GENM), MilliporeSigma, St. Louis, MO, USA
| | - Kyle D Fink
- Neurology Department, Stem Cell Program and Gene Therapy Center, UC Davis Health System, Sacramento, CA, USA; MIND Institute, UC Davis Health System, Sacramento, CA, USA
| | - Jill L Silverman
- MIND Institute, UC Davis Health System, Sacramento, CA, USA; Department of Psychiatry and Behavioral Sciences, UC Davis Health System, Sacramento, CA, USA
| | - David J Segal
- Genome Center, UC Davis, Davis, CA, USA; Department of Biochemistry and Molecular Medicine, UC Davis, Davis, CA, USA; MIND Institute, UC Davis Health System, Sacramento, CA, USA.
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11
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Antony I, Narasimhan M, Shen R, Prakasam R, Kaushik K, Chapman G, Kroll KL. Duplication Versus Deletion Through the Lens of 15q13.3: Clinical and Research Implications of Studying Copy Number Variants Associated with Neuropsychiatric Disorders in Induced Pluripotent Stem Cell-Derived Neurons. Stem Cell Rev Rep 2023; 19:639-650. [PMID: 36370261 PMCID: PMC10115185 DOI: 10.1007/s12015-022-10475-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2022] [Indexed: 11/15/2022]
Abstract
Copy number variants (CNVs), involving duplication or deletion of susceptible intervals of the human genome, underlie a range of neurodevelopmental and neuropsychiatric disorders. As accessible in vivo animal models of these disorders often cannot be generated, induced pluripotent stem cell (iPSC) models derived from patients carrying these CNVs can reveal alterations of brain development and neuronal function that contribute to these disorders. CNVs involving deletion versus duplication of a particular genomic interval often result both in distinct clinical phenotypes and in differential phenotypic penetrance. This review initially focuses on CNVs at 15q13.3, which contribute to autism spectrum disorder, attention deficit/hyperactivity disorder, and schizophrenia. Like most CNVs, deletions at 15q13.3 usually cause severe clinical phenotypes, while duplications instead result in highly variable penetrance, with some carriers exhibiting no clinical phenotype. Here, we describe cellular and molecular phenotypes seen in iPSC-derived neuronal models of 15q13.3 duplication and deletion, which may contribute both to the differential clinical consequences and phenotypic penetrance. We then relate this work to many other CNVs involving both duplication and deletion, summarizing findings from iPSC studies and their relationship to clinical phenotype. Together, this work highlights how CNVs involving duplication versus deletion can differentially alter neural development and function to contribute to neuropsychiatric disorders. iPSC-derived neuronal models of these disorders can be used both to understand the underlying neurodevelopmental alterations and to develop pharmacological or molecular approaches for phenotypic rescue that may suggest leads for patient intervention. Top: Deletion versus duplication of the same genomic interval results in different clinical phenotypes and degrees of phenotypic penetrance. Example findings schematized. Bottom: iPSC-derived neurons from individuals with these CNVs involving deletion versus duplication likewise often differential phenotypes (increases or decreases) in the categories shown. Figure created with BioRender.com.
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Affiliation(s)
- Irene Antony
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Mishka Narasimhan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Renata Shen
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Ramachandran Prakasam
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Komal Kaushik
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Gareth Chapman
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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12
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Human In Vitro Models of Epilepsy Using Embryonic and Induced Pluripotent Stem Cells. Cells 2022; 11:cells11243957. [PMID: 36552721 PMCID: PMC9776452 DOI: 10.3390/cells11243957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/25/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
The challenges in making animal models of complex human epilepsy phenotypes with varied aetiology highlights the need to develop alternative disease models that can address the limitations of animal models by effectively recapitulating human pathophysiology. The advances in stem cell technology provide an opportunity to use human iPSCs to make disease-in-a-dish models. The focus of this review is to report the current information and progress in the generation of epileptic patient-specific iPSCs lines, isogenic control cell lines, and neuronal models. These in vitro models can be used to study the underlying pathological mechanisms of epilepsies, anti-seizure medication resistance, and can also be used for drug testing and drug screening with their isogenic control cell lines.
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13
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Bossolasco P, Cimini S, Maderna E, Bardelli D, Canafoglia L, Cavallaro T, Ricci M, Silani V, Marucci G, Rossi G. GRN−/− iPSC-derived cortical neurons recapitulate the pathological findings of both frontotemporal lobar degeneration and neuronal ceroidolipofuscinosis. Neurobiol Dis 2022; 175:105891. [DOI: 10.1016/j.nbd.2022.105891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/27/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
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14
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Panov J, Kaphzan H. An Association Study of DNA Methylation and Gene Expression in Angelman Syndrome: A Bioinformatics Approach. Int J Mol Sci 2022; 23:ijms23169139. [PMID: 36012404 PMCID: PMC9409443 DOI: 10.3390/ijms23169139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/27/2022] [Accepted: 08/05/2022] [Indexed: 12/01/2022] Open
Abstract
Angelman syndrome (AS) is a neurodevelopmental disorder caused by the loss of function of the E3-ligase UBE3A. Despite multiple studies, AS pathophysiology is still obscure and has mostly been explored in rodent models of the disease. In recent years, a growing body of studies has utilized omics datasets in the attempt to focus research regarding the pathophysiology of AS. Here, for the first time, we utilized a multi-omics approach at the epigenomic level and the transcriptome level, for human-derived neurons. Using publicly available datasets for DNA methylation and gene expression, we found genome regions in proximity to gene promoters and intersecting with gene-body regions that were differentially methylated and differentially expressed in AS. We found that overall, the genome in AS postmortem brain tissue was hypo-methylated compared to healthy controls. We also found more upregulated genes than downregulated genes in AS. Many of these dysregulated genes in neurons obtained from AS patients are known to be critical for neuronal development and synaptic functioning. Taken together, our results suggest a list of dysregulated genes that may be involved in AS development and its pathological features. Moreover, these genes might also have a role in neurodevelopmental disorders similar to AS.
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15
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Jiang CC, Lin LS, Long S, Ke XY, Fukunaga K, Lu YM, Han F. Signalling pathways in autism spectrum disorder: mechanisms and therapeutic implications. Signal Transduct Target Ther 2022; 7:229. [PMID: 35817793 PMCID: PMC9273593 DOI: 10.1038/s41392-022-01081-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a prevalent and complex neurodevelopmental disorder which has strong genetic basis. Despite the rapidly rising incidence of autism, little is known about its aetiology, risk factors, and disease progression. There are currently neither validated biomarkers for diagnostic screening nor specific medication for autism. Over the last two decades, there have been remarkable advances in genetics, with hundreds of genes identified and validated as being associated with a high risk for autism. The convergence of neuroscience methods is becoming more widely recognized for its significance in elucidating the pathological mechanisms of autism. Efforts have been devoted to exploring the behavioural functions, key pathological mechanisms and potential treatments of autism. Here, as we highlight in this review, emerging evidence shows that signal transduction molecular events are involved in pathological processes such as transcription, translation, synaptic transmission, epigenetics and immunoinflammatory responses. This involvement has important implications for the discovery of precise molecular targets for autism. Moreover, we review recent insights into the mechanisms and clinical implications of signal transduction in autism from molecular, cellular, neural circuit, and neurobehavioural aspects. Finally, the challenges and future perspectives are discussed with regard to novel strategies predicated on the biological features of autism.
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Affiliation(s)
- Chen-Chen Jiang
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Li-Shan Lin
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Sen Long
- Department of Pharmacy, Hangzhou Seventh People's Hospital, Mental Health Center Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Xiao-Yan Ke
- Child Mental Health Research Center, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Kohji Fukunaga
- Department of CNS Drug Innovation, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
| | - Feng Han
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
- Institute of Brain Science, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China.
- Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215002, China.
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16
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Langouët M, Gorka D, Orniacki C, Dupont-Thibert CM, Chung MS, Glatt-Deeley HR, Germain N, Crandall LJ, Cotney JL, Stoddard CE, Lalande M, Chamberlain SJ. Specific ZNF274 binding interference at SNORD116 activates the maternal transcripts in Prader-Willi syndrome neurons. Hum Mol Genet 2021; 29:3285-3295. [PMID: 32977341 DOI: 10.1093/hmg/ddaa210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/15/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022] Open
Abstract
Prader-Willi syndrome (PWS) is characterized by neonatal hypotonia, developmental delay and hyperphagia/obesity. This disorder is caused by the absence of paternally expressed gene products from chromosome 15q11-q13. We previously demonstrated that knocking out ZNF274, a Kruppel-associated box-A-domain zinc finger protein capable of recruiting epigenetic machinery to deposit the H3K9me3 repressive histone modification, can activate expression from the normally silent maternal allele of SNORD116 in neurons derived from PWS induced pluripotent stem cells (iPSCs). However, ZNF274 has many other targets in the genome in addition to SNORD116. Depleting ZNF274 will surely affect the expression of other important genes and disrupt other pathways. Here, we used CRISPR/Cas9 to delete ZNF274 binding sites at the SNORD116 locus to determine whether activation of the maternal copy of SNORD116 could be achieved without altering ZNF274 protein levels. We obtained similar activation of gene expression from the normally silenced maternal allele in neurons derived from PWS iPSCs, compared with ZNF274 knockout, demonstrating that ZNF274 is directly involved in the repression of SNORD116. These results suggest that interfering with ZNF274 binding at the maternal SNORD116 locus is a potential therapeutic strategy for PWS.
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Affiliation(s)
- Maéva Langouët
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Dea Gorka
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Clarisse Orniacki
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Clémence M Dupont-Thibert
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Michael S Chung
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Heather R Glatt-Deeley
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Noelle Germain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Leann J Crandall
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
| | - Christopher E Stoddard
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Marc Lalande
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
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17
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Sirois CL, Bloom JE, Fink JJ, Gorka D, Keller S, Germain ND, Levine ES, Chamberlain SJ. Abundance and localization of human UBE3A protein isoforms. Hum Mol Genet 2021; 29:3021-3031. [PMID: 32833011 DOI: 10.1093/hmg/ddaa191] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023] Open
Abstract
Loss of UBE3A expression, a gene regulated by genomic imprinting, causes Angelman syndrome (AS), a rare neurodevelopmental disorder. The UBE3A gene encodes an E3 ubiquitin ligase with three known protein isoforms in humans. Studies in mouse suggest that the human isoforms may have differences in localization and neuronal function. A recent case study reported mild AS phenotypes in individuals lacking one specific isoform. Here we have used CRISPR/Cas9 to generate isogenic human embryonic stem cells (hESCs) that lack the individual protein isoforms. We demonstrate that isoform 1 accounts for the majority of UBE3A protein in hESCs and neurons. We also show that UBE3A predominantly localizes to the cytoplasm in both wild type and isoform-null cells. Finally, we show that neurons lacking isoform 1 display a less severe electrophysiological AS phenotype.
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Affiliation(s)
- Carissa L Sirois
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Judy E Bloom
- Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030, USA.,Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - James J Fink
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Dea Gorka
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Steffen Keller
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Noelle D Germain
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Eric S Levine
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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18
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Meganathan K, Prakasam R, Baldridge D, Gontarz P, Zhang B, Urano F, Bonni A, Maloney SE, Turner TN, Huettner JE, Constantino JN, Kroll KL. Altered neuronal physiology, development, and function associated with a common chromosome 15 duplication involving CHRNA7. BMC Biol 2021; 19:147. [PMID: 34320968 PMCID: PMC8317352 DOI: 10.1186/s12915-021-01080-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/30/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Copy number variants (CNVs) linked to genes involved in nervous system development or function are often associated with neuropsychiatric disease. While CNVs involving deletions generally cause severe and highly penetrant patient phenotypes, CNVs leading to duplications tend instead to exhibit widely variable and less penetrant phenotypic expressivity among affected individuals. CNVs located on chromosome 15q13.3 affecting the alpha-7 nicotinic acetylcholine receptor subunit (CHRNA7) gene contribute to multiple neuropsychiatric disorders with highly variable penetrance. However, the basis of such differential penetrance remains uncharacterized. Here, we generated induced pluripotent stem cell (iPSC) models from first-degree relatives with a 15q13.3 duplication and analyzed their cellular phenotypes to uncover a basis for the dissimilar phenotypic expressivity. RESULTS The first-degree relatives studied included a boy with autism and emotional dysregulation (the affected proband-AP) and his clinically unaffected mother (UM), with comparison to unrelated control models lacking this duplication. Potential contributors to neuropsychiatric impairment were modeled in iPSC-derived cortical excitatory and inhibitory neurons. The AP-derived model uniquely exhibited disruptions of cellular physiology and neurodevelopment not observed in either the UM or unrelated controls. These included enhanced neural progenitor proliferation but impaired neuronal differentiation, maturation, and migration, and increased endoplasmic reticulum (ER) stress. Both the neuronal migration deficit and elevated ER stress could be selectively rescued by different pharmacologic agents. Neuronal gene expression was also dysregulated in the AP, including reduced expression of genes related to behavior, psychological disorders, neuritogenesis, neuronal migration, and Wnt, axonal guidance, and GABA receptor signaling. The UM model instead exhibited upregulated expression of genes in many of these same pathways, suggesting that molecular compensation could have contributed to the lack of neurodevelopmental phenotypes in this model. However, both AP- and UM-derived neurons exhibited shared alterations of neuronal function, including increased action potential firing and elevated cholinergic activity, consistent with increased homomeric CHRNA7 channel activity. CONCLUSIONS These data define both diagnosis-associated cellular phenotypes and shared functional anomalies related to CHRNA7 duplication that may contribute to variable phenotypic penetrance in individuals with 15q13.3 duplication. The capacity for pharmacological agents to rescue some neurodevelopmental anomalies associated with diagnosis suggests avenues for intervention for carriers of this duplication and other CNVs that cause related disorders.
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Affiliation(s)
- Kesavan Meganathan
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Ramachandran Prakasam
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Fumihiko Urano
- Department of Medicine, Division of Endocrinology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Susan E. Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - James E. Huettner
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - John N. Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Kristen L. Kroll
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
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19
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Copping NA, McTighe SM, Fink KD, Silverman JL. Emerging Gene and Small Molecule Therapies for the Neurodevelopmental Disorder Angelman Syndrome. Neurotherapeutics 2021; 18:1535-1547. [PMID: 34528170 PMCID: PMC8608975 DOI: 10.1007/s13311-021-01082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2021] [Indexed: 02/07/2023] Open
Abstract
Angelman syndrome (AS) is a rare (~1:15,000) neurodevelopmental disorder characterized by severe developmental delay and intellectual disability, impaired communication skills, and a high prevalence of seizures, sleep disturbances, ataxia, motor deficits, and microcephaly. AS is caused by loss-of-function of the maternally inherited UBE3A gene. UBE3A is located on chromosome 15q11-13 and is biallelically expressed throughout the body but only maternally expressed in the brain due to an RNA antisense transcript that silences the paternal copy. There is currently no cure for AS, but advancements in small molecule drugs and gene therapies offer a promising approach for the treatment of the disorder. Here, we review AS and how loss-of-function of the maternal UBE3A contributes to the disorder. We also discuss the strengths and limitations of current animal models of AS. Furthermore, we examine potential small molecule drug and gene therapies for the treatment of AS and associated challenges faced by the therapeutic design. Finally, gene therapy offers the opportunity for precision medicine in AS and advancements in the treatment of this disorder can serve as a foundation for other single-gene neurodevelopmental disorders.
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Affiliation(s)
- Nycole A Copping
- School of Medicine, Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Research II Building 96, 4625 2nd Avenue, Suite 1001B, Davis, Sacramento, CA, 95817, USA
- Stem Cell Program and Gene Therapy Center, Department of Neurology, MIND Institute, University of California, Davis, Sacramento, CA, USA
| | | | - Kyle D Fink
- Stem Cell Program and Gene Therapy Center, Department of Neurology, MIND Institute, University of California, Davis, Sacramento, CA, USA
| | - Jill L Silverman
- School of Medicine, Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Research II Building 96, 4625 2nd Avenue, Suite 1001B, Davis, Sacramento, CA, 95817, USA.
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Adak P, Sinha S, Banerjee N. An Association Study of Gamma-Aminobutyric Acid Type A Receptor Variants and Susceptibility to Autism Spectrum Disorders. J Autism Dev Disord 2021; 51:4043-4053. [PMID: 33442857 DOI: 10.1007/s10803-020-04865-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2020] [Indexed: 10/22/2022]
Abstract
In this pilot study, we aim to identify the role of few genetic variants of GABA-receptor type A subunits GABRB3 (rs4906902, rs7171660), GABRG3 (rs208129, rs140679), GABRA5 (rs 140681) in the aetiology of autism spectrum disorders in a population of West Bengal. 192 ASD probands, their parents and 184 ethnically-matched healthy controls were recruited for the study. The rs4906902G and the rs140679T conferred significant risk towards ASD. rs7171660 and rs140679 had transmission bias in the family. Neither alleles of rs 208129 and rs 140681 showed significant over-representation in either groups. All these variants were associated with at least one deficit in ASD-associated phenotypes like 'relating to people', 'Imitation', 'emotional response', 'body use', 'taste, smell, touch response' and 'activity levels'.
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Affiliation(s)
- Pallabi Adak
- Manovikas Biomedical Research and Diagnostic Centre, Manovikas Kendra, 482 Madudah, Plot I-24, Sector J, E.M. Bypass, Kolkata, West Bengal, 700107, India
| | - Swagata Sinha
- Out Patient Department, Manovikas Kendra, Kolkata, West Bengal, 700107, India
| | - Nilanjana Banerjee
- Manovikas Biomedical Research and Diagnostic Centre, Manovikas Kendra, 482 Madudah, Plot I-24, Sector J, E.M. Bypass, Kolkata, West Bengal, 700107, India.
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Panov J, Kaphzan H. Bioinformatics analyses show dysregulation of calcium-related genes in Angelman syndrome mouse model. Neurobiol Dis 2020; 148:105180. [PMID: 33212289 DOI: 10.1016/j.nbd.2020.105180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Angelman syndrome (AS) is a genetic neurodevelopmental disorder caused by the loss of function of the UBE3A protein in the brain. In a previous study, we showed that activity-dependent calcium dynamics in hippocampal CA1 pyramidal neurons of AS mice is compromised, and its normalization rescues the hippocampal-dependent deficits. Therefore, we expected that the expression profiles of calcium-related genes would be altered in AS mice hippocampi. METHODS We analyzed mRNA sequencing data from AS model mice and WT controls in light of the newly published CaGeDB database of calcium-related genes. We validated our results in two independent RNA sequencing datasets from two additional different AS models: first one, a human neuroblastoma cell line where UBE3A expression was knocked down by siRNA, and the second, an iPSC-derived neurons from AS patient and healthy donor control. FINDINGS We found signatures of dysregulated calcium-related genes in AS mouse model hippocampus. Additionally, we show that these calcium-related genes function as signatures for AS in other human cellular models of AS, thus strengthening our findings. INTERPRETATION Our findings suggest the downstream implications and significance of the compromised calcium signaling in Angelman syndrome. Moreover, since AS share similar features with other autism spectrum disorders, we believe that these findings entail meaningful data and approach for other neurodevelopmental disorders, especially those with known alterations of calcium signaling. FUNDING This work was supported by the Angelman Syndrome Foundation and by the Israel Science Foundation, Grant Number 248/20.
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Affiliation(s)
- Julia Panov
- Sagol Department of Neurobiology, University of Haifa, Haifa 3498838, Israel
| | - Hanoch Kaphzan
- Sagol Department of Neurobiology, University of Haifa, Haifa 3498838, Israel.
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Hirose S, Tanaka Y, Shibata M, Kimura Y, Ishikawa M, Higurashi N, Yamamoto T, Ichise E, Chiyonobu T, Ishii A. Application of induced pluripotent stem cells in epilepsy. Mol Cell Neurosci 2020; 108:103535. [DOI: 10.1016/j.mcn.2020.103535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/10/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
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Saravanapandian V, Frohlich J, Hipp JF, Hyde C, Scheffler AW, Golshani P, Cook EH, Reiter LT, Senturk D, Jeste SS. Properties of beta oscillations in Dup15q syndrome. J Neurodev Disord 2020; 12:22. [PMID: 32791992 PMCID: PMC7425173 DOI: 10.1186/s11689-020-09326-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 07/30/2020] [Indexed: 11/21/2022] Open
Abstract
Background Duplications of 15q11.2-q13.1 (Dup15q syndrome) are highly penetrant for autism, intellectual disability, hypotonia, and epilepsy. The 15q region harbors genes critical for brain development, particularly UBE3A and a cluster of gamma-aminobutyric acid type A receptor (GABAAR) genes. We recently described an electrophysiological biomarker of the syndrome, characterized by excessive beta oscillations (12–30 Hz), resembling electroencephalogram (EEG) changes induced by allosteric modulation of GABAARs. In this follow-up study, we tested a larger cohort of children with Dup15q syndrome to comprehensively examine properties of this EEG biomarker that would inform its use in future clinical trials, specifically, its (1) relation to basic clinical features, such as age, duplication type, and epilepsy; (2) relation to behavioral characteristics, such as cognition and adaptive function; (3) stability over time; and (4) reproducibility of the signal in clinical EEG recordings. Methods We computed EEG power and beta peak frequency (BPF) in a cohort of children with Dup15q syndrome (N = 41, age range 9–189 months). To relate EEG parameters to clinical (study 1) and behavioral features (study 2), we examined age, duplication type, epilepsy, cognition, and daily living skills (DLS) as predictors of beta power and BPF. To evaluate stability over time (study 3), we derived the intraclass correlation coefficients (ICC) from beta power and BPF computed from children with multiple EEG recordings (N = 10, age range 18–161 months). To evaluate reproducibility in a clinical setting (study 4), we derived ICCs from beta power computed from children (N = 8, age range 19–96 months), who had undergone both research EEG and clinical EEG. Results The most promising relationships between EEG and clinical traits were found using BPF. BPF was predicted both by epilepsy status (R2 = 0.11, p = 0.038) and the DLS component of the Vineland Adaptive Behavior Scale (R2 = 0.17, p = 0.01). Beta power and peak frequency showed high stability across repeated visits (beta power ICC = 0.93, BPF ICC = 0.92). A reproducibility analysis revealed that beta power estimates are comparable between research and clinical EEG (ICC = 0.94). Conclusions In this era of precision health, with pharmacological and neuromodulatory therapies being developed and tested for specific genetic etiologies of neurodevelopmental disorders, quantification and examination of mechanistic biomarkers can greatly improve clinical trials. To this end, the robust beta oscillations evident in Dup15q syndrome are clinically reproducible and stable over time. With future preclinical and computational studies that will help disentangle the underlying mechanism, it is possible that this biomarker could serve as a robust measure of drug target engagement or a proximal outcome measure in future disease modifying intervention trials.
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Affiliation(s)
- Vidya Saravanapandian
- Center for Autism Research and Treatment, Semel Institute for Neuroscience, University of California Los Angeles, Los Angeles, CA, 90024, USA.
| | - Joel Frohlich
- Center for Autism Research and Treatment, Semel Institute for Neuroscience, University of California Los Angeles, Los Angeles, CA, 90024, USA.,Roche Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland.,Department of Psychology, University of California Los Angeles, 3423 Franz Hall, Los Angeles, CA, 90095, USA
| | - Joerg F Hipp
- Roche Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Carly Hyde
- Center for Autism Research and Treatment, Semel Institute for Neuroscience, University of California Los Angeles, Los Angeles, CA, 90024, USA
| | - Aaron W Scheffler
- Department of Biostatistics, University of California Los Angeles School of Public Health, Room 21-254C CHS, Los Angeles, CA, 90095, USA
| | - Peyman Golshani
- Department of Neurology and Semel Institute for Neuroscience, David Geffen School of Medicine, 710 Westwood Plaza, Los Angeles, CA, 90095, USA.,West Los Angeles VA Medical Center, 11301 Wilshire Blvd, Los Angeles, CA, 90073, USA
| | - Edwin H Cook
- Department of Psychiatry, University of Illinois at Chicago, 1747 W Roosevelt Road, Chicago, IL, 60608, USA
| | - Lawrence T Reiter
- Department of Neurology, Pediatrics and Anatomy & Neurobiology, The University of Tennessee Health Science Center, 855 Monroe Ave., Link, Memphis, TN, 415, USA
| | - Damla Senturk
- Department of Biostatistics, University of California Los Angeles School of Public Health, Room 21-254C CHS, Los Angeles, CA, 90095, USA
| | - Shafali S Jeste
- Center for Autism Research and Treatment, Semel Institute for Neuroscience, University of California Los Angeles, Los Angeles, CA, 90024, USA
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Transcriptome Analysis of iPSC-Derived Neurons from Rubinstein-Taybi Patients Reveals Deficits in Neuronal Differentiation. Mol Neurobiol 2020; 57:3685-3701. [PMID: 32562237 PMCID: PMC7399686 DOI: 10.1007/s12035-020-01983-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
Rubinstein-Taybi syndrome (RSTS) is a rare multisystem developmental disorder with moderate to severe intellectual disability caused by heterozygous mutations of either CREBBP or EP300 genes encoding CBP/p300 chromatin regulators. We explored the gene programs and processes underlying the morphological and functional alterations shown by iPSC-derived neurons modeling RSTS to bridge the molecular changes resulting from defective CBP/p300 to cognitive impairment. By global transcriptome analysis, we compared the differentially expressed genes (DEGs) marking the transition from iPSC-derived neural progenitors to cortical neurons (iNeurons) of five RSTS patients carrying private CREBBP/EP300 mutations and manifesting differently graded neurocognitive signs with those of four healthy controls. Our data shows a defective and altered neuroprogenitor to neuron transcriptional program in the cells from RSTS patients. First, transcriptional regulation is weaker in RSTS as less genes than in controls are modulated, including genes of key processes of mature functional neurons, such as those for voltage-gated channels and neurotransmitters and their receptors. Second, regulation is subverted as genes acting at pre-terminal stages of neural differentiation in cell polarity and adhesive functions (members of the cadherin family) and axon extension/guidance (members of the semaphorins and SLIT receptors families) are improperly upregulated. Impairment or delay of RSTS neuronal differentiation program is also evidenced by decreased modulation of the overall number of neural differentiation markers, significantly impacting the initial and final stages of the differentiation cascade. Last, extensive downregulation of genes for RNA/DNA metabolic processes confirms that RSTS is a global transcription disorder, consistent with a syndrome driven by chromatin dysregulation. Interestingly, the morphological and functional alterations we have previously appointed as biomarkers of RSTS iNeurons provide functional support to the herein designed transcriptome profile pointing to key dysregulated neuronal genes as main contributors to patients’ cognitive deficit. The impact of RSTS transcriptome may go beyond RSTS as comparison of dysregulated genes across modeled neurodevelopmental disorders could unveil convergent genes of cognitive impairment.
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Breen MS, Browne A, Hoffman GE, Stathopoulos S, Brennand K, Buxbaum JD, Drapeau E. Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan-McDermid syndrome and autism. Mol Autism 2020; 11:53. [PMID: 32560742 PMCID: PMC7304190 DOI: 10.1186/s13229-020-00355-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Phelan-McDermid syndrome (PMS) is a rare genetic disorder with high risk of autism spectrum disorder (ASD), intellectual disability, and language delay, and is caused by 22q13.3 deletions or mutations in the SHANK3 gene. To date, the molecular and pathway changes resulting from SHANK3 haploinsufficiency in PMS remain poorly understood. Uncovering these mechanisms is critical for understanding pathobiology of PMS and, ultimately, for the development of new therapeutic interventions. METHODS We developed human-induced pluripotent stem cell (hiPSC)-based models of PMS by reprogramming peripheral blood samples from individuals with PMS (n = 7) and their unaffected siblings (n = 6). For each participant, up to three hiPSC clones were generated and differentiated into induced neural progenitor cells (hiPSC-NPCs; n = 39) and induced forebrain neurons (hiPSC-neurons; n = 41). Genome-wide RNA-sequencing was applied to explore transcriptional differences between PMS probands and unaffected siblings. RESULTS Transcriptome analyses identified 391 differentially expressed genes (DEGs) in hiPSC-NPCs and 82 DEGs in hiPSC-neurons, when comparing cells from PMS probands and unaffected siblings (FDR < 5%). Genes under-expressed in PMS were implicated in Wnt signaling, embryonic development, and protein translation, while over-expressed genes were enriched for pre- and postsynaptic density genes, regulation of synaptic plasticity, and G-protein-gated potassium channel activity. Gene co-expression network analysis identified two modules in hiPSC-neurons that were over-expressed in PMS, implicating postsynaptic signaling and GDP binding, and both modules harbored a significant enrichment of genetic risk loci for developmental delay and intellectual disability. Finally, PMS-associated genes were integrated with other ASD hiPSC transcriptome findings and several points of convergence were identified, indicating altered Wnt signaling and extracellular matrix. LIMITATIONS Given the rarity of the condition, we could not carry out experimental validation in independent biological samples. In addition, functional and morphological phenotypes caused by loss of SHANK3 were not characterized here. CONCLUSIONS This is the largest human neural sample analyzed in PMS. Genome-wide RNA-sequencing in hiPSC-derived neural cells from individuals with PMS revealed both shared and distinct transcriptional signatures across hiPSC-NPCs and hiPSC-neurons, including many genes implicated in risk for ASD, as well as specific neurobiological pathways, including the Wnt pathway.
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Affiliation(s)
- Michael S Breen
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Browne
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sofia Stathopoulos
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Kristen Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - Elodie Drapeau
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
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Panov J, Simchi L, Feuermann Y, Kaphzan H. Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways. Int J Mol Sci 2020; 21:ijms21114156. [PMID: 32532103 PMCID: PMC7312912 DOI: 10.3390/ijms21114156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
The UBE3A gene encodes the ubiquitin E3-ligase protein, UBE3A, which is implicated in severe neurodevelopmental disorders. Lack of UBE3A expression results in Angelman syndrome, while UBE3A overexpression, due to genomic 15q duplication, results in autism. The cellular roles of UBE3A are not fully understood, yet a growing body of evidence indicates that these disorders involve mitochondrial dysfunction and increased oxidative stress. We utilized bioinformatics approaches to delineate the effects of murine Ube3a deletion on the expression of mitochondrial-related genes and pathways. For this, we generated an mRNA sequencing dataset from mouse embryonic fibroblasts (MEFs) in which both alleles of Ube3a gene were deleted and their wild-type controls. Since oxidative stress and mitochondrial dysregulation might not be exhibited in the resting baseline state, we also activated mitochondrial functioning in the cells of these two genotypes using TNFα application. Transcriptomes of the four groups of MEFs, Ube3a+/+ and Ube3a-/-, with or without the application of TNFα, were analyzed using various bioinformatics tools and machine learning approaches. Our results indicate that Ube3a deletion affects the gene expression profiles of mitochondrial-associated pathways. We further confirmed these results by analyzing other publicly available human transcriptome datasets of Angelman syndrome and 15q duplication syndrome.
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Drakulic D, Djurovic S, Syed YA, Trattaro S, Caporale N, Falk A, Ofir R, Heine VM, Chawner SJRA, Rodriguez-Moreno A, van den Bree MBM, Testa G, Petrakis S, Harwood AJ. Copy number variants (CNVs): a powerful tool for iPSC-based modelling of ASD. Mol Autism 2020; 11:42. [PMID: 32487215 PMCID: PMC7268297 DOI: 10.1186/s13229-020-00343-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Patients diagnosed with chromosome microdeletions or duplications, known as copy number variants (CNVs), present a unique opportunity to investigate the relationship between patient genotype and cell phenotype. CNVs have high genetic penetrance and give a good correlation between gene locus and patient clinical phenotype. This is especially effective for the study of patients with neurodevelopmental disorders (NDD), including those falling within the autism spectrum disorders (ASD). A key question is whether this correlation between genetics and clinical presentation at the level of the patient can be translated to the cell phenotypes arising from the neurodevelopment of patient induced pluripotent stem cells (iPSCs).Here, we examine how iPSCs derived from ASD patients with an associated CNV inform our understanding of the genetic and biological mechanisms underlying the aetiology of ASD. We consider selection of genetically characterised patient iPSCs; use of appropriate control lines; aspects of human neurocellular biology that can capture in vitro the patient clinical phenotype; and current limitations of patient iPSC-based studies. Finally, we consider how future research may be enhanced to maximise the utility of CNV patients for research of pathological mechanisms or therapeutic targets.
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Affiliation(s)
- Danijela Drakulic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, 152, Serbia
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, 5007, Bergen, Norway
| | - Yasir Ahmed Syed
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Sebastiano Trattaro
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, 20146, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Nicolò Caporale
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, 20146, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Rivka Ofir
- BGU-iPSC Core Facility, The Regenerative Medicine & Stem Cell (RMSC) Research Center, Ben Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Vivi M Heine
- Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Child and Youth Psychiatry, Emma Children's Hospital, Amsterdam UMC, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081, Amsterdam, The Netherlands
| | - Samuel J R A Chawner
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Antonio Rodriguez-Moreno
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Ctra. de Utrera, Km 1, 41013, Seville, Spain
| | - Marianne B M van den Bree
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, 20146, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, Via Cristina Belgioioso 171, 20157, Milan, Italy
| | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece.
| | - Adrian J Harwood
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK.
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Lopatkina ME, Lebedev IN. Transcriptome Analysis as a Tool for Investigation of Pathogenesis of Chromosomal Diseases. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420050099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Casamassa A, Ferrari D, Gelati M, Carella M, Vescovi AL, Rosati J. A Link between Genetic Disorders and Cellular Impairment, Using Human Induced Pluripotent Stem Cells to Reveal the Functional Consequences of Copy Number Variations in the Central Nervous System-A Close Look at Chromosome 15. Int J Mol Sci 2020; 21:ijms21051860. [PMID: 32182809 PMCID: PMC7084702 DOI: 10.3390/ijms21051860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 12/28/2022] Open
Abstract
Recent cutting-edge human genetics technology has allowed us to identify copy number variations (CNVs) and has provided new insights for understanding causative mechanisms of human diseases. A growing number of studies show that CNVs could be associated with physiological mechanisms linked to evolutionary trigger, as well as to the pathogenesis of various diseases, including cancer, autoimmune disease and mental disorders such as autism spectrum disorders, schizophrenia, intellectual disabilities or attention-deficit/hyperactivity disorder. Their incomplete penetrance and variable expressivity make diagnosis difficult and hinder comprehension of the mechanistic bases of these disorders. Additional elements such as co-presence of other CNVs, genomic background and environmental factors are involved in determining the final phenotype associated with a CNV. Genetically engineered animal models are helpful tools for understanding the behavioral consequences of CNVs. However, the genetic background and the biology of these animal model systems have sometimes led to confusing results. New cellular models obtained through somatic cellular reprogramming technology that produce induced pluripotent stem cells (iPSCs) from human subjects are being used to explore the mechanisms involved in the pathogenic consequences of CNVs. Considering the vast quantity of CNVs found in the human genome, we intend to focus on reviewing the current literature on the use of iPSCs carrying CNVs on chromosome 15, highlighting advantages and limits of this system with respect to mouse model systems.
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Affiliation(s)
- Alessia Casamassa
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy;
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, Viale Abramo Lincoln 5, 81100 Caserta, Italy
| | - Daniela Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
| | - Maurizio Gelati
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
| | - Massimo Carella
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
| | - Angelo Luigi Vescovi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
- Correspondence: (A.L.V.); (J.R.)
| | - Jessica Rosati
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy;
- Correspondence: (A.L.V.); (J.R.)
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Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons. Mol Autism 2019; 10:51. [PMID: 31893020 PMCID: PMC6936127 DOI: 10.1186/s13229-019-0306-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder with pronounced heritability in the general population. This is largely attributable to the effects of polygenic susceptibility, with inherited liability exhibiting distinct sex differences in phenotypic expression. Attempts to model ASD in human cellular systems have principally involved rare de novo mutations associated with ASD phenocopies. However, by definition, these models are not representative of polygenic liability, which accounts for the vast share of population-attributable risk. Methods Here, we performed what is, to our knowledge, the first attempt to model multiplex autism using patient-derived induced pluripotent stem cells (iPSCs) in a family manifesting incremental degrees of phenotypic expression of inherited liability (absent, intermediate, severe). The family members share an inherited variant of uncertain significance (VUS) in GPD2, a gene that was previously associated with developmental disability but here is insufficient by itself to cause ASD. iPSCs from three first-degree relatives and an unrelated control were differentiated into both cortical excitatory (cExN) and cortical inhibitory (cIN) neurons, and cellular phenotyping and transcriptomic analysis were conducted. Results cExN neurospheres from the two affected individuals were reduced in size, compared to those derived from unaffected related and unrelated individuals. This reduction was, at least in part, due to increased apoptosis of cells from affected individuals upon initiation of cExN neural induction. Likewise, cIN neural progenitor cells from affected individuals exhibited increased apoptosis, compared to both unaffected individuals. Transcriptomic analysis of both cExN and cIN neural progenitor cells revealed distinct molecular signatures associated with affectation, including the misregulation of suites of genes associated with neural development, neuronal function, and behavior, as well as altered expression of ASD risk-associated genes. Conclusions We have provided evidence of morphological, physiological, and transcriptomic signatures of polygenic liability to ASD from an analysis of cellular models derived from a multiplex autism family. ASD is commonly inherited on the basis of additive genetic liability. Therefore, identifying convergent cellular and molecular phenotypes resulting from polygenic and monogenic susceptibility may provide a critical bridge for determining which of the disparate effects of rare highly deleterious mutations might also apply to common autistic syndromes.
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Moslem M, Olive J, Falk A. Stem cell models of schizophrenia, what have we learned and what is the potential? Schizophr Res 2019; 210:3-12. [PMID: 30587427 DOI: 10.1016/j.schres.2018.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a complex disorder with clinical manifestations in early adulthood. However, it may start with disruption of brain development caused by genetic or environmental factors, or both. Early deteriorating effects of genetic/environmental factors on neural development might be key to described disease causing mechanisms. Establishing cellular models with cells from affected individual using the induced pluripotent stem cells (iPSC) technology could be used to mimic early neurodevelopment alterations caused by risk genes or environmental stressors. Indeed, cellular models have allowed identification and further study of risk factors and the biological pathways in which they are involved. New advancements in differentiation methods such as defined and robust monolayer protocols and cerebral 3D organoids have made it possible to faithfully mimic neural development and neuronal functionality while CRISPR-editing tools assist to engineer isogenic cell lines to precisely explore genetic variation in polygenic diseases such as schizophrenia. Here we review the current field of iPSC models of schizophrenia and how risk factors can be modelled as well as discussing the common biological pathways involved.
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Affiliation(s)
- Mohsen Moslem
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Jessica Olive
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Life Sciences, Imperial College London, United Kingdom.
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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A bipartite boundary element restricts UBE3A imprinting to mature neurons. Proc Natl Acad Sci U S A 2019; 116:2181-2186. [PMID: 30674673 DOI: 10.1073/pnas.1815279116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of function from the maternal allele of UBE3A, a gene encoding an E3 ubiquitin ligase. UBE3A is only expressed from the maternally inherited allele in mature human neurons due to tissue-specific genomic imprinting. Imprinted expression of UBE3A is restricted to neurons by expression of UBE3A antisense transcript (UBE3A-ATS) from the paternally inherited allele, which silences the paternal allele of UBE3A in cis However, the mechanism restricting UBE3A-ATS expression and UBE3A imprinting to neurons is not understood. We used CRISPR/Cas9-mediated genome editing to functionally define a bipartite boundary element critical for neuron-specific expression of UBE3A-ATS in humans. Removal of this element led to up-regulation of UBE3A-ATS without repressing paternal UBE3A However, increasing expression of UBE3A-ATS in the absence of the boundary element resulted in full repression of paternal UBE3A, demonstrating that UBE3A imprinting requires both the loss of function from the boundary element as well as the up-regulation of UBE3A-ATS These results suggest that manipulation of the competition between UBE3A-ATS and UBE3A may provide a potential therapeutic approach for AS.
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Langouët M, Glatt-Deeley HR, Chung MS, Dupont-Thibert CM, Mathieux E, Banda EC, Stoddard CE, Crandall L, Lalande M. Zinc finger protein 274 regulates imprinted expression of transcripts in Prader-Willi syndrome neurons. Hum Mol Genet 2019; 27:505-515. [PMID: 29228278 DOI: 10.1093/hmg/ddx420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/01/2017] [Indexed: 01/09/2023] Open
Abstract
Prader-Willi syndrome (PWS) is characterized by neonatal hypotonia, developmental delay and hyperphagia/obesity and is caused by the absence of paternal contribution to chromosome 15q11-q13. Using induced pluripotent stem cell (iPSC) models of PWS, we previously discovered an epigenetic complex that is comprised of the zinc-finger protein ZNF274 and the SET domain bifurcated 1 (SETDB1) histone H3 lysine 9 (H3K9) methyltransferase and that silences the maternal alleles at the PWS locus. Here, we have knocked out ZNF274 and rescued the expression of silent maternal alleles in neurons derived from PWS iPSC lines, without affecting DNA methylation at the PWS-Imprinting Center (PWS-IC). This suggests that the ZNF274 complex is a separate imprinting mark that represses maternal PWS gene expression in neurons and is a potential target for future therapeutic applications to rescue the PWS phenotype.
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Affiliation(s)
- Maéva Langouët
- Department of Genetics and Genome Sciences, School of Medicine
| | | | - Michael S Chung
- Department of Genetics and Genome Sciences, School of Medicine
| | | | - Elodie Mathieux
- Department of Genetics and Genome Sciences, School of Medicine
| | - Erin C Banda
- Department of Genetics and Genome Sciences, School of Medicine
| | | | - Leann Crandall
- Department of Genetics and Genome Sciences, School of Medicine
| | - Marc Lalande
- Department of Genetics and Genome Sciences, School of Medicine.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030-6403, USA
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Choi Y, Kim H, Choi M, Yang EJ, Takumi T, Kim HS. Fetal neural stem cells from a mouse model of 15q11-13 duplication syndrome exhibit altered differentiation into neurons and astrocytes. J Pharmacol Sci 2018; 139:249-253. [PMID: 30718079 DOI: 10.1016/j.jphs.2018.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 11/18/2022] Open
Abstract
The duplication of human chromosome 15q11-13 is known to be associated with an estimated 1.1% of autism cases. Here, we investigated whether differentiation into neurons and astrocytes is altered in fetal neural stem cells (FNSCs) isolated from the mouse model of 15q11-13 duplication syndrome (patDp/+ mice). In patDp/+ mice-derived FNSCs, multipotency was maintained for a longer period, the population of neurons was downregulated, and that of astrocytes was upregulated significantly after differentiation induction. These results suggest that the dysregulation of FNSCs differentiation could affect cortical development and behavioral deficits in the early postnatal stage shown in the patDp/+ mice.
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Affiliation(s)
- Yunjung Choi
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea
| | - Hyunju Kim
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea
| | - Moonseok Choi
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea
| | - Eun-Jeong Yang
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Hye-Sun Kim
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea; Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea; Seoul National University Bundang Hospital, Seongnam, 463-707, South Korea; Neuroscience Research Institute, College of Medicine, Seoul National University, 103 Daehakro, Jongro-gu, Seoul, 110-799, Republic of Korea.
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Abstract
UBE3A is a dual function protein consisting of ubiquitin ligase as well as transcriptional co-activator function. UBE3A gene is imprinted in the brain with preferential maternal-specific expression particularly in the neuron and loss of activity of the maternally inherited UBE3A causes Angelman syndrome (AS), characterized by severe mental retardation, lack of speech, seizures and autistic features. Interestingly, duplication, triplication, or gain-of-function mutations in the UBE3A gene are also linked with autism clinically distinguished by social impairments and stereotyped behaviors. These findings indicate that the expression and activity of UBE3A must be tightly regulated during brain development and UBE3A might be playing a crucial role in controlling synaptic function and plasticity through proteasome-mediated degradation as well as transcriptional regulation of its target proteins. In fact, several recent reports demonstrated the role of UBE3A in the modulation of synaptic function and plasticity. This review focuses on the critical role of UBE3A in regulating the synaptic function and how its altered activity is associated with autism.
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Affiliation(s)
- Naman Vatsa
- Cellular and Molecular Neuroscience Laboratory, National Brain Research Centre, Gurugram, India
| | - Nihar Ranjan Jana
- School of Bioscience, Indian Institute of Technology, Kharagpur, India
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Pólvora-Brandão D, Joaquim M, Godinho I, Aprile D, Álvaro AR, Onofre I, Raposo AC, Pereira de Almeida L, Duarte ST, da Rocha ST. Loss of hierarchical imprinting regulation at the Prader-Willi/Angelman syndrome locus in human iPSCs. Hum Mol Genet 2018; 27:3999-4011. [PMID: 30102380 PMCID: PMC6240739 DOI: 10.1093/hmg/ddy274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 12/13/2022] Open
Abstract
The human chr15q11-q13 imprinted cluster is linked to several disorders, including Prader-Willi (PWS) and Angelman (AS) syndromes. Recently, disease modeling approaches based on induced pluripotent stem cells (iPSCs) have been used to study these syndromes. A concern regarding the use of these cells for imprinted disease modeling is the numerous imprinting defects found in many iPSCs. Here, by reprogramming skin fibroblasts from a control and AS individuals, we generated several iPSC lines and addressed the stability of imprinting status across the PWS/AS domain. We focused on three important regulatory DNA elements which are all differentially methylated regions (DMRs), methylated on the maternal allele: the PWS imprinting center (PWS-IC), which is a germline DMR and the somatic NDN and MKRN3 DMRs, hierarchically controlled by PWS-IC. Normal PWS-IC methylation pattern was maintained in most iPSC lines; however, loss of maternal methylation in one out of five control iPSC lines resulted in a monoallelic to biallelic switch for many imprinted genes in this domain. Surprisingly, MKRN3 DMR was found aberrantly hypermethylated in all control and AS iPSCs, regardless of the methylation status of the PWS-IC master regulator. This suggests a loss of hierarchical control of imprinting at PWS/AS region. We confirmed these results in established iPSC lines derived using different reprogramming procedures. Overall, we show that hierarchy of imprinting control in donor cells might not apply to iPSCs, accounting for their spectrum of imprinting alterations. Such differences in imprinting regulation should be taken into consideration for the use of iPSCs in disease modeling.
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Affiliation(s)
- Duarte Pólvora-Brandão
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Mariana Joaquim
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Inês Godinho
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Domenico Aprile
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Rita Álvaro
- CNC - Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Isabel Onofre
- CNC - Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ana Cláudia Raposo
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Luís Pereira de Almeida
- CNC - Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra,Coimbra, Portugal
| | - Sofia T Duarte
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
- Hospital D. Estefânia, Centro Hospitalar Lisboa Central, Lisboa, Portugal
| | - Simão T da Rocha
- Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
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Quesnel-Vallières M, Weatheritt RJ, Cordes SP, Blencowe BJ. Autism spectrum disorder: insights into convergent mechanisms from transcriptomics. Nat Rev Genet 2018; 20:51-63. [DOI: 10.1038/s41576-018-0066-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Alari V, Russo S, Terragni B, Ajmone PF, Sironi A, Catusi I, Calzari L, Concolino D, Marotta R, Milani D, Giardino D, Mantegazza M, Gervasini C, Finelli P, Larizza L. iPSC-derived neurons of CREBBP- and EP300-mutated Rubinstein-Taybi syndrome patients show morphological alterations and hypoexcitability. Stem Cell Res 2018; 30:130-140. [PMID: 29883886 DOI: 10.1016/j.scr.2018.05.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/09/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022] Open
Abstract
Rubinstein-Taybi syndrome (RSTS) is a rare neurodevelopmental disorder characterized by distinctive facial features, growth retardation, broad thumbs and toes and mild to severe intellectual disability, caused by heterozygous mutations in either CREBBP or EP300 genes, encoding the homologous CBP and p300 lysine-acetyltransferases and transcriptional coactivators. No RSTS in vitro induced Pluripotent Stem Cell (iPSC)-neuronal model is available yet to achieve mechanistic insights on cognitive impairment of RSTS patients. We established iPSC-derived neurons (i-neurons) from peripheral blood cells of three CREBBP- and two EP300-mutated patients displaying different levels of intellectual disability, and four unaffected controls. Pan neuronal and cortical-specific markers were expressed by all patients' i-neurons. Altered morphology of patients' differentiating neurons, showing reduced branch length and increased branch number, and hypoexcitability of differentiated neurons emerged as potential disease biomarkers. Anomalous neuronal morphology and reduced excitability varied across different RSTS patients' i-neurons. Further studies are needed to validate these markers and assess whether they reflect cognitive and behavioural impairment of the donor patients.
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Affiliation(s)
- Valentina Alari
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy
| | - Silvia Russo
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy
| | - Benedetta Terragni
- Dept. of Neurophysiology and Diagnostic Epileptology, IRCCS Foundation C. Besta Neurological Institute, 20133 Milano, Italy
| | - Paola Francesca Ajmone
- Child and Adolescent Neuropsychiatric Service (UONPIA), Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Alessandra Sironi
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy
| | - Ilaria Catusi
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy
| | - Luciano Calzari
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy
| | - Daniela Concolino
- Pediatrics Unit, Department of Medical and Surgical Science, University "Magna Graecia", 88100 Catanzaro, Italy
| | - Rosa Marotta
- Pediatrics Unit, Department of Medical and Surgical Science, University "Magna Graecia", 88100 Catanzaro, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Daniela Giardino
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy
| | - Massimo Mantegazza
- Dept. of Neurophysiology and Diagnostic Epileptology, IRCCS Foundation C. Besta Neurological Institute, 20133 Milano, Italy; Institute of Molecular and Cellular Pharmacology (IPMC), CNRS UMR7275, LabEx ICST, 06560 Valbonne-Sophia Antipolis, France; Université Côte d'Azur (UCA), 06560 Valbonne-Sophia Antipolis, France
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy
| | - Palma Finelli
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy
| | - Lidia Larizza
- Laboratory of Medical Cytogenetics and Molecular Genetics, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, 20145 Milano, Italy.
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Fink JJ, Levine ES. Uncovering True Cellular Phenotypes: Using Induced Pluripotent Stem Cell-Derived Neurons to Study Early Insults in Neurodevelopmental Disorders. Front Neurol 2018; 9:237. [PMID: 29713304 PMCID: PMC5911479 DOI: 10.3389/fneur.2018.00237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/26/2018] [Indexed: 01/07/2023] Open
Abstract
Animal models of neurodevelopmental disorders have provided invaluable insights into the molecular-, cellular-, and circuit-level defects associated with a plethora of genetic disruptions. In many cases, these deficits have been linked to changes in disease-relevant behaviors, but very few of these findings have been translated to treatments for human disease. This may be due to significant species differences and the difficulty in modeling disorders that involve deletion or duplication of multiple genes. The identification of primary underlying pathophysiology in these models is confounded by the accumulation of secondary disease phenotypes in the mature nervous system, as well as potential compensatory mechanisms. The discovery of induced pluripotent stem cell technology now provides a tool to accurately model complex genetic neurogenetic disorders. Using this technique, patient-specific cell lines can be generated and differentiated into specific subtypes of neurons that can be used to identify primary cellular and molecular phenotypes. It is clear that impairments in synaptic structure and function are a common pathophysiology across neurodevelopmental disorders, and electrophysiological analysis at the earliest stages of neuronal development is critical for identifying changes in activity and excitability that can contribute to synaptic dysfunction and identify targets for disease-modifying therapies.
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Affiliation(s)
- James J Fink
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Eric S Levine
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, United States
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Takumi T, Tamada K. CNV biology in neurodevelopmental disorders. Curr Opin Neurobiol 2018; 48:183-192. [PMID: 29331932 DOI: 10.1016/j.conb.2017.12.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/27/2017] [Accepted: 12/10/2017] [Indexed: 12/29/2022]
Abstract
Copy number variants (CNVs), characterized in recent years by cutting-edge technology, add complexity to our knowledge of the human genome. CNVs contribute not only to human diversity but also to different kinds of diseases including neurodevelopmental delay, autism spectrum disorder and neuropsychiatric diseases. Interestingly, many pathogenic CNVs are shared among these diseases. Studies suggest that pathophysiology of disease may not be simply attributed to a single driver gene within a CNV but also that multifactorial effects may be important. Gene expression and the resulting phenotypes may also be affected by epigenetic alteration and chromosomal structural changes. Combined with human genetics and systems biology, integrative research by multi-dimensional approaches using animal and cell models of CNVs are expected to further understanding of pathophysiological mechanisms of neurodevelopmental disorders and neuropsychiatric disorders.
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Affiliation(s)
- Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan.
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
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Stem Cell Technology for (Epi)genetic Brain Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:443-475. [PMID: 28523560 DOI: 10.1007/978-3-319-53889-1_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the enormous efforts of the scientific community over the years, effective therapeutics for many (epi)genetic brain disorders remain unidentified. The common and persistent failures to translate preclinical findings into clinical success are partially attributed to the limited efficiency of current disease models. Although animal and cellular models have substantially improved our knowledge of the pathological processes involved in these disorders, human brain research has generally been hampered by a lack of satisfactory humanized model systems. This, together with our incomplete knowledge of the multifactorial causes in the majority of these disorders, as well as a thorough understanding of associated (epi)genetic alterations, has been impeding progress in gaining more mechanistic insights from translational studies. Over the last years, however, stem cell technology has been offering an alternative approach to study and treat human brain disorders. Owing to this technology, we are now able to obtain a theoretically inexhaustible source of human neural cells and precursors in vitro that offer a platform for disease modeling and the establishment of therapeutic interventions. In addition to the potential to increase our general understanding of how (epi)genetic alterations contribute to the pathology of brain disorders, stem cells and derivatives allow for high-throughput drugs and toxicity testing, and provide a cell source for transplant therapies in regenerative medicine. In the current chapter, we will demonstrate the validity of human stem cell-based models and address the utility of other stem cell-based applications for several human brain disorders with multifactorial and (epi)genetic bases, including Parkinson's disease (PD), Alzheimer's disease (AD), fragile X syndrome (FXS), Angelman syndrome (AS), Prader-Willi syndrome (PWS), and Rett syndrome (RTT).
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Autism spectrum disorders and disease modeling using stem cells. Cell Tissue Res 2017; 371:153-160. [PMID: 28918504 DOI: 10.1007/s00441-017-2685-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/19/2017] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorders (ASD) represent a variety of disorders characterized as complex lifelong neurodevelopment disabilities, which may affect the ability of communication and socialization, including typical comportments like repetitive and stereotyped behavior. Other comorbidities are usually present, such as echolalia, hypotonia, intellectual disability and difficulties in processing figured speech. Furthermore, some ASD individuals may present certain abilities, such as eidetic memory, outstanding musical or painting talents and special mathematical skills, among others. Considering the variability of the clinical symptoms, one autistic individual can be severely affected in communication while others can speak perfectly, sometimes having a vocabulary above average in early childhood. The same variability can be seen in other clinical symptoms, thus the "spectrum" can vary from severe to mild. Induced pluripotent stem cell technology has been used to model several neurological diseases, including syndromic and non-syndromic autism. We discuss how modeling the central nervous system cells in a dish may help to reach a better understanding of ASD pathology and variability, as well as personalize their treatment.
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Tamburini C, Li M. Understanding neurodevelopmental disorders using human pluripotent stem cell-derived neurons. Brain Pathol 2017; 27:508-517. [PMID: 28585386 PMCID: PMC8029066 DOI: 10.1111/bpa.12517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/23/2017] [Indexed: 12/18/2022] Open
Abstract
Research into psychiatric disorders has long been hindered by the lack of appropriate models. Induced pluripotent stem cells (iPSCs) offer an unlimited source of patient-specific cells, which in principle can be differentiated into all disease-relevant somatic cell types to create in vitro models of the disorder of interest. Here, neuronal differentiation protocols available for this purpose and the current progress on iPSCs-based models of schizophrenia, autism spectrum disorders and bipolar disorder were reviewed. We also discuss the impact of the recently developed CRISPR/Cas9 genome editing tool in the disease modeling field. Genetically engineered mutation of disease risk alleles in well characterized reference "control" hPSCs or correction of disease risk variants in patient iPSCs has been used as a powerful means to establish causality of the identified cellular pathology. Together, iPSC reprogramming and CRISPR/CAS9 genome editing technology have already significantly contributed to our understanding of the developmental origin of some major psychiatric disorders. The challenge ahead is the identification of shared mechanisms in their etiology, which will ultimately be relevant to the development of new treatments.
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Affiliation(s)
- Claudia Tamburini
- Neuroscience and Mental Health Research Institute, School of Medicine and School of BiosciencesCardiff UniversityCardiffUnited Kingdom
| | - Meng Li
- Neuroscience and Mental Health Research Institute, School of Medicine and School of BiosciencesCardiff UniversityCardiffUnited Kingdom
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Abstract
Autism spectrum disorders (ASDs) are diagnosed on the basis of three behavioral features, namely, (1) deficits in social communication, (2) absence or delay in language and (3) stereotypy. The consensus regarding the neurological pathogenesis of ASDs is aberrant synaptogenesis and synapse function. Further, it is now widely accepted that ASD is neurodevelopmental in nature, placing emphasis on derangements occurring at the level of intra- and intercellular signaling during corticogenesis. At present, there is an ever-growing list of mutations in putative susceptibility genes in affected individuals, preventing effective transformation of knowledge gathered from basic science research to the clinic. In response, the focus of ASD biology has shifted toward the identification of cellular signaling pathways that are common to various ASD-related mutations in hopes that these shared pathways may serve as more promising treatment targets than targeting individual genes or proteins. To this end, the endogenous cannabinoid (endocannabinoid, eCB) system has recently emerged as a promising therapeutic target in the field of ASD research. The eCB system is altered in several neurological disorders, but the role of these bioactive lipids in ASD etiology remains poorly understood. In this perspective, we review current evidence linking eCB signaling to ASDs and put forth the notion that continued focus on eCBs in autism research may provide valuable insight into pathophysiology and treatment strategies. In addition to its role in modulating transmitter release at mature synapses, the eCB signaling system plays important roles in many aspects of cortical development, and disruption of these effects of eCBs may also be related to ASD pathophysiology.
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Affiliation(s)
- Mason L Yeh
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06032, USA
| | - Eric S Levine
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06032, USA
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45
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Fink JJ, Robinson TM, Germain ND, Sirois CL, Bolduc KA, Ward AJ, Rigo F, Chamberlain SJ, Levine ES. Disrupted neuronal maturation in Angelman syndrome-derived induced pluripotent stem cells. Nat Commun 2017; 8:15038. [PMID: 28436452 PMCID: PMC5413969 DOI: 10.1038/ncomms15038] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/16/2017] [Indexed: 01/15/2023] Open
Abstract
Angelman syndrome (AS) is a neurogenetic disorder caused by deletion of the maternally inherited UBE3A allele and is characterized by developmental delay, intellectual disability, ataxia, seizures and a happy affect. Here, we explored the underlying pathophysiology using induced pluripotent stem cell-derived neurons from AS patients and unaffected controls. AS-derived neurons showed impaired maturation of resting membrane potential and action potential firing, decreased synaptic activity and reduced synaptic plasticity. These patient-specific differences were mimicked by knocking out UBE3A using CRISPR/Cas9 or by knocking down UBE3A using antisense oligonucleotides. Importantly, these phenotypes could be rescued by pharmacologically unsilencing paternal UBE3A expression. Moreover, selective effects of UBE3A disruption at late stages of in vitro development suggest that changes in action potential firing and synaptic activity may be secondary to altered resting membrane potential. Our findings provide a cellular phenotype for investigating pathogenic mechanisms underlying AS and identifying novel therapeutic strategies.
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Affiliation(s)
- James J Fink
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, Connecticut 06030, USA
| | - Tiwanna M Robinson
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, Connecticut 06030, USA
| | - Noelle D Germain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, Connecticut 06030, USA
| | - Carissa L Sirois
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, Connecticut 06030, USA
| | - Kaitlyn A Bolduc
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, Connecticut 06030, USA
| | - Amanda J Ward
- Ionis Pharmaceuticals, Carlsbad, California 92010, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, California 92010, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, Connecticut 06030, USA
| | - Eric S Levine
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, Connecticut 06030, USA
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Flaherty EK, Brennand KJ. Using hiPSCs to model neuropsychiatric copy number variations (CNVs) has potential to reveal underlying disease mechanisms. Brain Res 2017; 1655:283-293. [PMID: 26581337 PMCID: PMC4865445 DOI: 10.1016/j.brainres.2015.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/16/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022]
Abstract
Schizophrenia is a neuropsychological disorder with a strong heritable component; genetic risk for schizophrenia is conferred by both common variants of relatively small effect and rare variants with high penetrance. Genetically engineered mouse models can recapitulate rare variants, displaying some behavioral defects associated with schizophrenia; however, these mouse models cannot recapitulate the full genetic architecture underlying the disorder. Patient-derived human induced pluripotent stem cells (hiPSCs) present an alternative approach for studying rare variants, in the context of all other risk alleles. Genome editing technologies, such as CRISPR-Cas9, enable the generation of isogenic hiPSC lines with which to examine the functional contribution of single variants within any genetic background. Studies of these rare variants using hiPSCs have the potential to identify commonly disrupted pathways in schizophrenia and allow for the identification of new therapeutic targets. This article is part of a Special Issue entitled SI:StemsCellsinPsychiatry.
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Affiliation(s)
- Erin K Flaherty
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, 1425 Madison Ave, New York, NY 10029, United States
| | - Kristen J Brennand
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, 1425 Madison Ave, New York, NY 10029, United States.
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47
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A new era of disease modeling and drug discovery using induced pluripotent stem cells. Arch Pharm Res 2016; 40:1-12. [DOI: 10.1007/s12272-016-0871-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/27/2016] [Indexed: 12/21/2022]
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48
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Picinelli C, Lintas C, Piras IS, Gabriele S, Sacco R, Brogna C, Persico AM. Recurrent 15q11.2 BP1-BP2 microdeletions and microduplications in the etiology of neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1088-1098. [PMID: 27566550 DOI: 10.1002/ajmg.b.32480] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/22/2016] [Indexed: 01/04/2023]
Abstract
Rare and common CNVs can contribute to the etiology of neurodevelopmental disorders. One of the recurrent genomic aberrations associated with these phenotypes and proposed as a susceptibility locus is the 15q11.2 BP1-BP2 CNV encompassing TUBGCP5, CYFIP1, NIPA2, and NIPA1. Characterizing by array-CGH a cohort of 243 families with various neurodevelopmental disorders, we identified five patients carrying the 15q11.2 duplication and one carrying the deletion. All CNVs were confirmed by qPCR and were inherited, except for one duplication where parents were not available. The phenotypic spectrum of CNV carriers was broad but mainly neurodevelopmental, in line with all four genes being implicated in axonal growth and neural connectivity. Phenotypically normal and mildly affected carriers complicate the interpretation of this aberration. This variability may be due to reduced penetrance or altered gene dosage on a particular genetic background. We evaluated the expression levels of the four genes in peripheral blood RNA and found the expected reduction in the deleted case, while duplicated carriers displayed high interindividual variability. These data suggest that differential expression of these genes could partially account for differences in clinical phenotypes, especially among duplication carriers. Furthermore, urinary Mg2+ levels appear negatively correlated with NIPA2 gene copy number, suggesting they could potentially represent a useful biomarker, whose reliability will need replication in larger samples. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Chiara Picinelli
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy.,Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Carla Lintas
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Ignazio Stefano Piras
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy.,Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Stefano Gabriele
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Roberto Sacco
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Claudia Brogna
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Antonio Maria Persico
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy.,Unit of Child and Adolescent Neuropsychiatry, "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
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Lin YC, Frei JA, Kilander MBC, Shen W, Blatt GJ. A Subset of Autism-Associated Genes Regulate the Structural Stability of Neurons. Front Cell Neurosci 2016; 10:263. [PMID: 27909399 PMCID: PMC5112273 DOI: 10.3389/fncel.2016.00263] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a range of neurological conditions that affect individuals’ ability to communicate and interact with others. People with ASD often exhibit marked qualitative difficulties in social interaction, communication, and behavior. Alterations in neurite arborization and dendritic spine morphology, including size, shape, and number, are hallmarks of almost all neurological conditions, including ASD. As experimental evidence emerges in recent years, it becomes clear that although there is broad heterogeneity of identified autism risk genes, many of them converge into similar cellular pathways, including those regulating neurite outgrowth, synapse formation and spine stability, and synaptic plasticity. These mechanisms together regulate the structural stability of neurons and are vulnerable targets in ASD. In this review, we discuss the current understanding of those autism risk genes that affect the structural connectivity of neurons. We sub-categorize them into (1) cytoskeletal regulators, e.g., motors and small RhoGTPase regulators; (2) adhesion molecules, e.g., cadherins, NCAM, and neurexin superfamily; (3) cell surface receptors, e.g., glutamatergic receptors and receptor tyrosine kinases; (4) signaling molecules, e.g., protein kinases and phosphatases; and (5) synaptic proteins, e.g., vesicle and scaffolding proteins. Although the roles of some of these genes in maintaining neuronal structural stability are well studied, how mutations contribute to the autism phenotype is still largely unknown. Investigating whether and how the neuronal structure and function are affected when these genes are mutated will provide insights toward developing effective interventions aimed at improving the lives of people with autism and their families.
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Affiliation(s)
- Yu-Chih Lin
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Jeannine A Frei
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Michaela B C Kilander
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Wenjuan Shen
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Gene J Blatt
- Laboratory of Autism Neurocircuitry, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
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50
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Temme SJ, Maher BJ, Christian KM. Using Induced Pluripotent Stem Cells to Investigate Complex Genetic Psychiatric Disorders. Curr Behav Neurosci Rep 2016; 3:275-284. [PMID: 28191386 DOI: 10.1007/s40473-016-0100-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE OF REVIEW Induced pluripotent stem cells (iPSCs) can be generated from human patient tissue samples, differentiated into any somatic cell type, and studied under controlled culture conditions. We review how iPSCs are used to investigate genetic factors and biological mechanisms underlying psychiatric disorders, and considerations for synthesizing data across studies. RECENT FINDINGS Results from patient specific-iPSC studies often reveal cellular phenotypes consistent with postmortem and brain imaging studies. Unpredicted findings illustrate the power of iPSCs as a discovery tool, but may also be attributable to limitations in modeling dynamic neural networks or difficulty in identifying the most affected neural subtype or developmental stage. SUMMARY Technological advances in differentiation protocols and organoid generation will enhance our ability to model the salient pathology underlying psychiatric disorders using iPSCs. The field will also benefit from context-driven interpretations of iPSC studies that recognize all potential sources of variability, including differences in patient symptomatology, genetic risk factors and affected cellular subtype.
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Affiliation(s)
- Stephanie J Temme
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Brady J Maher
- Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kimberly M Christian
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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