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Bhattacharya A, Parlanti P, Cavallo L, Farrow E, Spivey T, Renieri A, Mari F, Manzini MC. A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A. Hum Mol Genet 2024; 33:1229-1240. [PMID: 38652285 DOI: 10.1093/hmg/ddae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/07/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous with hundreds of identified risk genes, most affecting only a few patients. Novel missense variants in these genes are being discovered as clinical exome sequencing is now routinely integrated into diagnosis, yet most of them are annotated as variants of uncertain significance (VUS). VUSs are a major roadblock in using patient genetics to inform clinical action. We developed a framework to characterize VUSs in Coiled-coil and C2 domain containing 1A (CC2D1A), a gene causing autosomal recessive ID with comorbid ASD in 40% of cases. We analyzed seven VUSs (p.Pro319Leu, p.Ser327Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, p.Arg886His and p.Glu910Lys) from four cases of individuals with ID and ASD. Variants were cloned and overexpressed in HEK293 individually and in their respective heterozygous combination. CC2D1A is a signaling scaffold that positively regulates PKA-CREB signaling by repressing phosphodiesterase 4D (PDE4D) to prevent cAMP degradation. After testing multiple parameters including direct interaction between PDE4D and CC2D1A, cAMP levels and CREB activation, we found that the most sensitive readout was CREB transcriptional activity using a luciferase assay. Compared to WT CC2D1A, five VUSs (p.Pro319Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, and p.Arg886His) led to significantly blunted response to forskolin induced CREB activation. This luciferase assay approach can be scaled up to annotate ~150 CC2D1A VUSs that are currently listed in ClinVar. Since CREB activation is a common denominator for multiple ASD/ID genes, our paradigm can also be adapted for their VUSs.
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Affiliation(s)
- Aniket Bhattacharya
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Paola Parlanti
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Luca Cavallo
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Edward Farrow
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Tyler Spivey
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - M Chiara Manzini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
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2
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Vacharasin JM, Ward JA, McCord MM, Cox K, Imitola J, Lizarraga SB. Neuroimmune mechanisms in autism etiology - untangling a complex problem using human cellular models. OXFORD OPEN NEUROSCIENCE 2024; 3:kvae003. [PMID: 38665176 PMCID: PMC11044813 DOI: 10.1093/oons/kvae003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 04/28/2024]
Abstract
Autism spectrum disorder (ASD) affects 1 in 36 people and is more often diagnosed in males than in females. Core features of ASD are impaired social interactions, repetitive behaviors and deficits in verbal communication. ASD is a highly heterogeneous and heritable disorder, yet its underlying genetic causes account only for up to 80% of the cases. Hence, a subset of ASD cases could be influenced by environmental risk factors. Maternal immune activation (MIA) is a response to inflammation during pregnancy, which can lead to increased inflammatory signals to the fetus. Inflammatory signals can cross the placenta and blood brain barriers affecting fetal brain development. Epidemiological and animal studies suggest that MIA could contribute to ASD etiology. However, human mechanistic studies have been hindered by a lack of experimental systems that could replicate the impact of MIA during fetal development. Therefore, mechanisms altered by inflammation during human pre-natal brain development, and that could underlie ASD pathogenesis have been largely understudied. The advent of human cellular models with induced pluripotent stem cell (iPSC) and organoid technology is closing this gap in knowledge by providing both access to molecular manipulations and culturing capability of tissue that would be otherwise inaccessible. We present an overview of multiple levels of evidence from clinical, epidemiological, and cellular studies that provide a potential link between higher ASD risk and inflammation. More importantly, we discuss how stem cell-derived models may constitute an ideal experimental system to mechanistically interrogate the effect of inflammation during the early stages of brain development.
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Affiliation(s)
- Janay M Vacharasin
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
- Department of Biological Sciences, Francis Marion University, 4822 East Palmetto Street, Florence, S.C. 29506, USA
| | - Joseph A Ward
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute of Brain Science, Brown University, 70 Ship Street, Providence, RI 02903, USA
| | - Mikayla M McCord
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Kaitlin Cox
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Jaime Imitola
- Laboratory of Neural Stem Cells and Functional Neurogenetics, UConn Health, Departments of Neuroscience, Neurology, Genetics and Genome Sciences, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-5357, USA
| | - Sofia B Lizarraga
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute of Brain Science, Brown University, 70 Ship Street, Providence, RI 02903, USA
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3
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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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4
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Kitamura RA, Maxwell KG, Ye W, Kries K, Brown CM, Augsornworawat P, Hirsch Y, Johansson MM, Weiden T, Ekstein J, Cohen J, Klee J, Leslie K, Simeonov A, Henderson MJ, Millman JR, Urano F. Multidimensional analysis and therapeutic development using patient iPSC-derived disease models of Wolfram syndrome. JCI Insight 2022; 7:156549. [PMID: 36134655 PMCID: PMC9675478 DOI: 10.1172/jci.insight.156549] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Wolfram syndrome is a rare genetic disorder largely caused by pathogenic variants in the WFS1 gene and manifested by diabetes mellitus, optic nerve atrophy, and progressive neurodegeneration. Recent genetic and clinical findings have revealed Wolfram syndrome as a spectrum disorder. Therefore, a genotype-phenotype correlation analysis is needed for diagnosis and therapeutic development. Here, we focus on the WFS1 c.1672C>T, p.R558C variant, which is highly prevalent in the Ashkenazi Jewish population. Clinical investigation indicated that patients carrying the homozygous WFS1 c.1672C>T, p.R558C variant showed mild forms of Wolfram syndrome phenotypes. Expression of WFS1 p.R558C was more stable compared with the other known recessive pathogenic variants associated with Wolfram syndrome. Human induced pluripotent stem cell-derived (iPSC-derived) islets (SC-islets) homozygous for WFS1 c.1672C>T variant recapitulated genotype-related Wolfram syndrome phenotypes. Enhancing residual WFS1 function through a combination treatment of chemical chaperones mitigated detrimental effects caused by the WFS1 c.1672C>T, p.R558C variant and increased insulin secretion in SC-islets. Thus, the WFS1 c.1672C>T, p.R558C variant causes a mild form of Wolfram syndrome phenotypes, which can be remitted with a combination treatment of chemical chaperones. We demonstrate that our patient iPSC-derived disease model provides a valuable platform for further genotype-phenotype analysis and therapeutic development for Wolfram syndrome.
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Affiliation(s)
- Rie Asada Kitamura
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kristina G Maxwell
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wenjuan Ye
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Kelly Kries
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Cris M Brown
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Punn Augsornworawat
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, New York, USA
| | - Martin M Johansson
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, New York, USA
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Joseph Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, New York, USA
| | - Joshua Cohen
- Amylyx Pharmaceuticals Inc., Cambridge, Massachusetts, USA
| | - Justin Klee
- Amylyx Pharmaceuticals Inc., Cambridge, Massachusetts, USA
| | - Kent Leslie
- Amylyx Pharmaceuticals Inc., Cambridge, Massachusetts, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Jeffrey R Millman
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Fumihiko Urano
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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5
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Lewis EMA, Chapman G, Kaushik K, Determan J, Antony I, Meganathan K, Narasimhan M, Gontarz P, Zhang B, Kroll KL. Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2. Sci Rep 2022; 12:15636. [PMID: 36115870 PMCID: PMC9482661 DOI: 10.1038/s41598-022-19654-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in the chromodomain helicase DNA binding protein 2 (CHD2) gene are associated with neurodevelopmental disorders. However, mechanisms by which CHD2 regulates human brain development remain largely uncharacterized. Here, we used a human embryonic stem cell model of cortical interneuron (hcIN) development to elucidate its roles in this process. We identified genome-wide CHD2 binding profiles during hcIN differentiation, defining direct CHD2 targets related to neurogenesis in hcIN progenitors and to neuronal function in hcINs. CHD2 bound sites were frequently coenriched with histone H3 lysine 27 acetylation (H3K27ac) and associated with high gene expression, indicating roles for CHD2 in promoting gene expression during hcIN development. Binding sites for different classes of transcription factors were enriched at CHD2 bound regions during differentiation, suggesting transcription factors that may cooperatively regulate stage-specific gene expression with CHD2. We also demonstrated that CHD2 haploinsufficiency altered CHD2 and H3K27ac coenrichment on chromatin and expression of associated genes, decreasing acetylation and expression of cell cycle genes while increasing acetylation and expression of neuronal genes, to cause precocious differentiation. Together, these data describe CHD2 direct targets and mechanisms by which CHD2 prevents precocious hcIN differentiation, which are likely to be disrupted by pathogenic CHD2 mutation to cause neurodevelopmental disorders.
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Affiliation(s)
- E M A Lewis
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - G Chapman
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - K Kaushik
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - J Determan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - I Antony
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - K Meganathan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - M Narasimhan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - P Gontarz
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - B Zhang
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - K L Kroll
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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6
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Rao SR, Kostic A, Baillargeon P, Fernandez-Vega V, de Anda MR, Fletcher K, Shumate J, Scampavia L, Buxbaum JD, Spicer TP. Screening for modulators of autism spectrum disorder using induced human neurons. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:128-139. [PMID: 35123134 DOI: 10.1016/j.slasd.2022.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental disorder. There are no drugs to treat the core symptoms. De novo mutations often play an important role in ASD and multiple high-risk loci have been identified in the last decade. These mutations range from copy number variants to small insertion/deletion and single nucleotide variants. Large-scale exome sequencing has identified over 100 risk genes that are associated with ASD. Both etiological heterogeneity and unavailability of human neurons remain major hurdles in understanding the pathophysiology of ASD and testing of new drug candidates. Hence, the most achievable and relevant model to screen for potential drugs is human neurons from inducible pluripotent stem cells (iPSCs), including those from individuals with genetic mutations. In this study, we tested stem cells from individuals carrying mutations in ADNP, FOXP1 or SHANK3. They were scaled and reprogrammed to glutamatergic neurons and assessed for the effects of their specific mutations on neurite outgrowth. High Content Analysis allowed us to observe phenotypic differences between ASD neurons compared to controls, in terms of neuron number, neurite number and neurite length per neuron. Further, neurons were derived from both patient derived and genetically modified iPSCs with DDX3X mutation which were tested against 5088 drug like compounds. We assessed individual compound effects on the induced neurons to determine if they elicited changes that would indicate neurite growth (neuroprotection) or, alternatively, reduce outgrowth and hence appear neurotoxic. This report includes all methods, phenotypic outcomes, and results for the largest ASD small molecule screening effort done to date.
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Affiliation(s)
- Sumitha Rajendra Rao
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Ana Kostic
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Pierre Baillargeon
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Virneliz Fernandez-Vega
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Mitzy Rios de Anda
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Kelty Fletcher
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Justin Shumate
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Louis Scampavia
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Timothy P Spicer
- The Scripps Research Molecular Screening Center, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
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7
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Neural Transcriptomic Analysis of Sex Differences in Autism Spectrum Disorder: Current Insights and Future Directions. Biol Psychiatry 2022; 91:53-60. [PMID: 33551190 DOI: 10.1016/j.biopsych.2020.11.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/18/2022]
Abstract
Autism spectrum disorder (ASD) is consistently diagnosed 3 to 5 times more frequently in males than females, a dramatically sex-biased prevalence that suggests the involvement of sex-differential biological factors in modulating risk. The genomic scale of transcriptomic analyses of human brain tissue can provide an unbiased approach for identifying genes and associated functional processes at the intersection of sex-differential and ASD-impacted neurobiology. Several studies characterizing gene expression changes in the ASD brain have been published in recent years with increasing sample size and cellular resolution. These studies report several convergent patterns across data sets and genetically heterogeneous samples in the ASD brain, including elevated expression of gene sets associated with glial and immune function, and reduced expression of gene sets associated with neuronal and synaptic functions. Assessment of neurotypical cortex tissue has reported parallel patterns by sex, with male-elevated expression of overlapping sets of glial/immune-related genes and female-biased expression of neuron-associated genes, suggesting potential roles for these cell types in sex-differential ASD risk mechanisms. However, validating and further exploring these mechanisms is challenged by the available data, as existing studies of ASD brain include a limited number of female ASD donors and focus predominantly on cortex regions not known to show pronounced sex-differential morphology or function. With this review, we summarize convergent findings from several landmark studies of the transcriptome in ASD brain and their relationship to sex-differential gene expression, and we discuss limitations and remaining questions regarding transcriptomic analysis of sex differences in ASD.
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8
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Vasic V, Jones MSO, Haslinger D, Knaus LS, Schmeisser MJ, Novarino G, Chiocchetti AG. Translating the Role of mTOR- and RAS-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment. Genes (Basel) 2021; 12:genes12111746. [PMID: 34828352 PMCID: PMC8624393 DOI: 10.3390/genes12111746] [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: 09/29/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/23/2022] Open
Abstract
Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems.
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Affiliation(s)
- Verica Vasic
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany; (V.V.); (M.J.S.)
| | - Mattson S. O. Jones
- Autism Therapy and Research Center of Excellence, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, 60528 Frankfurt am Main, Germany; (M.S.O.J.); (D.H.)
- Center for Personalized Translational Epilepsy Research (CePTER), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
| | - Denise Haslinger
- Autism Therapy and Research Center of Excellence, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, 60528 Frankfurt am Main, Germany; (M.S.O.J.); (D.H.)
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria; (L.S.K.); (G.N.)
| | - Lisa S. Knaus
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria; (L.S.K.); (G.N.)
| | - Michael J. Schmeisser
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany; (V.V.); (M.J.S.)
- Focus Program Translational Neurosciences (FTN), University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Gaia Novarino
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria; (L.S.K.); (G.N.)
| | - Andreas G. Chiocchetti
- Autism Therapy and Research Center of Excellence, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, 60528 Frankfurt am Main, Germany; (M.S.O.J.); (D.H.)
- Center for Personalized Translational Epilepsy Research (CePTER), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-69-6301-80658
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9
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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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10
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Zhang S, Zhang X, Purmann C, Ma S, Shrestha A, Davis KN, Ho M, Huang Y, Pattni R, Hung Wong W, Bernstein JA, Hallmayer J, Urban AE. Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons. Biol Psychiatry 2021; 89:497-509. [PMID: 32919612 PMCID: PMC9359316 DOI: 10.1016/j.biopsych.2020.06.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The 15q13.3 microdeletion is associated with several neuropsychiatric disorders, including autism and schizophrenia. Previous association and functional studies have investigated the potential role of several genes within the deletion in neuronal dysfunction, but the molecular effects of the deletion as a whole remain largely unknown. METHODS Induced pluripotent stem cells, from 3 patients with the 15q13.3 microdeletion and 3 control subjects, were generated and converted into induced neurons. We analyzed the effects of the 15q13.3 microdeletion on genome-wide gene expression, DNA methylation, chromatin accessibility, and sensitivity to cisplatin-induced DNA damage. Furthermore, we measured gene expression changes in induced neurons with CRISPR (clustered regularly interspaced short palindromic repeats) knockouts of individual 15q13.3 microdeletion genes. RESULTS In both induced pluripotent stem cells and induced neurons, gene copy number change within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression and no compensatory changes in DNA methylation or chromatin accessibility, supporting the model that haploinsufficiency of genes within the deleted region drives the disorder. Furthermore, we observed global effects of the microdeletion on the transcriptome and epigenome, with disruptions in several neuropsychiatric disorder-associated pathways and gene families, including Wnt signaling, ribosome function, DNA binding, and clustered protocadherins. Individual gene knockouts mirrored many of the observed changes in an overlapping fashion between knockouts. CONCLUSIONS Our multiomics analysis of the 15q13.3 microdeletion revealed downstream effects in pathways previously associated with neuropsychiatric disorders and indications of interactions between genes within the deletion. This molecular systems analysis can be applied to other chromosomal aberrations to further our etiological understanding of neuropsychiatric disorders.
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Affiliation(s)
- Siming Zhang
- Department of Genetics, School of Humanities and Science, Stanford University, Stanford, California
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Shining Ma
- Department of Pediatrics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Anima Shrestha
- School of Medicine, Stanford University, and Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Kasey N Davis
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Yiling Huang
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Wing Hung Wong
- Department of Pediatrics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Jonathan A Bernstein
- Department of Human Biology, School of Humanities and Science, Stanford University, Stanford, California
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Alexander E Urban
- Department of Genetics, School of Humanities and Science, Stanford University, Stanford, California; Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California.
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11
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Pintacuda G, Martín JM, Eggan KC. Mind the translational gap: using iPS cell models to bridge from genetic discoveries to perturbed pathways and therapeutic targets. Mol Autism 2021; 12:10. [PMID: 33557935 PMCID: PMC7869517 DOI: 10.1186/s13229-021-00417-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a group of neurodevelopmental disorders characterized by impaired social interactions as well as the presentation of restrictive and repetitive behaviors. ASD is highly heritable but genetically heterogenous with both common and rare genetic variants collaborating to predispose individuals to the disorder. In this review, we synthesize recent efforts to develop human induced pluripotent stem cell (iPSC)-derived models of ASD-related phenotypes. We firstly address concerns regarding the relevance and validity of available neuronal iPSC-derived models. We then critically evaluate the robustness of various differentiation and cell culture protocols used for producing cell types of relevance to ASD. By exploring iPSC models of ASD reported thus far, we examine to what extent cellular and neuronal phenotypes with potential relevance to ASD can be linked to genetic variants found to underlie it. Lastly, we outline promising strategies by which iPSC technology can both enhance the power of genetic studies to identify ASD risk factors and nominate pathways that are disrupted across groups of ASD patients that might serve as common points for therapeutic intervention.
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Affiliation(s)
- Greta Pintacuda
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Jacqueline M Martín
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin C Eggan
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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12
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Hathy E, Szabó E, Varga N, Erdei Z, Tordai C, Czehlár B, Baradits M, Jezsó B, Koller J, Nagy L, Molnár MJ, Homolya L, Nemoda Z, Apáti Á, Réthelyi JM. Investigation of de novo mutations in a schizophrenia case-parent trio by induced pluripotent stem cell-based in vitro disease modeling: convergence of schizophrenia- and autism-related cellular phenotypes. Stem Cell Res Ther 2020; 11:504. [PMID: 33246498 PMCID: PMC7694414 DOI: 10.1186/s13287-020-01980-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/18/2020] [Indexed: 12/30/2022] Open
Abstract
Background De novo mutations (DNMs) have been implicated in the etiology of schizophrenia (SZ), a chronic debilitating psychiatric disorder characterized by hallucinations, delusions, cognitive dysfunction, and decreased community functioning. Several DNMs have been identified by examining SZ cases and their unaffected parents; however, in most cases, the biological significance of these mutations remains elusive. To overcome this limitation, we have developed an approach of using induced pluripotent stem cell (iPSC) lines from each member of a SZ case-parent trio, in order to investigate the effects of DNMs in cellular progenies of interest, particularly in dentate gyrus neuronal progenitors. Methods We identified a male SZ patient characterized by early disease onset and negative symptoms, who is a carrier of 3 non-synonymous DNMs in genes LRRC7, KHSRP, and KIR2DL1. iPSC lines were generated from his and his parents’ peripheral blood mononuclear cells using Sendai virus-based reprogramming and differentiated into neuronal progenitor cells (NPCs) and hippocampal dentate gyrus granule cells. We used RNASeq to explore transcriptomic differences and calcium (Ca2+) imaging, cell proliferation, migration, oxidative stress, and mitochondrial assays to characterize the investigated NPC lines. Results NPCs derived from the SZ patient exhibited transcriptomic differences related to Wnt signaling, neuronal differentiation, axonal guidance and synaptic function, and decreased Ca2+ reactivity to glutamate. Moreover, we could observe increased cellular proliferation and alterations in mitochondrial quantity and morphology. Conclusions The approach of reprograming case-parent trios represents an opportunity for investigating the molecular effects of disease-causing mutations and comparing these in cell lines with reduced variation in genetic background. Our results are indicative of a partial overlap between schizophrenia and autism-related phenotypes in the investigated family. Limitations Our study investigated only one family; therefore, the generalizability of findings is limited. We could not derive iPSCs from two other siblings to test for possible genetic effects in the family that are not driven by DNMs. The transcriptomic and functional assays were limited to the NPC stage, although these variables should also be investigated at the mature neuronal stage.
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Affiliation(s)
- Edit Hathy
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Eszter Szabó
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Nóra Varga
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Zsuzsa Erdei
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Csongor Tordai
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Boróka Czehlár
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Máté Baradits
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Bálint Jezsó
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Júlia Koller
- Institute of Rare Disorders and Genomic Medicine, Semmelweis University, Budapest, Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Mária Judit Molnár
- Institute of Rare Disorders and Genomic Medicine, Semmelweis University, Budapest, Hungary
| | - László Homolya
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary
| | - Zsófia Nemoda
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Ágota Apáti
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Center for Natural Sciences, 1117 Magyar tudósok körútja 2, Budapest, Hungary.
| | - János M Réthelyi
- National Brain Research Project (NAP) Molecular Psychiatry Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary. .,Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa utca 6, Budapest, 1083, Hungary.
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13
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Gordon A, Geschwind DH. Human in vitro models for understanding mechanisms of autism spectrum disorder. Mol Autism 2020; 11:26. [PMID: 32299488 PMCID: PMC7164291 DOI: 10.1186/s13229-020-00332-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
Early brain development is a critical epoch for the development of autism spectrum disorder (ASD). In vivo animal models have, until recently, been the principal tool used to study early brain development and the changes occurring in neurodevelopmental disorders such as ASD. In vitro models of brain development represent a significant advance in the field. Here, we review the main methods available to study human brain development in vitro and the applications of these models for studying ASD and other psychiatric disorders. We discuss the main findings from stem cell models to date focusing on cell cycle and proliferation, cell death, cell differentiation and maturation, and neuronal signaling and synaptic stimuli. To be able to generalize the results from these studies, we propose a framework of experimental design and power considerations for using in vitro models to study ASD. These include both technical issues such as reproducibility and power analysis and conceptual issues such as the brain region and cell types being modeled.
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Affiliation(s)
- Aaron Gordon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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