201
|
Xie Y, Zhang X, Liu F, Qin W, Fu J, Xue K, Yu C. Brain mRNA Expression Associated with Cortical Volume Alterations in Autism Spectrum Disorder. Cell Rep 2021; 32:108137. [PMID: 32937121 DOI: 10.1016/j.celrep.2020.108137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/23/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022] Open
Abstract
Numerous studies report abnormal cerebral cortex volume (CCV) in autism spectrum disorder (ASD); however, genes related to CCV abnormalities in ASD remain largely unknown. Here, we identify genes associated with CCV alterations in ASD by performing spatial correlations between the gene expression of 6 donated brains and neuroimaging data from 1,404 ASD patients and 1,499 controls. Based on spatial correlations between gene expression and CCV differences from two independent meta-analyses and between gene expression and individual CCV distributions of 404 patients and 496 controls, we identify 417 genes associated with both CCV differences and individual CCV distributions. These genes are enriched for genetic association signals and genes downregulated in the ASD post-mortem brain. The expression patterns of these genes are correlated with brain activation patterns of language-related neural processes frequently impaired in ASD. These findings highlight a model whereby genetic risk impacts gene expression (downregulated), which leads to CCV alterations in ASD.
Collapse
Affiliation(s)
- Yingying Xie
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, 300052 Tianjin, China
| | - Xue Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, 300052 Tianjin, China
| | - Feng Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, 300052 Tianjin, China
| | - Wen Qin
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, 300052 Tianjin, China
| | - Jilian Fu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, 300052 Tianjin, China
| | - Kaizhong Xue
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, 300052 Tianjin, China
| | - Chunshui Yu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, 300052 Tianjin, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, P.R. China.
| |
Collapse
|
202
|
Griesi-Oliveira K, Fogo MS, Pinto BGG, Alves AY, Suzuki AM, Morales AG, Ezquina S, Sosa OJ, Sutton GJ, Sunaga-Franze DY, Bueno AP, Seabra G, Sardinha L, Costa SS, Rosenberg C, Zachi EC, Sertie AL, Martins-de-Souza D, Reis EM, Voineagu I, Passos-Bueno MR. Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder. Mol Psychiatry 2021; 26:1589-1605. [PMID: 32060413 PMCID: PMC8159745 DOI: 10.1038/s41380-020-0669-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/11/2019] [Accepted: 01/28/2020] [Indexed: 01/02/2023]
Abstract
Evaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question, but larger cohorts and different ASD endophenotypes still need to be investigated. Moreover, whether changes seen in this in vitro model reflect previous findings in ASD postmortem brains and how consistent they are across the studies remain underexplored questions. We examined the transcriptome of iPSC-derived neuronal cells from a normocephalic ASD cohort composed mostly of high-functioning individuals and from non-ASD individuals. ASD patients presented expression dysregulation of a module of co-expressed genes involved in protein synthesis in neuronal progenitor cells (NPC), and a module of genes related to synapse/neurotransmission and a module related to translation in neurons. Proteomic analysis in NPC revealed potential molecular links between the modules dysregulated in NPC and in neurons. Remarkably, the comparison of our results to a series of transcriptome studies revealed that the module related to synapse has been consistently found as upregulated in iPSC-derived neurons-which has an expression profile more closely related to fetal brain-while downregulated in postmortem brain tissue, indicating a reliable association of this network to the disease and suggesting that its dysregulation might occur in different directions across development in ASD individuals. Therefore, the expression pattern of this network might be used as biomarker for ASD and should be experimentally explored as a therapeutic target.
Collapse
Affiliation(s)
- K Griesi-Oliveira
- Hospital Israelita Albert Einstein, São Paulo, Brazil.
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - M S Fogo
- Hospital Israelita Albert Einstein, São Paulo, Brazil
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - B G G Pinto
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - A Y Alves
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - A M Suzuki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - A G Morales
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - S Ezquina
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - O J Sosa
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - G J Sutton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - D Y Sunaga-Franze
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - A P Bueno
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - G Seabra
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - L Sardinha
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - S S Costa
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - C Rosenberg
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - E C Zachi
- Núcleo de Neurociências e Comportamento, Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil
| | - A L Sertie
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - D Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), São Paulo, Brazil
- Experimental Medicine Research Cluster (EMC), University of Campinas, Campinas, Brazil
| | - E M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - I Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - M R Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| |
Collapse
|
203
|
Mehta SQ, Behl S, Day PL, Delgado AM, Larson NB, Stromback LR, Huebner AR, DeGrado TR, Davis JM, Jannetto PJ, Howie F, Pandey MK. Evaluation of Zn, Cu, and Se Levels in the North American Autism Spectrum Disorder Population. Front Mol Neurosci 2021; 14:665686. [PMID: 33994944 PMCID: PMC8116541 DOI: 10.3389/fnmol.2021.665686] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Metal ion dyshomeostasis and disparate levels of biometals like zinc (Zn), copper (Cu), and selenium (Se) have been implicated as a potential causative factor for Autism Spectrum Disorder (ASD). In this study, we have enrolled 129 children (aged 2–4 years) in North America, of which 64 children had a diagnosis of ASD and 65 were controls. Hair, nail, and blood samples were collected and quantitatively analyzed for Zn, Cu and Se using inductively coupled plasma mass spectrometry (ICP-MS). Of the analyzed biometals, serum Se (116.83 ± 14.84 ng/mL) was found to be significantly lower in male ASD cases compared to male healthy controls (128.21 ± 9.11 ng/mL; p < 0.005). A similar trend was found for nail Se levels in ASD (1.01 ± 0.15 mcg/g) versus that of controls (1.11 ± 0.17 mcg/g) with a p-value of 0.0132 using a stratified Wilcoxon rank sum testing. The level of Se in ASD cohort was co-analyzed for psychometric correlation and found a negative correlation between total ADOS score and serum Se levels. However, we did not observe any significant difference in Zn, Cu, and Zn/Cu ratio in ASD cases versus controls in this cohort of North American children. Further studies are recommended to better understand the biology of the relationship between Se and ASD status.
Collapse
Affiliation(s)
- Sunil Q Mehta
- Division of Developmental and Behavioral Pediatrics, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Supriya Behl
- Children's Research Center, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Patrick L Day
- Metals Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Adriana M Delgado
- Children's Research Center, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Nicholas B Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Lindsay R Stromback
- Children's Research Center, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Andrea R Huebner
- Division of Developmental and Behavioral Pediatrics, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Timothy R DeGrado
- Divisions of Nuclear Medicine and Research, Department of Radiology, Mayo Clinic, Rochester, MN, United States
| | - Jessica M Davis
- Division of Community Pediatric and Adolescent Medicine, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Paul J Jannetto
- Metals Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Flora Howie
- Division of Developmental and Behavioral Pediatrics, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, United States
| | - Mukesh K Pandey
- Divisions of Nuclear Medicine and Research, Department of Radiology, Mayo Clinic, Rochester, MN, United States
| |
Collapse
|
204
|
Cederquist GY, Tchieu J, Callahan SJ, Ramnarine K, Ryan S, Zhang C, Rittenhouse C, Zeltner N, Chung SY, Zhou T, Chen S, Betel D, White RM, Tomishima M, Studer L. A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes. Cell Stem Cell 2021; 27:35-49.e6. [PMID: 32619517 DOI: 10.1016/j.stem.2020.06.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 01/12/2023]
Abstract
Autism is a clinically heterogeneous neurodevelopmental disorder characterized by impaired social interactions, restricted interests, and repetitive behaviors. Despite significant advances in the genetics of autism, understanding how genetic changes perturb brain development and affect clinical symptoms remains elusive. Here, we present a multiplex human pluripotent stem cell (hPSC) platform, in which 30 isogenic disease lines are pooled in a single dish and differentiated into prefrontal cortex (PFC) lineages to efficiently test early-developmental hypotheses of autism. We define subgroups of autism mutations that perturb PFC neurogenesis and are correlated to abnormal WNT/βcatenin responses. Class 1 mutations (8 of 27) inhibit while class 2 mutations (5 of 27) enhance PFC neurogenesis. Remarkably, autism patient data reveal that individuals carrying subclass-specific mutations differ clinically in their corresponding language acquisition profiles. Our study provides a framework to disentangle genetic heterogeneity associated with autism and points toward converging molecular and developmental pathways of diverse autism-associated mutations.
Collapse
Affiliation(s)
- Gustav Y Cederquist
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Jason Tchieu
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Scott J Callahan
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Cancer Genetics and Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Gerstner Graduate School of Biomedical Sciences, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Kiran Ramnarine
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Sean Ryan
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chelsea Rittenhouse
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Nadja Zeltner
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Center for Molecular Medicine, Department of Cellular Biology, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sun Young Chung
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Ting Zhou
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Doron Betel
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Richard M White
- Cancer Genetics and Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Mark Tomishima
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA.
| |
Collapse
|
205
|
Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun 2021; 12:2277. [PMID: 33859189 PMCID: PMC8050063 DOI: 10.1038/s41467-021-22266-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/28/2021] [Indexed: 12/19/2022] Open
Abstract
Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We reveal key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrates that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a is associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease implicates critical cell types, developmental stages, genes, and regulatory mechanisms. The single cell multi-omics atlas reveals key chromatin remodeling events and gene expression dynamics associated with kidney development.
Collapse
Affiliation(s)
- Zhen Miao
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ziyuan Ma
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rojesh Shrestha
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tamas Aranyi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy Kwan
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayano Kondo
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Marco Pontoglio
- Epigenetics and Development Laboratory, Université de Paris Inserm U1151/CNRS UMR 8253, Institut Necker Enfants Malades, Paris, France
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mingyao Li
- Department of Epidemiology and Biostatistics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
206
|
Darki F, Nyström P, McAlonan G, Bölte S, Falck-Ytter T. T1-Weighted/T2-Weighted Ratio Mapping at 5 Months Captures Individual Differences in Behavioral Development and Differentiates Infants at Familial Risk for Autism from Controls. Cereb Cortex 2021; 31:4068-4077. [PMID: 33825851 PMCID: PMC8328213 DOI: 10.1093/cercor/bhab069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
Identifying structural measures that capture early brain development and are sensitive to individual differences in behavior is a priority in developmental neuroscience, with potential implications for our understanding of both typical and atypical populations. T1-weighted/T2-weighted (T1w/T2w) ratio mapping, which previously has been linked to myelination, represents an interesting candidate measure in this respect, as an accessible measure from standard magnetic resonance imaging (MRI) sequences. Yet, its value as an early infancy measure remains largely unexplored. Here, we compared T1w/T2w ratio in 5-month-old infants at familial risk (n = 27) for autism spectrum disorder (ASD) to those without elevated autism risk (n = 16). We found lower T1w/T2w ratio in infants at high risk for ASD within widely distributed regions, spanning both white and gray matter. In regions differing between groups, higher T1w/T2w ratio was robustly associated with higher age at scan (range: ~ 4–6.5 months), implying sensitivity to maturation at short developmental timescales. Further, higher T1w/T2w ratio within these regions was associated with higher scores on measures of concurrent developmental level. These findings suggest that T1w/T2w ratio is a developmentally sensitive measure that should be explored further in future studies of both typical and atypical infant populations.
Collapse
Affiliation(s)
- Fahimeh Darki
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Stockholm Health Care Services, Region Stockholm, SE-11330 Stockholm, Sweden.,Department of Psychology, Uppsala University, SE 75142 Uppsala, Sweden
| | - Pär Nyström
- Department of Psychology, Uppsala University, SE 75142 Uppsala, Sweden
| | - Grainne McAlonan
- The Sackler Institute and Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, South London and Maudsley NHS Foundation Trust, WC2R 2LS UK
| | - Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Stockholm Health Care Services, Region Stockholm, SE-11330 Stockholm, Sweden.,Child and Adolescent Psychiatry, Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.,Curtin Autism Research Group, School of Occupational Therapy, Social Work and Speech Pathology, Curtin University, WA 6102 Perth, Western Australia
| | - Terje Falck-Ytter
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet & Stockholm Health Care Services, Region Stockholm, SE-11330 Stockholm, Sweden.,Department of Psychology, Uppsala University, SE 75142 Uppsala, Sweden.,The Swedish Collegium for Advanced Study (SCAS), SE-752 38 Uppsala, Sweden
| |
Collapse
|
207
|
Bhat SA, Yousuf A, Mushtaq Z, Kumar V, Qurashi A. Fragile X Premutation rCGG Repeats Impair Synaptic Growth and Synaptic Transmission at Drosophila larval Neuromuscular Junction. Hum Mol Genet 2021; 30:1677-1692. [PMID: 33772546 DOI: 10.1093/hmg/ddab087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 11/14/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disease that develops in some premutation (PM) carriers of the FMR1 gene with alleles bearing 55-200 CGG repeats. The discovery of a broad spectrum of clinical and cell developmental abnormalities among PM carriers with or without FXTAS and in model systems suggests that neurodegeneration seen in FXTAS could be the inevitable end-result of pathophysiological processes set during early development. Hence, it is imperative to trace early PM-induced pathological abnormalities. Previous studies have shown that transgenic Drosophila carrying PM-length CGG repeats are sufficient to cause neurodegeneration. Here, we used the same transgenic model to understand the effect of CGG repeats on the structure and function of the developing nervous system. We show that presynaptic expression of CGG repeats restricts synaptic growth, reduces the number of synaptic boutons, leads to aberrant presynaptic varicosities, and impairs synaptic transmission at the larval neuromuscular junctions. The postsynaptic analysis shows that both glutamate receptors and subsynaptic reticulum proteins were normal. However, a high percentage of boutons show a reduced density of Bruchpilot protein, a key component of presynaptic active zones required for vesicle release. The electrophysiological analysis shows a significant reduction in quantal content, a measure of total synaptic vesicles released per excitation potential. Together, these findings suggest that synapse perturbation caused by rCGG repeats mediates presynaptically during larval NMJ development. We also suggest that the stress-activated c-Jun N-terminal kinase protein Basket and CIDE-N protein Drep-2 positively mediate Bruchpilot active zone defects caused by rCGG repeats.
Collapse
Affiliation(s)
- Sajad A Bhat
- Department of Biotechnology, University of Kashmir, Srinagar, JK, 190006, India
| | - Aadil Yousuf
- Department of Biotechnology, University of Kashmir, Srinagar, JK, 190006, India
| | - Zeeshan Mushtaq
- Laboratory of Neurogenetics, IISER-Bhopal, Bhopal, MP, 462066, India
| | - Vimlesh Kumar
- Laboratory of Neurogenetics, IISER-Bhopal, Bhopal, MP, 462066, India
| | - Abrar Qurashi
- Department of Biotechnology, University of Kashmir, Srinagar, JK, 190006, India
| |
Collapse
|
208
|
Hoffmann A, Spengler D. Single-Cell Transcriptomics Supports a Role of CHD8 in Autism. Int J Mol Sci 2021; 22:3261. [PMID: 33806835 PMCID: PMC8004931 DOI: 10.3390/ijms22063261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/16/2022] Open
Abstract
Chromodomain helicase domain 8 (CHD8) is one of the most frequently mutated and most penetrant genes in the autism spectrum disorder (ASD). Individuals with CHD8 mutations show leading symptoms of autism, macrocephaly, and facial dysmorphisms. The molecular and cellular mechanisms underpinning the early onset and development of these symptoms are still poorly understood and prevent timely and more efficient therapies of patients. Progress in this area will require an understanding of "when, why and how cells deviate from their normal trajectories". High-throughput single-cell RNA sequencing (sc-RNAseq) directly quantifies information-bearing RNA molecules that enact each cell's biological identity. Here, we discuss recent insights from sc-RNAseq of CRISPR/Cas9-editing of Chd8/CHD8 during mouse neocorticogenesis and human cerebral organoids. Given that the deregulation of the balance between excitation and inhibition (E/I balance) in cortical and subcortical circuits is thought to represent a major etiopathogenetic mechanism in ASD, we focus on the question of whether, and to what degree, results from current sc-RNAseq studies support this hypothesis. Beyond that, we discuss the pros and cons of these approaches and further steps to be taken to harvest the full potential of these transformative techniques.
Collapse
Affiliation(s)
| | - Dietmar Spengler
- Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany;
| |
Collapse
|
209
|
Comorbidities associated with genetic abnormalities in children with intellectual disability. Sci Rep 2021; 11:6563. [PMID: 33753861 PMCID: PMC7985145 DOI: 10.1038/s41598-021-86131-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/02/2021] [Indexed: 12/03/2022] Open
Abstract
Intellectual disability (ID) has emerged as the commonest manifestation of underlying genomic abnormalities. Given that molecular genetic tests for diagnosis of ID usually require high costs and yield relatively low diagnostic rates, identification of additional phenotypes or comorbidities may increase the genetic diagnostic yield and are valuable clues for pediatricians in general practice. Here, we enrolled consecutively 61 children with unexplained moderate or severe ID and performed chromosomal microarray (CMA) and sequential whole-exome sequencing (WES) analysis on them. We identified 13 copy number variants in 12 probands and 24 variants in 25 probands, and the total diagnostic rate was 60.7%. The genetic abnormalities were commonly found in ID patients with movement disorder (100%) or with autistic spectrum disorder (ASD) (93.3%). Univariate analysis showed that ASD was the significant risk factor of genetic abnormality (P = 0.003; OR 14, 95% CI 1.7–115.4). At least 14 ID-ASD associated genes were identified, and the majority of ID-ASD associated genes (85.7%) were found to be expressed in the cerebellum based on database analysis. In conclusion, genetic testing on ID children, particularly in those with ASD is highly recommended. ID and ASD may share common cerebellar pathophysiology.
Collapse
|
210
|
Lichtman D, Bergmann E, Kavushansky A, Cohen N, Levy NS, Levy AP, Kahn I. Structural and functional brain-wide alterations in A350V Iqsec2 mutant mice displaying autistic-like behavior. Transl Psychiatry 2021; 11:181. [PMID: 33753721 PMCID: PMC7985214 DOI: 10.1038/s41398-021-01289-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/21/2022] Open
Abstract
IQSEC2 is an X-linked gene that is associated with autism spectrum disorder (ASD), intellectual disability, and epilepsy. IQSEC2 is a postsynaptic density protein, localized on excitatory synapses as part of the NMDA receptor complex and is suggested to play a role in AMPA receptor trafficking and mediation of long-term depression. Here, we present brain-wide structural volumetric and functional connectivity characterization in a novel mouse model with a missense mutation in the IQ domain of IQSEC2 (A350V). Using high-resolution structural and functional MRI, we show that animals with the A350V mutation display increased whole-brain volume which was further found to be specific to the cerebral cortex and hippocampus. Moreover, using a data-driven approach we identify putative alterations in structure-function relations of the frontal, auditory, and visual networks in A350V mice. Examination of these alterations revealed an increase in functional connectivity between the anterior cingulate cortex and the dorsomedial striatum. We also show that corticostriatal functional connectivity is correlated with individual variability in social behavior only in A350V mice, as assessed using the three-chamber social preference test. Our results at the systems-level bridge the impact of previously reported changes in AMPA receptor trafficking to network-level disruption and impaired social behavior. Further, the A350V mouse model recapitulates similarly reported brain-wide changes in other ASD mouse models, with substantially different cellular-level pathologies that nonetheless result in similar brain-wide alterations, suggesting that novel therapeutic approaches in ASD that result in systems-level rescue will be relevant to IQSEC2 mutations.
Collapse
Affiliation(s)
- Daniela Lichtman
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Eyal Bergmann
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Alexandra Kavushansky
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Nadav Cohen
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Nina S Levy
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Andrew P Levy
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel.
| | - Itamar Kahn
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel.
| |
Collapse
|
211
|
Radio FC, Pang K, Ciolfi A, Levy MA, Hernández-García A, Pedace L, Pantaleoni F, Liu Z, de Boer E, Jackson A, Bruselles A, McConkey H, Stellacci E, Lo Cicero S, Motta M, Carrozzo R, Dentici ML, McWalter K, Desai M, Monaghan KG, Telegrafi A, Philippe C, Vitobello A, Au M, Grand K, Sanchez-Lara PA, Baez J, Lindstrom K, Kulch P, Sebastian J, Madan-Khetarpal S, Roadhouse C, MacKenzie JJ, Monteleone B, Saunders CJ, Jean Cuevas JK, Cross L, Zhou D, Hartley T, Sawyer SL, Monteiro FP, Secches TV, Kok F, Schultz-Rogers LE, Macke EL, Morava E, Klee EW, Kemppainen J, Iascone M, Selicorni A, Tenconi R, Amor DJ, Pais L, Gallacher L, Turnpenny PD, Stals K, Ellard S, Cabet S, Lesca G, Pascal J, Steindl K, Ravid S, Weiss K, Castle AMR, Carter MT, Kalsner L, de Vries BBA, van Bon BW, Wevers MR, Pfundt R, Stegmann APA, Kerr B, Kingston HM, Chandler KE, Sheehan W, Elias AF, Shinde DN, Towne MC, Robin NH, Goodloe D, Vanderver A, Sherbini O, Bluske K, Hagelstrom RT, Zanus C, Faletra F, Musante L, Kurtz-Nelson EC, Earl RK, Anderlid BM, Morin G, van Slegtenhorst M, Diderich KEM, Brooks AS, Gribnau J, Boers RG, Finestra TR, Carter LB, Rauch A, Gasparini P, Boycott KM, Barakat TS, Graham JM, Faivre L, Banka S, Wang T, Eichler EE, Priolo M, Dallapiccola B, Vissers LELM, Sadikovic B, Scott DA, Holder JL, Tartaglia M. SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females. Am J Hum Genet 2021; 108:502-516. [PMID: 33596411 PMCID: PMC8008487 DOI: 10.1016/j.ajhg.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.
Collapse
Affiliation(s)
| | - Kaifang Pang
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ciolfi
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Andrés Hernández-García
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lucia Pedace
- Oncohaematology Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Zhandong Liu
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Adam Jackson
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Emilia Stellacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marialetizia Motta
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Rosalba Carrozzo
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | | | | | - Christophe Philippe
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Joanne Baez
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | | | - Peggy Kulch
- Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - Jessica Sebastian
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Suneeta Madan-Khetarpal
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | | | | | - Berrin Monteleone
- Clinical genetics, NYU Langone Long Island School of Medicine, Mineola, NY 11501, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - July K Jean Cuevas
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Laura Cross
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Sarah L Sawyer
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | | | | | - Fernando Kok
- Mendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil
| | | | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Eva Morava
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | - Romano Tenconi
- Dipartimento di Pediatria, Università di Padova, 35137 Padua, Italy
| | - David J Amor
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Lynn Pais
- Medical and Populations Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | | | - Karen Stals
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sian Ellard
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sara Cabet
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Gaetan Lesca
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Joset Pascal
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Sarit Ravid
- Pediatric Neurology Unit, Ruth Children's Hospital, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa 3109601, Israel
| | - Alison M R Castle
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Melissa T Carter
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Louisa Kalsner
- Connecticut Children's Medical Center, University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marijke R Wevers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, 6229 HX Maastricht, the Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Helen M Kingston
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Willow Sheehan
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | | | | | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dana Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Omar Sherbini
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Krista Bluske
- Illumina Clinical Services Laboratory, San Diego, CA 92122, USA
| | | | - Caterina Zanus
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | | | - Rachel K Earl
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Gilles Morin
- CA de Génétique Clinique & Oncogénétique, CHU Amiens-Picardie, 80054 Amiens, France
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Teresa Robert Finestra
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Lauren B Carter
- Department of Pediatrics, Division of Medical Genetics, Levine Children's Hospital Atrium Health, Charlotte, NC 28203, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy; Department of Medicine, Surgery & Health Science, University of Trieste, 34143 Trieste, Italy
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Laurence Faivre
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD et Institut GIMI, 77908 Dijon, France; UMR 1231 GAD, Inserm - Université Bourgogne-Franche Comté, 77908 Dijon, France
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Manuela Priolo
- UOSD Genetica Medica del Grande Ospedale Metropolitano "Bianchi Melacrino Morelli" di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jimmy Lloyd Holder
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
| |
Collapse
|
212
|
Disruption of RFX family transcription factors causes autism, attention-deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior. Genet Med 2021; 23:1028-1040. [PMID: 33658631 DOI: 10.1038/s41436-021-01114-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/30/2022] Open
Abstract
PURPOSE We describe a novel neurobehavioral phenotype of autism spectrum disorder (ASD), intellectual disability, and/or attention-deficit/hyperactivity disorder (ADHD) associated with de novo or inherited deleterious variants in members of the RFX family of genes. RFX genes are evolutionarily conserved transcription factors that act as master regulators of central nervous system development and ciliogenesis. METHODS We assembled a cohort of 38 individuals (from 33 unrelated families) with de novo variants in RFX3, RFX4, and RFX7. We describe their common clinical phenotypes and present bioinformatic analyses of expression patterns and downstream targets of these genes as they relate to other neurodevelopmental risk genes. RESULTS These individuals share neurobehavioral features including ASD, intellectual disability, and/or ADHD; other frequent features include hypersensitivity to sensory stimuli and sleep problems. RFX3, RFX4, and RFX7 are strongly expressed in developing and adult human brain, and X-box binding motifs as well as RFX ChIP-seq peaks are enriched in the cis-regulatory regions of known ASD risk genes. CONCLUSION These results establish a likely role of deleterious variation in RFX3, RFX4, and RFX7 in cases of monogenic intellectual disability, ADHD and ASD, and position these genes as potentially critical transcriptional regulators of neurobiological pathways associated with neurodevelopmental disease pathogenesis.
Collapse
|
213
|
Adhya D, Swarup V, Nagy R, Dutan L, Shum C, Valencia-Alarcón EP, Jozwik KM, Mendez MA, Horder J, Loth E, Nowosiad P, Lee I, Skuse D, Flinter FA, Murphy D, McAlonan G, Geschwind DH, Price J, Carroll J, Srivastava DP, Baron-Cohen S. Atypical Neurogenesis in Induced Pluripotent Stem Cells From Autistic Individuals. Biol Psychiatry 2021; 89:486-496. [PMID: 32826066 PMCID: PMC7843956 DOI: 10.1016/j.biopsych.2020.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/12/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Autism is a heterogeneous collection of disorders with a complex molecular underpinning. Evidence from postmortem brain studies have indicated that early prenatal development may be altered in autism. Induced pluripotent stem cells (iPSCs) generated from individuals with autism with macrocephaly also indicate prenatal development as a critical period for this condition. But little is known about early altered cellular events during prenatal stages in autism. METHODS iPSCs were generated from 9 unrelated individuals with autism without macrocephaly and with heterogeneous genetic backgrounds, and 6 typically developing control individuals. iPSCs were differentiated toward either cortical or midbrain fates. Gene expression and high throughput cellular phenotyping was used to characterize iPSCs at different stages of differentiation. RESULTS A subset of autism-iPSC cortical neurons were RNA-sequenced to reveal autism-specific signatures similar to postmortem brain studies, indicating a potential common biological mechanism. Autism-iPSCs differentiated toward a cortical fate displayed impairments in the ability to self-form into neural rosettes. In addition, autism-iPSCs demonstrated significant differences in rate of cell type assignment of cortical precursors and dorsal and ventral forebrain precursors. These cellular phenotypes occurred in the absence of alterations in cell proliferation during cortical differentiation, differing from previous studies. Acquisition of cell fate during midbrain differentiation was not different between control- and autism-iPSCs. CONCLUSIONS Taken together, our data indicate that autism-iPSCs diverge from control-iPSCs at a cellular level during early stage of neurodevelopment. This suggests that unique developmental differences associated with autism may be established at early prenatal stages.
Collapse
Affiliation(s)
- Dwaipayan Adhya
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom; Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Vivek Swarup
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Roland Nagy
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Lucia Dutan
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Carole Shum
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Eva P Valencia-Alarcón
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | | | - Maria Andreina Mendez
- Department of Forensic and Neurodevelopmental Sciences, Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jamie Horder
- Department of Forensic and Neurodevelopmental Sciences, Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Eva Loth
- Department of Forensic and Neurodevelopmental Sciences, Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Paulina Nowosiad
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Irene Lee
- Behavioural and Brain Sciences Unit, Population Policy Practice Programme, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - David Skuse
- Behavioural and Brain Sciences Unit, Population Policy Practice Programme, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Frances A Flinter
- Department of Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Declan Murphy
- Department of Forensic and Neurodevelopmental Sciences, Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Grainne McAlonan
- Department of Forensic and Neurodevelopmental Sciences, Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California; Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
| | - Jason Carroll
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom.
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
214
|
Gordon A, Yoon SJ, Tran SS, Makinson CD, Park JY, Andersen J, Valencia AM, Horvath S, Xiao X, Huguenard JR, Pașca SP, Geschwind DH. Long-term maturation of human cortical organoids matches key early postnatal transitions. Nat Neurosci 2021; 24:331-342. [PMID: 33619405 PMCID: PMC8109149 DOI: 10.1038/s41593-021-00802-y] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023]
Abstract
Human stem-cell-derived models provide the promise of accelerating our understanding of brain disorders, but not knowing whether they possess the ability to mature beyond mid- to late-fetal stages potentially limits their utility. We leveraged a directed differentiation protocol to comprehensively assess maturation in vitro. Based on genome-wide analysis of the epigenetic clock and transcriptomics, as well as RNA editing, we observe that three-dimensional human cortical organoids reach postnatal stages between 250 and 300 days, a timeline paralleling in vivo development. We demonstrate the presence of several known developmental milestones, including switches in the histone deacetylase complex and NMDA receptor subunits, which we confirm at the protein and physiological levels. These results suggest that important components of an intrinsic in vivo developmental program persist in vitro. We further map neurodevelopmental and neurodegenerative disease risk genes onto in vitro gene expression trajectories to provide a resource and webtool (Gene Expression in Cortical Organoids, GECO) to guide disease modeling.
Collapse
Affiliation(s)
- Aaron Gordon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Se-Jin Yoon
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Stephen S Tran
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Department of Integrative Biology, University of California Los Angeles, Angeles, CA, USA
| | - Christopher D Makinson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Jin Young Park
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Jimena Andersen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Alfredo M Valencia
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Xinshu Xiao
- Department of Integrative Biology, University of California Los Angeles, Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
215
|
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.
Collapse
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.
| |
Collapse
|
216
|
Huang K, Wu Y, Shin J, Zheng Y, Siahpirani AF, Lin Y, Ni Z, Chen J, You J, Keles S, Wang D, Roy S, Lu Q. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PLoS Genet 2021; 17:e1009309. [PMID: 33539344 PMCID: PMC7888619 DOI: 10.1371/journal.pgen.1009309] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/17/2021] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
Recent advances in consortium-scale genome-wide association studies (GWAS) have highlighted the involvement of common genetic variants in autism spectrum disorder (ASD), but our understanding of their etiologic roles, especially the interplay with rare variants, is incomplete. In this work, we introduce an analytical framework to quantify the transmission disequilibrium of genetically regulated gene expression from parents to offspring. We applied this framework to conduct a transcriptome-wide association study (TWAS) on 7,805 ASD proband-parent trios, and replicated our findings using 35,740 independent samples. We identified 31 associations at the transcriptome-wide significance level. In particular, we identified POU3F2 (p = 2.1E-7), a transcription factor mainly expressed in developmental brain. Gene targets regulated by POU3F2 showed a 2.7-fold enrichment for known ASD genes (p = 2.0E-5) and a 2.7-fold enrichment for loss-of-function de novo mutations in ASD probands (p = 7.1E-5). These results provide a novel connection between rare and common variants, whereby ASD genes affected by very rare mutations are regulated by an unlinked transcription factor affected by common genetic variations.
Collapse
Affiliation(s)
- Kunling Huang
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yuchang Wu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Junha Shin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alireza Fotuhi Siahpirani
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yupei Lin
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zheng Ni
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jiawen Chen
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jing You
- University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sunduz Keles
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Qiongshi Lu
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
217
|
Extrinsic Regulators of mRNA Translation in Developing Brain: Story of WNTs. Cells 2021; 10:cells10020253. [PMID: 33525513 PMCID: PMC7911671 DOI: 10.3390/cells10020253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/16/2021] [Accepted: 01/21/2021] [Indexed: 12/30/2022] Open
Abstract
Extrinsic molecules such as morphogens can regulate timed mRNA translation events in developing neurons. In particular, Wingless-type MMTV integration site family, member 3 (Wnt3), was shown to regulate the translation of Foxp2 mRNA encoding a Forkhead transcription factor P2 in the neocortex. However, the Wnt receptor that possibly mediates these translation events remains unknown. Here, we report Frizzled member 7 (Fzd7) as the Wnt3 receptor that lays downstream in Wnt3-regulated mRNA translation. Fzd7 proteins co-localize with Wnt3 ligands in developing neocortices. In addition, the Fzd7 proteins overlap in layer-specific neuronal subpopulations expressing different transcription factors, Foxp1 and Foxp2. When Fzd7 was silenced, we found decreased Foxp2 protein expression and increased Foxp1 protein expression, respectively. The Fzd7 silencing also disrupted the migration of neocortical glutamatergic neurons. In contrast, Fzd7 overexpression reversed the pattern of migratory defects and Foxp protein expression that we found in the Fzd7 silencing. We further discovered that Fzd7 is required for Wnt3-induced Foxp2 mRNA translation. Surprisingly, we also determined that the Fzd7 suppression of Foxp1 protein expression is not Wnt3 dependent. In conclusion, it is exhibited that the interaction between Wnt3 and Fzd7 regulates neuronal identity and the Fzd7 receptor functions as a downstream factor in ligand Wnt3 signaling for mRNA translation. In particular, the Wnt3-Fzd7 signaling axis determines the deep layer Foxp2-expressing neurons of developing neocortices. Our findings also suggest that Fzd7 controls the balance of the expression for Foxp transcription factors in developing neocortical neurons. These discoveries are presented in our manuscript within a larger framework of this review on the role of extrinsic factors in regulating mRNA translation.
Collapse
|
218
|
3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. Cell 2021; 184:723-740.e21. [PMID: 33508230 DOI: 10.1016/j.cell.2021.01.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 11/09/2020] [Accepted: 12/31/2020] [Indexed: 02/06/2023]
Abstract
Elucidating the regulatory mechanisms of human brain evolution is essential to understanding human cognition and mental disorders. We generated multi-omics profiles and constructed a high-resolution map of 3D genome architecture of rhesus macaque during corticogenesis. By comparing the 3D genomes of human, macaque, and mouse brains, we identified many human-specific chromatin structure changes, including 499 topologically associating domains (TADs) and 1,266 chromatin loops. The human-specific loops are significantly enriched in enhancer-enhancer interactions, and the regulated genes show human-specific expression changes in the subplate, a transient zone of the developing brain critical for neural circuit formation and plasticity. Notably, many human-specific sequence changes are located in the human-specific TAD boundaries and loop anchors, which may generate new transcription factor binding sites and chromatin structures in human. Collectively, the presented data highlight the value of comparative 3D genome analyses in dissecting the regulatory mechanisms of brain development and evolution.
Collapse
|
219
|
Willsey HR, Exner CRT, Xu Y, Everitt A, Sun N, Wang B, Dea J, Schmunk G, Zaltsman Y, Teerikorpi N, Kim A, Anderson AS, Shin D, Seyler M, Nowakowski TJ, Harland RM, Willsey AJ, State MW. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron 2021; 109:788-804.e8. [PMID: 33497602 DOI: 10.1016/j.neuron.2021.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022]
Abstract
Gene Ontology analyses of autism spectrum disorders (ASD) risk genes have repeatedly highlighted synaptic function and transcriptional regulation as key points of convergence. However, these analyses rely on incomplete knowledge of gene function across brain development. Here we leverage Xenopus tropicalis to study in vivo ten genes with the strongest statistical evidence for association with ASD. All genes are expressed in developing telencephalon at time points mapping to human mid-prenatal development, and mutations lead to an increase in the ratio of neural progenitor cells to maturing neurons, supporting previous in silico systems biological findings implicating cortical neurons in ASD vulnerability, but expanding the range of convergent functions to include neurogenesis. Systematic chemical screening identifies that estrogen, via Sonic hedgehog signaling, rescues this convergent phenotype in Xenopus and human models of brain development, suggesting a resilience factor that may mitigate a range of ASD genetic risks.
Collapse
Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Galina Schmunk
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yefim Zaltsman
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nia Teerikorpi
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Albert Kim
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aoife S Anderson
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Shin
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Meghan Seyler
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
220
|
Transcriptional subtyping explains phenotypic variability in genetic subtypes of autism spectrum disorder. Dev Psychopathol 2021; 32:1353-1361. [PMID: 32912353 DOI: 10.1017/s0954579420000784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autism spectrum disorder (ASD) is a common neurodevelopmental disorder characterized by deficits in social communication and presence of restricted, repetitive behaviors, and interests. However, individuals with ASD vary significantly in their challenges and abilities in these and other developmental domains. Gene discovery in ASD has accelerated in the past decade, and genetic subtyping has yielded preliminary evidence of utility in parsing phenotypic heterogeneity through genomic subtypes. Recent advances in transcriptomics have provided additional dimensions with which to refine genetic subtyping efforts. In the current study, we investigate phenotypic differences among transcriptional subtypes defined by neurobiological spatiotemporal co-expression patterns. Of the four transcriptional subtypes examined, participants with mutations to genes typically expressed highly in all brain regions prenatally, and those with differential postnatal cerebellar expression relative to other brain regions, showed lower cognitive and adaptive skills, higher severity of social communication deficits, and later acquisition of speech and motor milestones, compared to those with mutations to genes highly expressed during the postnatal period across brain regions. These findings suggest higher-order characterization of genetic subtypes based on neurobiological expression patterns may be a promising approach to parsing phenotypic heterogeneity among those with ASD and related neurodevelopmental disorders.
Collapse
|
221
|
Peng J, Zhou Y, Wang K. Multiplex gene and phenotype network to characterize shared genetic pathways of epilepsy and autism. Sci Rep 2021; 11:952. [PMID: 33441621 PMCID: PMC7806931 DOI: 10.1038/s41598-020-78654-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
It is well established that epilepsy and autism spectrum disorder (ASD) commonly co-occur; however, the underlying biological mechanisms of the co-occurence from their genetic susceptibility are not well understood. Our aim in this study is to characterize genetic modules of subgroups of epilepsy and autism genes that have similar phenotypic manifestations and biological functions. We first integrate a large number of expert-compiled and well-established epilepsy- and ASD-associated genes in a multiplex network, where one layer is connected through protein-protein interaction (PPI) and the other layer through gene-phenotype associations. We identify two modules in the multiplex network, which are significantly enriched in genes associated with both epilepsy and autism as well as genes highly expressed in brain tissues. We find that the first module, which represents the Gene Ontology category of ion transmembrane transport, is more epilepsy-focused, while the second module, representing synaptic signaling, is more ASD-focused. However, because of their enrichment in common genes and association with both epilepsy and ASD phenotypes, these modules point to genetic etiologies and biological processes shared between specific subtypes of epilepsy and ASD. Finally, we use our analysis to prioritize new candidate genes for epilepsy (i.e. ANK2, CACNA1E, CACNA2D3, GRIA2, DLG4) for further validation. The analytical approaches in our study can be applied to similar studies in the future to investigate the genetic connections between different human diseases.
Collapse
Affiliation(s)
- Jacqueline Peng
- grid.25879.310000 0004 1936 8972School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Yunyun Zhou
- grid.239552.a0000 0001 0680 8770Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Kai Wang
- grid.239552.a0000 0001 0680 8770Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| |
Collapse
|
222
|
Morphological study of embryonic Chd8 +/- mouse brains using light-sheet microscopy. BMC Res Notes 2021; 14:23. [PMID: 33436073 PMCID: PMC7802325 DOI: 10.1186/s13104-020-05436-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/28/2020] [Indexed: 01/24/2023] Open
Abstract
Objective Autism spectrum disorder (ASD) encompasses a group of neurodevelopmental conditions that remain poorly understood due to their genetic complexity. CHD8 is a risk allele strongly associated with ASD, and heterozygous Chd8 loss-of-function mice have been reported to exhibit macrocephaly in early postnatal stages. In this work, we sought to identify measurable brain alterations in early embryonic development. Results We performed light-sheet fluorescence microscopy imaging of N-cadherin stained and optically cleared Chd8+/− and wild-type mouse brains at embryonic day 12.5 (E12.5). We report a detailed morphometric characterization of embryonic brain shapes and cortical neuroepithelial apical architecture. While Chd8+/− characteristic expansion of the forebrain and midbrain was not observed this early in embryogenesis, a tendency for a decreased lateral ventricular sphericity and an increased intraocular distance in Chd8+/− brains was found compared to controls. This study advocates the use of high-resolution microscopy technologies and multi-scale morphometric analyses of target brain regions to explore the etiology and cellular basis of Chd8 haploinsufficiency.
Collapse
|
223
|
Song L, Pan S, Zhang Z, Jia L, Chen WH, Zhao XM. STAB: a spatio-temporal cell atlas of the human brain. Nucleic Acids Res 2021; 49:D1029-D1037. [PMID: 32976581 PMCID: PMC7778989 DOI: 10.1093/nar/gkaa762] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/17/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022] Open
Abstract
The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available. Here, we present STAB (a Spatio-Temporal cell Atlas of the human Brain), a database consists of single-cell transcriptomes across multiple brain regions and developmental periods. Right now, STAB contains single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With STAB, the landscape of cell types and their regional heterogeneity and temporal dynamics across the human brain can be clearly seen, which can help to understand both the development of the normal human brain and the etiology of neuropsychiatric disorders. STAB is available at http://stab.comp-sysbio.org.
Collapse
Affiliation(s)
- Liting Song
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Shaojun Pan
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Zichao Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Longhao Jia
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, Hubei, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Shanghai 200433, China
| |
Collapse
|
224
|
Goldberg EM. Getting a Foot IN the Door: GABAergic INterneuron-Specific Enhancers. Epilepsy Curr 2021; 21:114-116. [PMID: 33412946 PMCID: PMC8010863 DOI: 10.1177/1535759720985841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Viral Manipulation of Functionally Distinct Interneurons in Mice, Non-Human Primates and Humans Vormstein-Schneider D, Lin JD, Pelkey KA, Chittajallu R, Guo B, Arias-Garcia MA, Allaway K, Sakopoulos S, Schneider G, Stevenson O, Vergara J, Sharma J, Zhang Q, Franken TP, Smith J, Ibrahim LA, Mastro KJ, Sabri E, Huang S, Favuzzi E, Burbridge T, Xu Q, Guo L, Vogel I, Sanchez V, Saldi GA, Gorissen BL, Yuan X, Zaghloul KA, Devinsky O, Sabatini BL, Batista-Brito R, Reynolds J, Feng G, Fu Z, McBain CJ, Fishell G, Dimidschstein J. Nat Neurosci. 2020;23(12):1629-1636. doi:10.1038/s41593-020-0692-9 Recent success in identifying gene-regulatory elements in the context of recombinant adeno-associated virus vectors has enabled cell-type-restricted gene expression. However, within the cerebral cortex, these tools are largely limited to broad classes of neurons. To overcome this limitation, we developed a strategy that led to the identification of multiple new enhancers to target functionally distinct neuronal subtypes. By investigating the regulatory landscape of the disease gene Scn1a, we discovered enhancers selective for parvalbumin (PV) and vasoactive intestinal peptide-expressing interneurons. Demonstrating the functional utility of these elements, we show that the PV-specific enhancer allowed for the selective targeting and manipulation of these neurons across vertebrate species, including humans. Finally, we demonstrate that our selection method is generalizable and characterizes additional PV-specific enhancers with exquisite specificity within distinct brain regions. Altogether, these viral tools can be used for cell type–specific circuit manipulation and hold considerable promise for use in therapeutic interventions.
Collapse
|
225
|
Xie X, Li L, Wu H, Hou F, Chen Y, Xue Q, Zhou Y, Zhang J, Gong J, Song R. Comprehensive Integrative Analyses Identify TIGD5 rs75547282 as a Risk Variant for Autism Spectrum Disorder. Autism Res 2021; 14:631-644. [PMID: 33393181 DOI: 10.1002/aur.2466] [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] [Received: 05/27/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
Although recent genome-wide association studies have identified risk loci that strongly associates with autism spectrum disorder (ASD), how to pinpoint the causal genes remains a challenge. We aimed to pinpoint the potential causal genes and explore the possible susceptibility and mechanism. A convergent functional genomics (CFG) method was used to prioritize the candidate genes by combining lines of evidence, including Sherlock analysis, spatio-temporal expression patterns, expression analysis, protein-protein interactions, co-expression and association with brain structure. A higher score in the CFG approach suggested that more evidence supported this gene as an ASD risk gene. We screened genes with higher CFG scores for candidate functional single nucleotide polymorphisms (SNPs). A genotyping experiment (602 ASD children and 604 healthy sex-matched children) and the dual-luciferase reporter gene assay were followed to validate the effects of SNPs. We identified three genes (MAPT, ZNF285, and TIGD5) as candidate causal genes using the CFG approach. The genotyping experiment showed that TIGD5 rs75547282 was associated with an increased risk of ASD under the dominant model (OR = 1.37, 95% CI = 1.09-1.72, P = 0.006) though the statistical power was limited (5.2%). The T allele of rs75547282 activated the expression of TIGD5 compared with the C allele in the dual-luciferase reporter assay. Our study indicates that such comprehensive integrative analyses may be an effective way to explore promising ASD susceptibility variants and needs to be further investigated in future research. Genotyping experiments should, however, be based on a larger population sample to increase statistical power. LAY SUMMARY: We set out to pinpoint the potential causal genes of ASD and explore the possible susceptibility and mechanism by combining lines of evidence from different analyses. Our results show that TIGD5 rs75547282 is associated with the risk of ASD in the Han Chinese population. In addition, a similar framework to seek promising ASD risk variants could be further investigated in future research Autism Res 2021, 14: 631-644. © 2021 International Society for Autism Research and Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Xinyan Xie
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Li
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Hao Wu
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Hou
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Yanlin Chen
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Qi Xue
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhou
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiajia Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Jianhua Gong
- Maternity and Children Health Care Hospital of Luohu District, Shenzhen, China
| | - Ranran Song
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
226
|
Lee T, Lee H. Shared Blood Transcriptomic Signatures between Alzheimer's Disease and Diabetes Mellitus. Biomedicines 2021; 9:34. [PMID: 33406707 PMCID: PMC7823888 DOI: 10.3390/biomedicines9010034] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/29/2022] Open
Abstract
Alzheimer's disease (AD) and diabetes mellitus (DM) are known to have a shared molecular mechanism. We aimed to identify shared blood transcriptomic signatures between AD and DM. Blood expression datasets for each disease were combined and a co-expression network was used to construct modules consisting of genes with similar expression patterns. For each module, a gene regulatory network based on gene expression and protein-protein interactions was established to identify hub genes. We selected one module, where COPS4, PSMA6, GTF2B, GTF2F2, and SSB were identified as dysregulated transcription factors that were common between AD and DM. These five genes were also differentially co-expressed in disease-related tissues, such as the brain in AD and the pancreas in DM. Our study identified gene modules that were dysregulated in both AD and DM blood samples, which may contribute to reveal common pathophysiology between two diseases.
Collapse
Affiliation(s)
- Taesic Lee
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Hyunju Lee
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
- Artificial Intelligence Graduate School, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| |
Collapse
|
227
|
Shohat S, Amelan A, Shifman S. Convergence and Divergence in the Genetics of Psychiatric Disorders From Pathways to Developmental Stages. Biol Psychiatry 2021; 89:32-40. [PMID: 32682568 DOI: 10.1016/j.biopsych.2020.05.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
In the past decade, the identification of susceptibility genes for psychiatric disorders has become routine, but understanding the biology underlying these discoveries has proven extremely difficult. The large number of potential risk genes and the genetic overlap between disorders are major obstacles for studying the etiology of these conditions. Systems biology approaches relying on gene ontologies, gene coexpression, and protein-protein interactions are used to identify convergence of the genes in relation to biological processes, cell types, brain areas, and developmental stages. Across psychiatric disorders, there is a clear enrichment for genes expressed in the brain and especially in the cortex, but a higher resolution is vastly dependent on sample size and statistical power. There is indication that susceptibility genes tend to be expressed in the brain during periods preceding the typical onset of the disorders. Thus, the role of genes in prenatal brain development is more pronounced for childhood-onset disorders, such as autism spectrum disorder and attention-deficit/hyperactivity disorder, but is much less so for bipolar disorder and depression. One of the most consistent findings across multiple disorders and classes of genetic variants is the role of genes intolerant to mutations in psychiatric disorders, yet this association is more pronounced for disorders with a clear neurodevelopmental component. Notwithstanding, a detailed understanding of the neurobiology of psychiatric disorders is still lacking. It is possible that it will only be revealed by studying the risk genes at the level of the development and function of neuronal networks and circuits.
Collapse
Affiliation(s)
- Shahar Shohat
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alana Amelan
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sagiv Shifman
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
228
|
Chiola S, Napan KL, Wang Y, Lazarenko RM, Armstrong CJ, Cui J, Shcheglovitov A. Defective AMPA-mediated synaptic transmission and morphology in human neurons with hemizygous SHANK3 deletion engrafted in mouse prefrontal cortex. Mol Psychiatry 2021; 26:4670-4686. [PMID: 33558651 PMCID: PMC8349370 DOI: 10.1038/s41380-021-01023-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/18/2020] [Accepted: 01/08/2021] [Indexed: 01/12/2023]
Abstract
Genetic abnormalities in synaptic proteins are common in individuals with autism; however, our understanding of the cellular and molecular mechanisms disrupted by these abnormalities is limited. SHANK3 is a postsynaptic scaffolding protein of excitatory synapses that has been found mutated or deleted in most patients with 22q13 deletion syndrome and about 2% of individuals with idiopathic autism and intellectual disability. Here, we generated CRISPR/Cas9-engineered human pluripotent stem cells (PSCs) with complete hemizygous SHANK3 deletion (SHANK3+/-), which is the most common genetic abnormality in patients, and investigated the synaptic and morphological properties of SHANK3-deficient PSC-derived cortical neurons engrafted in the mouse prefrontal cortex. We show that human PSC-derived neurons integrate into the mouse cortex by acquiring appropriate cortical layer identities and by receiving and sending anatomical projections from/to multiple different brain regions. We also demonstrate that SHANK3-deficient human neurons have reduced AMPA-, but not NMDA- or GABA-mediated synaptic transmission and exhibit impaired dendritic arbors and spines, as compared to isogenic control neurons co-engrafted in the same brain region. Together, this study reveals specific synaptic and morphological deficits caused by SHANK3 hemizygosity in human cortical neurons at different developmental stages under physiological conditions and validates the use of co-engrafted control and mutant human neurons as a new platform for studying connectivity deficits in genetic neurodevelopmental disorders associated with autism.
Collapse
Affiliation(s)
- Simone Chiola
- grid.223827.e0000 0001 2193 0096Departments of Neurobiology, University of Utah, Salt Lake City, UT USA
| | - Kandy L. Napan
- grid.223827.e0000 0001 2193 0096Departments of Neurobiology, University of Utah, Salt Lake City, UT USA
| | - Yueqi Wang
- grid.223827.e0000 0001 2193 0096Departments of Neurobiology, University of Utah, Salt Lake City, UT USA ,grid.223827.e0000 0001 2193 0096Neuroscience Graduate Program, University of Utah, Salt Lake City, UT USA
| | - Roman M. Lazarenko
- grid.152326.10000 0001 2264 7217Departments of Pharmacology, Vanderbilt University, Nashville, TN USA
| | - Celeste J. Armstrong
- grid.223827.e0000 0001 2193 0096Departments of Neurobiology, University of Utah, Salt Lake City, UT USA
| | - Jun Cui
- grid.41891.350000 0001 2156 6108Department of Cell Biology and Neurosciences, Montana State University, Bozeman, MT USA
| | - Aleksandr Shcheglovitov
- Departments of Neurobiology, University of Utah, Salt Lake City, UT, USA. .,Neuroscience Graduate Program, University of Utah, Salt Lake City, UT, USA. .,Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA. .,Department of Adult Psychiatry, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
229
|
Enriquez KD, Gupta AR, Hoffman EJ. Signaling Pathways and Sex Differential Processes in Autism Spectrum Disorder. Front Psychiatry 2021; 12:716673. [PMID: 34690830 PMCID: PMC8531220 DOI: 10.3389/fpsyt.2021.716673] [Citation(s) in RCA: 4] [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: 05/29/2021] [Accepted: 09/02/2021] [Indexed: 12/21/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders associated with deficits in social communication and restrictive, repetitive patterns of behavior, that affect up to 1 in 54 children. ASDs clearly demonstrate a male bias, occurring ~4 times more frequently in males than females, though the basis for this male predominance is not well-understood. In recent years, ASD risk gene discovery has accelerated, with many whole-exome sequencing studies identifying genes that converge on common pathways, such as neuronal communication and regulation of gene expression. ASD genetics studies have suggested that there may be a "female protective effect," such that females may have a higher threshold for ASD risk, yet its etiology is not well-understood. Here, we review common biological pathways implicated by ASD genetics studies as well as recent analyses of sex differential processes in ASD using imaging genomics, transcriptomics, and animal models. Additionally, we discuss recent investigations of ASD risk genes that have suggested a potential role for estrogens as modulators of biological pathways in ASD, and highlight relevant molecular and cellular pathways downstream of estrogen signaling as potential avenues for further investigation.
Collapse
Affiliation(s)
- Kristen D Enriquez
- Program on Neurogenetics, Child Study Center, Yale University School of Medicine, New Haven, CT, United States
| | - Abha R Gupta
- Program on Neurogenetics, Child Study Center, Yale University School of Medicine, New Haven, CT, United States.,Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT, United States
| | - Ellen J Hoffman
- Program on Neurogenetics, Child Study Center, Yale University School of Medicine, New Haven, CT, United States.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT, United States
| |
Collapse
|
230
|
Zhang Y, Wang R, Liu Z, Jiang S, Du L, Qiu K, Li F, Wang Q, Jin J, Chen X, Li Z, Wu J, Zhang N. Distinct genetic patterns of shared and unique genes across four neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2021; 186:3-15. [PMID: 32929885 DOI: 10.1002/ajmg.b.32821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023]
Abstract
Neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), developmental disorders (DD) and epileptic encephalopathy (EE), have a strong clinical comorbidity, which indicates a common genetic etiology across various disorders. However, the underlying genetic mechanisms of comorbidity and specificity remain unknown across neurodevelopmental disorders. Based on de novo mutations, we compared systematically the functional characteristics between shared and unique genes under these disorders, as well as the spatiotemporal trajectory of development in brain and common molecular pathways of all shared genes. We observed that shared genes present more constrained against functional rare genetic variation, and harbor more pathogenic rare variants than do unique genes in each disorder. Furthermore, 71 shared genes formed two clusters related to synaptic transmission, transcription regulation and chromatin regulator. Particularly, we also found that two core genes STXBP1 and SCN2A, that were shared by the four neurodevelopmental disorders showed prominent pleiotropy. Our findings shed light on the shared and specific patterns across neurodevelopmental disorders and will enable us to further comprehend the etiology and provide valuable information for the diagnosis of neurodevelopmental disorders.
Collapse
Affiliation(s)
- Yijia Zhang
- Reproductive Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruochen Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kairui Qiu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jing Jin
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Medicine & Technology School of Zunyi Medical University, Zunyi, China
| |
Collapse
|
231
|
Searles Quick VB, Wang B, State MW. Leveraging large genomic datasets to illuminate the pathobiology of autism spectrum disorders. Neuropsychopharmacology 2021; 46:55-69. [PMID: 32668441 PMCID: PMC7688655 DOI: 10.1038/s41386-020-0768-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
"Big data" approaches in the form of large-scale human genomic studies have led to striking advances in autism spectrum disorder (ASD) genetics. Similar to many other psychiatric syndromes, advances in genotyping technology, allowing for inexpensive genome-wide assays, has confirmed the contribution of polygenic inheritance involving common alleles of small effect, a handful of which have now been definitively identified. However, the past decade of gene discovery in ASD has been most notable for the application, in large family-based cohorts, of high-density microarray studies of submicroscopic chromosomal structure as well as high-throughput DNA sequencing-leading to the identification of an increasingly long list of risk regions and genes disrupted by rare, de novo germline mutations of large effect. This genomic architecture offers particular advantages for the illumination of biological mechanisms but also presents distinctive challenges. While the tremendous locus heterogeneity and functional pleiotropy associated with the more than 100 identified ASD-risk genes and regions is daunting, a growing armamentarium of comprehensive, large, foundational -omics databases, across species and capturing developmental trajectories, are increasingly contributing to a deeper understanding of ASD pathology.
Collapse
Affiliation(s)
- Veronica B Searles Quick
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA.
| |
Collapse
|
232
|
Identification of key genes and convergent pathways disrupted in autism spectrum disorder via comprehensive bioinformatic analysis. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
233
|
Griesi-Oliveira K, Passos-Bueno MR. Reply to Lombardo, 2020: An additional route of investigation: what are the mechanisms controlling ribosomal protein genes dysregulation in autistic neuronal cells? Mol Psychiatry 2021; 26:1436-1437. [PMID: 32467646 PMCID: PMC8159728 DOI: 10.1038/s41380-020-0792-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 02/04/2023]
Affiliation(s)
| | - Maria Rita Passos-Bueno
- grid.11899.380000 0004 1937 0722Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
234
|
Dickinson A, Daniel M, Marin A, Gaonkar B, Dapretto M, McDonald NM, Jeste S. Multivariate Neural Connectivity Patterns in Early Infancy Predict Later Autism Symptoms. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2021; 6:59-69. [PMID: 32798139 PMCID: PMC7736067 DOI: 10.1016/j.bpsc.2020.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Functional brain connectivity is altered in children and adults with autism spectrum disorder (ASD). Functional disruption during infancy could provide earlier markers of ASD, thus providing a crucial opportunity to improve developmental outcomes. Using a whole-brain multivariate approach, we asked whether electroencephalography measures of neural connectivity at 3 months of age predict autism symptoms at 18 months. METHODS Spontaneous electroencephalography data were collected from 65 infants with and without familial risk for ASD at 3 months of age. Neural connectivity patterns were quantified using phase coherence in the alpha range (6-12 Hz). Support vector regression analysis was used to predict ASD symptoms at age 18 months, with ASD symptoms quantified by the Toddler Module of the Autism Diagnostic Observation Schedule, Second Edition. RESULTS Autism Diagnostic Observation Schedule scores predicted by support vector regression algorithms trained on 3-month electroencephalography data correlated highly with Autism Diagnostic Observation Schedule scores measured at 18 months (r = .76, p = .02, root-mean-square error = 2.38). Specifically, lower frontal connectivity and higher right temporoparietal connectivity at 3 months predicted higher ASD symptoms at 18 months. The support vector regression model did not predict cognitive abilities at 18 months (r = .15, p = .36), suggesting specificity of these brain patterns to ASD. CONCLUSIONS Using a data-driven, unbiased analytic approach, neural connectivity across frontal and temporoparietal regions at 3 months predicted ASD symptoms at 18 months. Identifying early neural differences that precede an ASD diagnosis could promote closer monitoring of infants who show signs of neural risk and provide a crucial opportunity to mediate outcomes through early intervention.
Collapse
Affiliation(s)
- Abigail Dickinson
- Semel Institute of Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, California.
| | - Manjari Daniel
- Semel Institute of Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Andrew Marin
- Department of Psychology, University of California, San Diego, San Diego, California
| | - Bilwaj Gaonkar
- Department of Neurosurgery, Ronald Reagan UCLA Medical Center, University of California, Los Angeles, California
| | - Mirella Dapretto
- Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, Los Angeles, California
| | - Nicole M McDonald
- Semel Institute of Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Shafali Jeste
- Semel Institute of Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, California
| |
Collapse
|
235
|
Hernandez LM, Kim M, Hoftman GD, Haney JR, de la Torre-Ubieta L, Pasaniuc B, Gandal MJ. Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders. Biol Psychiatry 2021; 89:54-64. [PMID: 32792264 PMCID: PMC7718368 DOI: 10.1016/j.biopsych.2020.06.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
Over the past decade, large-scale genetic studies have successfully identified hundreds of genetic variants robustly associated with risk for psychiatric disorders. However, mechanistic insight and clinical translation continue to lag the pace of risk variant identification, hindered by the sheer number of targets and their predominant noncoding localization, as well as pervasive pleiotropy and incomplete penetrance. Successful next steps require identification of "causal" genetic variants and their proximal biological consequences; placing variants within biologically defined functional contexts, reflecting specific molecular pathways, cell types, circuits, and developmental windows; and characterizing the downstream, convergent neurobiological impact of polygenicity within an individual. Here, we discuss opportunities and challenges of high-throughput transcriptomic profiling in the human brain, and how transcriptomic approaches can help pinpoint mechanisms underlying genetic risk for psychiatric disorders at a scale necessary to tackle daunting levels of polygenicity. These include transcriptome-wide association studies for risk gene prioritization through integration of genome-wide association studies with expression quantitative trait loci. We outline transcriptomic results that inform our understanding of the brain-level molecular pathology of psychiatric disorders, including autism spectrum disorder, bipolar disorder, major depressive disorder, and schizophrenia. Finally, we discuss systems-level approaches for integration of distinct genetic, genomic, and phenotypic levels, including combining spatially resolved gene expression and human neuroimaging maps. Results highlight the importance of understanding gene expression (dys)regulation across human brain development as a major contributor to psychiatric disease pathogenesis, from common variants acting as expression quantitative trait loci to rare variants enriched for gene expression regulatory pathways.
Collapse
Affiliation(s)
- Leanna M Hernandez
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Minsoo Kim
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gil D Hoftman
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Jillian R Haney
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Luis de la Torre-Ubieta
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Bogdan Pasaniuc
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Michael J Gandal
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.
| |
Collapse
|
236
|
Abstract
Recent progress in the identification of genes and genomic regions contributing to autism spectrum disorder (ASD) has had a broad impact on our understanding of the nature of genetic risk for a range of psychiatric disorders, on our understanding of ASD biology, and on defining the key challenges now facing the field in efforts to translate gene discovery into an actionable understanding of pathology. While these advances have not yet had a transformative impact on clinical practice, there is nonetheless cause for real optimism: reliable lists of risk genes are large and growing rapidly; the identified encoded proteins have already begun to point to a relatively small number of areas of biology, where parallel advances in neuroscience and functional genomics are yielding profound insights; there is strong evidence pointing to mid-fetal prefrontal cortical development as one nexus of vulnerability for some of the largest-effect ASD risk genes; and there are multiple plausible paths forward toward rational therapeutics development that, while admittedly challenging, constitute fundamental departures from what was possible prior to the era of successful gene discovery.
Collapse
Affiliation(s)
- Devanand S Manoli
- Department of Psychiatry and Behavioral Sciences, Neuroscience Graduate Program, and Weill Institute for Neurosciences, University of California, San Francisco
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, Neuroscience Graduate Program, and Weill Institute for Neurosciences, University of California, San Francisco
| |
Collapse
|
237
|
Urresti J, Zhang P, Moran-Losada P, Yu NK, Negraes PD, Trujillo CA, Antaki D, Amar M, Chau K, Pramod AB, Diedrich J, Tejwani L, Romero S, Sebat J, Yates III JR, Muotri AR, Iakoucheva LM. Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism. Mol Psychiatry 2021; 26:7560-7580. [PMID: 34433918 PMCID: PMC8873019 DOI: 10.1038/s41380-021-01243-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 11/09/2022]
Abstract
Reciprocal deletion and duplication of the 16p11.2 region is the most common copy number variation (CNV) associated with autism spectrum disorders. We generated cortical organoids from skin fibroblasts of patients with 16p11.2 CNV to investigate impacted neurodevelopmental processes. We show that organoid size recapitulates macrocephaly and microcephaly phenotypes observed in the patients with 16p11.2 deletions and duplications. The CNV dosage affects neuronal maturation, proliferation, and synapse number, in addition to its effect on organoid size. We demonstrate that 16p11.2 CNV alters the ratio of neurons to neural progenitors in organoids during early neurogenesis, with a significant excess of neurons and depletion of neural progenitors observed in deletions. Transcriptomic and proteomic profiling revealed multiple pathways dysregulated by the 16p11.2 CNV, including neuron migration, actin cytoskeleton, ion channel activity, synaptic-related functions, and Wnt signaling. The level of the active form of small GTPase RhoA was increased in both, deletions and duplications. Inhibition of RhoA activity rescued migration deficits, but not neurite outgrowth. This study provides insights into potential neurobiological mechanisms behind the 16p11.2 CNV during neocortical development.
Collapse
Affiliation(s)
- Jorge Urresti
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Pan Zhang
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Patricia Moran-Losada
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Nam-Kyung Yu
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Priscilla D. Negraes
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Cleber A. Trujillo
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Danny Antaki
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Megha Amar
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Kevin Chau
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Akula Bala Pramod
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Jolene Diedrich
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Leon Tejwani
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Sarah Romero
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Jonathan Sebat
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Beyster Center for Psychiatric Genomics, La Jolla, CA USA
| | - John R. Yates III
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Alysson R. Muotri
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Kavli Institute for Brain and Mind, La Jolla, CA USA ,Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA USA
| | - Lilia M. Iakoucheva
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| |
Collapse
|
238
|
Meyerink BL, Tiwari NK, Pilaz LJ. Ariadne's Thread in the Developing Cerebral Cortex: Mechanisms Enabling the Guiding Role of the Radial Glia Basal Process during Neuron Migration. Cells 2020; 10:E3. [PMID: 33375033 PMCID: PMC7822038 DOI: 10.3390/cells10010003] [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: 11/26/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Radial neuron migration in the developing cerebral cortex is a complex journey, starting in the germinal zones and ending in the cortical plate. In mice, migratory distances can reach several hundreds of microns, or millimeters in humans. Along the migratory path, radially migrating neurons slither through cellularly dense and complex territories before they reach their final destination in the cortical plate. This task is facilitated by radial glia, the neural stem cells of the developing cortex. Indeed, radial glia have a unique bipolar morphology, enabling them to serve as guides for neuronal migration. The key guiding structure of radial glia is the basal process, which traverses the entire thickness of the developing cortex. Neurons recognize the basal process as their guide and maintain physical interactions with this structure until the end of migration. Thus, the radial glia basal process plays a key role during radial migration. In this review, we highlight the pathways enabling neuron-basal process interactions during migration, as well as the known mechanisms regulating the morphology of the radial glia basal process. Throughout, we describe how dysregulation of these interactions and of basal process morphology can have profound effects on cortical development, and therefore lead to neurodevelopmental diseases.
Collapse
Affiliation(s)
- Brandon L. Meyerink
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA; (B.L.M.); (N.K.T.)
- Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
| | - Neeraj K. Tiwari
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA; (B.L.M.); (N.K.T.)
| | - Louis-Jan Pilaz
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA; (B.L.M.); (N.K.T.)
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
| |
Collapse
|
239
|
Reilly J, Gallagher L, Leader G, Shen S. Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation. PLoS One 2020; 15:e0242773. [PMID: 33338084 PMCID: PMC7748153 DOI: 10.1371/journal.pone.0242773] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous disorder that is often accompanied with many co-morbidities. Recent genetic studies have identified various pathways from hundreds of candidate risk genes with varying levels of association to ASD. However, it is unknown which pathways are specific to the core symptoms or which are shared by the co-morbidities. We hypothesised that critical ASD candidates should appear widely across different scoring systems, and that comorbidity pathways should be constituted by genes expressed in the relevant tissues. We analysed the Simons Foundation for Autism Research Initiative (SFARI) database and four independently published scoring systems and identified 292 overlapping genes. We examined their mRNA expression using the Genotype-Tissue Expression (GTEx) database and validated protein expression levels using the human protein atlas (HPA) dataset. This led to clustering of the overlapping ASD genes into 2 groups; one with 91 genes primarily expressed in the central nervous system (CNS geneset) and another with 201 genes expressed in both CNS and peripheral tissues (CNS+PT geneset). Bioinformatic analyses showed a high enrichment of CNS development and synaptic transmission in the CNS geneset, and an enrichment of synapse, chromatin remodelling, gene regulation and endocrine signalling in the CNS+PT geneset. Calcium signalling and the glutamatergic synapse were found to be highly interconnected among pathways in the combined geneset. Our analyses demonstrate that 2/3 of ASD genes are expressed beyond the brain, which may impact peripheral function and involve in ASD co-morbidities, and relevant pathways may be explored for the treatment of ASD co-morbidities.
Collapse
Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, Biomedical Science Building, National University of Ireland (NUI) Galway, Galway, Ireland
- * E-mail: (JR); (SS)
| | - Louise Gallagher
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity Centre for Health Sciences—Trinity College Dublin, St. James’s Hospital, Dublin, Ireland
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland (NUI) Galway, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, Biomedical Science Building, National University of Ireland (NUI) Galway, Galway, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
- * E-mail: (JR); (SS)
| |
Collapse
|
240
|
Mann C, Schäfer T, Bletsch A, Gudbrandsen M, Daly E, Suckling J, Bullmore ET, Lombardo MV, Lai MC, Craig MC, Baron-Cohen S, Murphy DGM, Ecker C. Examining volumetric gradients based on the frustum surface ratio in the brain in autism spectrum disorder. Hum Brain Mapp 2020; 42:953-966. [PMID: 33295656 PMCID: PMC7856638 DOI: 10.1002/hbm.25270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 11/19/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that is accompanied by neurodevelopmental differences in regional cortical volume (CV), and a potential layer‐specific pathology. Conventional measures of CV, however, do not indicate how volume is distributed across cortical layers. In a sample of 92 typically developing (TD) controls and 92 adult individuals with ASD (aged 18–52 years), we examined volumetric gradients by quantifying the degree to which CV is weighted from the pial to the white surface of the brain. Overall, the spatial distribution of Frustum Surface Ratio (FSR) followed the gyral and sulcal pattern of the cortex and approximated a bimodal Gaussian distribution caused by a linear mixture of vertices on gyri and sulci. Measures of FSR were highly correlated with vertex‐wise estimates of mean curvature, sulcal depth, and pial surface area, although none of these features explained more than 76% variability in FSR on their own. Moreover, in ASD, we observed a pattern of predominant increases in the degree of FSR relative to TD controls, with an atypical neurodevelopmental trajectory. Our findings suggest a more outward‐weighted gradient of CV in ASD, which may indicate a larger contribution of supragranular layers to regional differences in CV.
Collapse
Affiliation(s)
- Caroline Mann
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital, Goethe University, Frankfurt am Main, Germany.,Brain Imaging Center, Goethe-University, Frankfurt am Main, Germany
| | - Tim Schäfer
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital, Goethe University, Frankfurt am Main, Germany.,Brain Imaging Center, Goethe-University, Frankfurt am Main, Germany
| | - Anke Bletsch
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital, Goethe University, Frankfurt am Main, Germany.,Brain Imaging Center, Goethe-University, Frankfurt am Main, Germany
| | - Maria Gudbrandsen
- Department of Forensic and Neurodevelopmental Sciences, and the Sackler Institute for Translational Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, United Kingdom
| | - Eileen Daly
- Department of Forensic and Neurodevelopmental Sciences, and the Sackler Institute for Translational Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, United Kingdom
| | - John Suckling
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Edward T Bullmore
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Michael V Lombardo
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.,Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Meng-Chuan Lai
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.,Centre for Addiction and Mental Health and The Hospital for Sick Children, Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Michael C Craig
- Department of Forensic and Neurodevelopmental Sciences, and the Sackler Institute for Translational Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, United Kingdom.,National Autism Unit, Bethlem Royal Hospital, London, United Kingdom
| | | | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Declan G M Murphy
- Department of Forensic and Neurodevelopmental Sciences, and the Sackler Institute for Translational Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, United Kingdom
| | - Christine Ecker
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital, Goethe University, Frankfurt am Main, Germany.,Brain Imaging Center, Goethe-University, Frankfurt am Main, Germany.,Department of Forensic and Neurodevelopmental Sciences, and the Sackler Institute for Translational Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, United Kingdom
| |
Collapse
|
241
|
Doostparast Torshizi A, Ionita-Laza I, Wang K. Cell Type-Specific Annotation and Fine Mapping of Variants Associated With Brain Disorders. Front Genet 2020; 11:575928. [PMID: 33343624 PMCID: PMC7744805 DOI: 10.3389/fgene.2020.575928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Common genetic variants confer susceptibility to a large number of complex brain disorders. Given that such variants predominantly localize in non-coding regions of the human genome, there is a significant challenge to predict and characterize their functional consequences. More importantly, most available computational methods, generally defined as context-free methods, output prediction scores regarding the functionality of genetic variants irrespective of the context, i.e., the tissue or cell-type affected by a disease, limiting the ability to predict the functional consequences of common variants on brain disorders. In this study, we introduce a comparative multi-step pipeline to investigate the relative effectiveness of context-specific and context-free approaches to prioritize disease causal variants. As an experimental case, we focused on schizophrenia (SCZ), a debilitating neuropsychiatric disease for which a large number of susceptibility variants is identified from genome-wide association studies. We tested over two dozen available methods and examined potential associations between the cell/tissue-specific mapping scores and open chromatin accessibility, and provided a prioritized map of SCZ risk loci for in vitro or in-vivo functional analysis. We found extensive differences between context-free and tissue-specific approaches and showed how they may play complementary roles. As a proof of concept, we found a few sets of genes, through a consensus mapping of both categories, including FURIN to be among the top hits. We showed that the genetic variants in this gene and related genes collectively dysregulate gene expression patterns in stem cell-derived neurons and characterize SCZ phenotypic manifestations, while genes which were not shared among highly prioritized candidates in both approaches did not demonstrate such characteristics. In conclusion, by combining context-free and tissue-specific predictions, our pipeline enables prioritization of the most likely disease-causal common variants in complex brain disorders.
Collapse
Affiliation(s)
- Abolfazl Doostparast Torshizi
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Columbia University, New York, NY, United States
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
242
|
Pei G, Wang YY, Simon LM, Dai Y, Zhao Z, Jia P. Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders. Genome Res 2020; 31:146-158. [PMID: 33272935 PMCID: PMC7849392 DOI: 10.1101/gr.265769.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022]
Abstract
As the most complex organ of the human body, the brain is composed of diverse regions, each consisting of distinct cell types and their respective cellular interactions. Human brain development involves a finely tuned cascade of interactive events. These include spatiotemporal gene expression changes and dynamic alterations in cell-type composition. However, our understanding of this process is still largely incomplete owing to the difficulty of brain spatiotemporal transcriptome collection. In this study, we developed a tensor-based approach to impute gene expression on a transcriptome-wide level. After rigorous computational benchmarking, we applied our approach to infer missing data points in the widely used BrainSpan resource and completed the entire grid of spatiotemporal transcriptomics. Next, we conducted deconvolutional analyses to comprehensively characterize major cell-type dynamics across the entire BrainSpan resource to estimate the cellular temporal changes and distinct neocortical areas across development. Moreover, integration of these results with GWAS summary statistics for 13 brain-associated traits revealed multiple novel trait–cell-type associations and trait-spatiotemporal relationships. In summary, our imputed BrainSpan transcriptomic data provide a valuable resource for the research community and our findings help further studies of the transcriptional and cellular dynamics of the human brain and related diseases.
Collapse
Affiliation(s)
- Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yin-Ying Wang
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Lukas M Simon
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| |
Collapse
|
243
|
Abstract
The formation of the human brain, which contains nearly 100 billion neurons making an average of 1000 connections each, represents an astonishing feat of self-organization. Despite impressive progress, our understanding of how neurons form the nervous system and enable function is very fragmentary, especially for the human brain. New technologies that produce large volumes of high-resolution measurements-big data-are now being brought to bear on this problem. Single-cell molecular profiling methods allow the exploration of neural diversity with increasing spatial and temporal resolution. Advances in human genetics are shedding light on the genetic architecture of neurodevelopmental disorders, and new approaches are revealing plausible neurobiological mechanisms underlying these conditions. Here, we review the opportunities and challenges of integrating large-scale genomics and genetics for the study of brain development.
Collapse
Affiliation(s)
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK. .,MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| |
Collapse
|
244
|
Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. Curr Opin Genet Dev 2020; 65:126-137. [PMID: 32659636 DOI: 10.1016/j.gde.2020.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022]
Abstract
The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes.
Collapse
Affiliation(s)
| | - Jasmin Morandell
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Gaia Novarino
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
| |
Collapse
|
245
|
Spiess K, Won H. Regulatory landscape in brain development and disease. Curr Opin Genet Dev 2020; 65:53-60. [PMID: 32563855 PMCID: PMC7746596 DOI: 10.1016/j.gde.2020.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/06/2020] [Accepted: 05/01/2020] [Indexed: 01/16/2023]
Abstract
Although many regulatory elements in the non-coding genome are linked to brain development and disease, deciphering their function has been challenging due to the lack of a genomic toolbox. However, recent advances in high throughput sequencing techniques have allowed us to begin decoding its function, enhancing our understanding of the regulatory landscape that underpins human traits and brain disorders. Here, we review how the regulatory landscape of the human brain undergoes dynamic changes across neurodevelopment, different cell types, and human evolution. We then discuss how regulatory landscapes shed light onto the molecular basis of neuropsychiatric disorders and guide the development of specifically targeted molecular therapies. Finally, we offer some thoughts on how these discoveries might impact the direction of future studies.
Collapse
Affiliation(s)
- Keeley Spiess
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hyejung Won
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| |
Collapse
|
246
|
Wamsley B, Geschwind DH. Functional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease. Curr Opin Genet Dev 2020; 65:117-125. [PMID: 32634676 PMCID: PMC8171040 DOI: 10.1016/j.gde.2020.05.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/24/2020] [Indexed: 12/30/2022]
Abstract
Neurodegenerative and neuropsychiatric disorders are pervasive and debilitating conditions characterized by diverse clinical syndromes and comorbidities, whose origins are as complex and heterogeneous as their associated phenotypes. Risk for these disorders involves substantial genetic liability, which has fueled large-scale genetic studies that have led to a flood of discoveries. In turn, these discoveries have exposed substantial gaps in our knowledge with regards to the complicated genetic architecture of each disorder and the substantial amount of genetic overlap among disorders, which implies some degree of shared pathophysiology underlying these clinically distinct, multifactorial disorders. Understanding the role of specific genetic variants will involve resolving the connections between molecular pathways, heterogeneous cell types, specific circuits and disease pathogenesis at the tissue and patient level. We consider the current known genetic basis of these disorders and highlight the utility of molecular systems approaches that establish the function of genetic variation in the context of specific neurobiological networks, cell-types, and life stages. Beyond expanding our knowledge of disease mechanisms, understanding these relationships provides promise for early detection and potential therapeutic interventions.
Collapse
Affiliation(s)
- Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Program in Neurobehavioral Genetics and Center for Autism Research and Treatment Semel Institute and Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
247
|
Christian DL, Wu DY, Martin JR, Moore JR, Liu YR, Clemens AW, Nettles SA, Kirkland NM, Papouin T, Hill CA, Wozniak DF, Dougherty JD, Gabel HW. DNMT3A Haploinsufficiency Results in Behavioral Deficits and Global Epigenomic Dysregulation Shared across Neurodevelopmental Disorders. Cell Rep 2020; 33:108416. [PMID: 33238114 PMCID: PMC7716597 DOI: 10.1016/j.celrep.2020.108416] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 09/17/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Mutations in DNA methyltransferase 3A (DNMT3A) have been detected in autism and related disorders, but how these mutations disrupt nervous system function is unknown. Here, we define the effects of DNMT3A mutations associated with neurodevelopmental disease. We show that diverse mutations affect different aspects of protein activity but lead to shared deficiencies in neuronal DNA methylation. Heterozygous DNMT3A knockout mice mimicking DNMT3A disruption in disease display growth and behavioral alterations consistent with human phenotypes. Strikingly, in these mice, we detect global disruption of neuron-enriched non-CG DNA methylation, a binding site for the Rett syndrome protein MeCP2. Loss of this methylation leads to enhancer and gene dysregulation that overlaps with models of Rett syndrome and autism. These findings define the effects of DNMT3A haploinsufficiency in the brain and uncover disruption of the non-CG methylation pathway as a convergence point across neurodevelopmental disorders.
Collapse
Affiliation(s)
- Diana L Christian
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - J Russell Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Yiran R Liu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Nicole M Kirkland
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - David F Wozniak
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA.
| |
Collapse
|
248
|
Hu VW, Bi C. Phenotypic Subtyping and Re-analyses of Existing Transcriptomic Data from Autistic Probands in Simplex Families Reveal Differentially Expressed and ASD Trait-Associated Genes. Front Neurol 2020; 11:578972. [PMID: 33281715 PMCID: PMC7689346 DOI: 10.3389/fneur.2020.578972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 12/25/2022] Open
Abstract
Autism spectrum disorder (ASD) describes a collection of neurodevelopmental disorders characterized by core symptoms that include social communication deficits and repetitive, stereotyped behaviors often coupled with restricted interests. Primary challenges to understanding and treating ASD are the genetic and phenotypic heterogeneity of cases that complicates all omics analyses as well as a lack of information on relationships among genes, pathways, and autistic traits. In this study, we re-analyze existing transcriptomic data from simplex families by subtyping individuals with ASD according to multivariate cluster analyses of clinical ADI-R scores that encompass a broad range of behavioral symptoms. We also correlate multiple ASD traits, such as deficits in verbal and non-verbal communication, play and social skills, ritualistic behaviors, and savant skills, with expression profiles using Weighted Gene Correlation Network Analyses (WGCNA). Our results show that subtyping greatly enhances the ability to identify differentially expressed genes involved in specific canonical pathways and biological functions associated with ASD within each phenotypic subgroup. Moreover, using WGCNA, we identify gene modules that correlate significantly with specific ASD traits. Network prediction analyses of the genes in these modules reveal canonical pathways as well as neurological functions and disorders relevant to the pathobiology of ASD. Finally, we compare the WGCNA-derived data on autistic traits in simplex families with analogous data from multiplex families using transcriptomic data from our previous studies. The comparison reveals overlapping trait-associated pathways as well as upstream regulators of the module-associated genes that may serve as useful targets for a precision medicine approach to ASD.
Collapse
Affiliation(s)
- Valerie W Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Chongfeng Bi
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| |
Collapse
|
249
|
Prem S, Millonig JH, DiCicco-Bloom E. Dysregulation of Neurite Outgrowth and Cell Migration in Autism and Other Neurodevelopmental Disorders. ADVANCES IN NEUROBIOLOGY 2020; 25:109-153. [PMID: 32578146 DOI: 10.1007/978-3-030-45493-7_5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite decades of study, elucidation of the underlying etiology of complex developmental disorders such as autism spectrum disorder (ASD), schizophrenia (SCZ), intellectual disability (ID), and bipolar disorder (BPD) has been hampered by the inability to study human neurons, the heterogeneity of these disorders, and the relevance of animal model systems. Moreover, a majority of these developmental disorders have multifactorial or idiopathic (unknown) causes making them difficult to model using traditional methods of genetic alteration. Examination of the brains of individuals with ASD and other developmental disorders in both post-mortem and MRI studies shows defects that are suggestive of dysregulation of embryonic and early postnatal development. For ASD, more recent genetic studies have also suggested that risk genes largely converge upon the developing human cerebral cortex between weeks 8 and 24 in utero. Yet, an overwhelming majority of studies in autism rodent models have focused on postnatal development or adult synaptic transmission defects in autism related circuits. Thus, studies looking at early developmental processes such as proliferation, cell migration, and early differentiation, which are essential to build the brain, are largely lacking. Yet, interestingly, a few studies that did assess early neurodevelopment found that alterations in brain structure and function associated with neurodevelopmental disorders (NDDs) begin as early as the initial formation and patterning of the neural tube. By the early to mid-2000s, the derivation of human embryonic stem cells (hESCs) and later induced pluripotent stem cells (iPSCs) allowed us to study living human neural cells in culture for the first time. Specifically, iPSCs gave us the unprecedented ability to study cells derived from individuals with idiopathic disorders. Studies indicate that iPSC-derived neural cells, whether precursors or "matured" neurons, largely resemble cortical cells of embryonic humans from weeks 8 to 24. Thus, these cells are an excellent model to study early human neurodevelopment, particularly in the context of genetically complex diseases. Indeed, since 2011, numerous studies have assessed developmental phenotypes in neurons derived from individuals with both genetic and idiopathic forms of ASD and other NDDs. However, while iPSC-derived neurons are fetal in nature, they are post-mitotic and thus cannot be used to study developmental processes that occur before terminal differentiation. Moreover, it is important to note that during the 8-24-week window of human neurodevelopment, neural precursor cells are actively undergoing proliferation, migration, and early differentiation to form the basic cytoarchitecture of the brain. Thus, by studying NPCs specifically, we could gain insight into how early neurodevelopmental processes contribute to the pathogenesis of NDDs. Indeed, a few studies have explored NPC phenotypes in NDDs and have uncovered dysregulations in cell proliferation. Yet, few studies have explored migration and early differentiation phenotypes of NPCs in NDDs. In this chapter, we will discuss cell migration and neurite outgrowth and the role of these processes in neurodevelopment and NDDs. We will begin by reviewing the processes that are important in early neurodevelopment and early cortical development. We will then delve into the roles of neurite outgrowth and cell migration in the formation of the brain and how errors in these processes affect brain development. We also provide review of a few key molecules that are involved in the regulation of neurite outgrowth and migration while discussing how dysregulations in these molecules can lead to abnormalities in brain structure and function thereby highlighting their contribution to pathogenesis of NDDs. Then we will discuss whether neurite outgrowth, migration, and the molecules that regulate these processes are associated with ASD. Lastly, we will review the utility of iPSCs in modeling NDDs and discuss future goals for the study of NDDs using this technology.
Collapse
Affiliation(s)
- Smrithi Prem
- Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - James H Millonig
- Department of Neuroscience and Cell Biology, Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Emanuel DiCicco-Bloom
- Department of Neuroscience and Cell Biology/Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.
| |
Collapse
|
250
|
Wang J, Wang L. Prediction and prioritization of autism-associated long non-coding RNAs using gene expression and sequence features. BMC Bioinformatics 2020; 21:505. [PMID: 33160303 PMCID: PMC7648398 DOI: 10.1186/s12859-020-03843-5] [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: 07/15/2020] [Accepted: 10/27/2020] [Indexed: 01/04/2023] Open
Abstract
Background Autism spectrum disorders (ASD) refer to a range of neurodevelopmental conditions, which are genetically complex and heterogeneous with most of the genetic risk factors also found in the unaffected general population. Although all the currently known ASD risk genes code for proteins, long non-coding RNAs (lncRNAs) as essential regulators of gene expression have been implicated in ASD. Some lncRNAs show altered expression levels in autistic brains, but their roles in ASD pathogenesis are still unclear. Results In this study, we have developed a new machine learning approach to predict candidate lncRNAs associated with ASD. Particularly, the knowledge learnt from protein-coding ASD risk genes was transferred to the prediction and prioritization of ASD-associated lncRNAs. Both developmental brain gene expression data and transcript sequence were found to contain relevant information for ASD risk gene prediction. During the pre-training phase of model construction, an autoencoder network was implemented for a representation learning of the gene expression data, and a random-forest-based feature selection was applied to the transcript-sequence-derived k-mers. Our models, including logistic regression, support vector machine and random forest, showed robust performance based on tenfold cross-validations as well as candidate prioritization with hypothetical loci. We then utilized the models to predict and prioritize a list of candidate lncRNAs, including some reported to be cis-regulators of known ASD risk genes, for further investigation.
Conclusions Our results suggest that ASD risk genes can be accurately predicted using developmental brain gene expression data and transcript sequence features, and the models may provide useful information for functional characterization of the candidate lncRNAs associated with ASD.
Collapse
Affiliation(s)
- Jun Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA. .,Center for Human Genetics, Clemson University, Clemson, SC, 29634, USA.
| |
Collapse
|