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Zhang S, Yang J, Ji D, Meng X, Zhu C, Zheng G, Glessner J, Qu HQ, Cui Y, Liu Y, Wang W, Li X, Zhang H, Xiu Z, Sun Y, Sun L, Li J, Hakonarson H, Li J, Xia Q. NASP gene contributes to autism by epigenetic dysregulation of neural and immune pathways. J Med Genet 2024; 61:677-688. [PMID: 38443156 DOI: 10.1136/jmg-2023-109385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Epigenetics makes substantial contribution to the aetiology of autism spectrum disorder (ASD) and may harbour a unique opportunity to prevent the development of ASD. We aimed to identify novel epigenetic genes involved in ASD aetiology. METHODS Trio-based whole exome sequencing was conducted on ASD families. Genome editing technique was used to knock out the candidate causal gene in a relevant cell line. ATAC-seq, ChIP-seq and RNA-seq were performed to investigate the functional impact of knockout (KO) or mutation in the candidate gene. RESULTS We identified a novel candidate gene NASP (nuclear autoantigenic sperm protein) for epigenetic dysregulation in ASD in a Chinese nuclear family including one proband with autism and comorbid atopic disease. The de novo likely gene disruptive variant tNASP(Q289X) subjects the expression of tNASP to nonsense-mediated decay. tNASP KO increases chromatin accessibility, promotes the active promoter state of genes enriched in synaptic signalling and leads to upregulated expression of genes in the neural signalling and immune signalling pathways. Compared with wild-type tNASP, tNASP(Q289X) enhances chromatin accessibility of the genes with enriched expression in the brain. RNA-seq revealed that genes involved in neural and immune signalling are affected by the tNASP mutation, consistent with the phenotypic impact and molecular effects of nasp-1 mutations in Caenorhabditis elegans. Two additional patients with ASD were found carrying deletion or deleterious mutation in the NASP gene. CONCLUSION We identified novel epigenetic mechanisms mediated by tNASP which may contribute to the pathogenesis of ASD and its immune comorbidity.
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Affiliation(s)
- Sipeng Zhang
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dandan Ji
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinyi Meng
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Chonggui Zhu
- Department of Endocrinology, Tianjin Medical University General Hospital, Tianjin, China
| | - Gang Zheng
- National Supercomputer Center in Tianjin (NSCC-TJ), Tianjin, China
| | - Joseph Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui-Qi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yuechen Cui
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yichuan Liu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Wang
- The Institute of Psychology of the Chinese Academy of Sciences, Beijing, China
| | - Xiumei Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hao Zhang
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhanjie Xiu
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yan Sun
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ling Sun
- Laboratory of Biological Psychiatry, Institute of Mental Health, Tianjin Anding Hospital, Tianjin Medical University, Tianjin, China
| | - Jie Li
- Laboratory of Biological Psychiatry, Institute of Mental Health, Tianjin Anding Hospital, Tianjin Medical University, Tianjin, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jin Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Qianghua Xia
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Zheng L, Jiao Y, Zhong H, Tan Y, Yin Y, Liu Y, Liu D, Wu M, Wang G, Huang J, Wang P, Qin M, Wang M, Xiao Y, Lv T, Luo Y, Hu H, Hou ST, Kui L. Human-derived fecal microbiota transplantation alleviates social deficits of the BTBR mouse model of autism through a potential mechanism involving vitamin B 6 metabolism. mSystems 2024; 9:e0025724. [PMID: 38780265 DOI: 10.1128/msystems.00257-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by social communication deficiencies and stereotypic behaviors influenced by hereditary and/or environmental risk factors. There are currently no approved medications for treating the core symptoms of ASD. Human fecal microbiota transplantation (FMT) has emerged as a potential intervention to improve autistic symptoms, but the underlying mechanisms are not fully understood. In this study, we evaluated the effects of human-derived FMT on behavioral and multi-omics profiles of the BTBR mice, an established model for ASD. FMT effectively alleviated the social deficits in the BTBR mice and normalized their distinct plasma metabolic profile, notably reducing the elevated long-chain acylcarnitines. Integrative analysis linked these phenotypic changes to specific Bacteroides species and vitamin B6 metabolism. Indeed, vitamin B6 supplementation improved the social behaviors in BTBR mice. Collectively, these findings shed new light on the interplay between FMT and vitamin B6 metabolism and revealed a potential mechanism underlying the therapeutic role of FMT in ASD.IMPORTANCEAccumulating evidence supports the beneficial effects of human fecal microbiota transplantation (FMT) on symptoms associated with autism spectrum disorder (ASD). However, the precise mechanism by which FMT induces a shift in the microbiota and leads to symptom improvement remains incompletely understood. This study integrated data from colon-content metagenomics, colon-content metabolomics, and plasma metabolomics to investigate the effects of FMT treatment on the BTBR mouse model for ASD. The analysis linked the amelioration of social deficits following FMT treatment to the restoration of mitochondrial function and the modulation of vitamin B6 metabolism. Bacterial species and compounds with beneficial roles in vitamin B6 metabolism and mitochondrial function may further contribute to improving FMT products and designing novel therapies for ASD treatment.
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Affiliation(s)
- Lifeng Zheng
- Brain Research Centre and Department of Neuroscience, Southern University of Science and Technology, Shenzhen, China
- Xbiome Co. Ltd., Shenzhen, China
| | - Yinming Jiao
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Haolin Zhong
- Brain Research Centre and Department of Neuroscience, Southern University of Science and Technology, Shenzhen, China
| | - Yan Tan
- Xbiome Co. Ltd., Shenzhen, China
| | | | | | - Ding Liu
- Xbiome Co. Ltd., Shenzhen, China
| | - Manli Wu
- Xbiome Co. Ltd., Shenzhen, China
| | - Guoyun Wang
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | | | - Ping Wang
- Shenzhen Institute for Drug Control, Shenzhen, China
| | - Meirong Qin
- Shenzhen Institute for Drug Control, Shenzhen, China
| | - Mingbang Wang
- Microbiome Therapy Center, South China Hospital, Medical School, Shenzhen University, Shenzhen, China
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Yang Xiao
- Department of Hematology, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Tiying Lv
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yangzi Luo
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Han Hu
- Xbiome Co. Ltd., Shenzhen, China
| | - Sheng-Tao Hou
- Brain Research Centre and Department of Neuroscience, Southern University of Science and Technology, Shenzhen, China
| | - Ling Kui
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
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Topa H, Benoit-Pilven C, Tukiainen T, Pietiläinen O. X-chromosome inactivation in human iPSCs provides insight into X-regulated gene expression in autosomes. Genome Biol 2024; 25:144. [PMID: 38822397 PMCID: PMC11143737 DOI: 10.1186/s13059-024-03286-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/17/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Variation in X chromosome inactivation (XCI) in human-induced pluripotent stem cells (hiPSCs) can impact their ability to model biological sex biases. The gene-wise landscape of X chromosome gene dosage remains unresolved in female hiPSCs. To characterize patterns of de-repression and escape from inactivation, we performed a systematic survey of allele specific expression in 165 female hiPSC lines. RESULTS XCI erosion is non-random and primarily affects genes that escape XCI in human tissues. Individual genes and cell lines vary in the frequency and degree of de-repression. Bi-allelic expression increases gradually after modest decrease of XIST in cultures, whose loss is commonly used to mark lines with eroded XCI. We identify three clusters of female lines at different stages of XCI. Increased XCI erosion amplifies female-biased expression at hypomethylated sites and regions normally occupied by repressive histone marks, lowering male-biased differences in the X chromosome. In autosomes, erosion modifies sex differences in a dose-dependent way. Male-biased genes are enriched for hypermethylated regions, and de-repression of XIST-bound autosomal genes in female lines attenuates normal male-biased gene expression in eroded lines. XCI erosion can compensate for a dominant loss of function effect in several disease genes. CONCLUSIONS We present a comprehensive view of X chromosome gene dosage in hiPSCs and implicate a direct mechanism for XCI erosion in regulating autosomal gene expression in trans. The uncommon and variable reactivation of X chromosome genes in female hiPSCs can provide insight into X chromosome's role in regulating gene expression and sex differences in humans.
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Affiliation(s)
- Hande Topa
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Clara Benoit-Pilven
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Olli Pietiläinen
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
- The Stanley Center for Psychiatric Research at the Broad Institute, of MIT and Harvard, Cambridge, MA, USA.
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Yue F, Yang X, Liu N, Liu R, Zhang H. Prenatal diagnosis and pregnancy outcomes in fetuses with ventriculomegaly. Front Med (Lausanne) 2024; 11:1349171. [PMID: 38784233 PMCID: PMC11111914 DOI: 10.3389/fmed.2024.1349171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Objective Genetic etiology plays a critical role in fetal ventriculomegaly (VM). However, the studies on chromosomal copy number variants (CNVs) in fetal VM are limited. This study aimed to investigate the chromosomal CNVs in fetuses with mild to moderate VM, and explore its genotype-phenotype correlation. Methods A total of 242 fetuses with mild to moderate VM detected by prenatal ultrasound were enrolled in our study from October 2018 to October 2022. All cases underwent chromosomal microarray analysis (CMA) and G-banding simultaneously. All VM cases were classified different subgroups according to the maternal age, severity, VM distribution and presence/absence of other ultrasound abnormalities. The pregnancy outcomes and health conditions after birth were followed up. We also performed a pooled analysis regarding likely pathogenic and pathogenic CNVs (LP/P CNVs) for VM. Results The detection rate of chromosomal abnormalities by karyotyping was 9.1% (22/242), whereas it was 16.5% (40/242) when CMA was conducted (P < 0.05). The total detection rate of chromosomal abnormalities by karyotyping and CMA was 21.1% (51/242). A 12.0% incremental yield of CMA over karyotyping was observed. The detection rate of total genetic variants in fetuses with bilateral VM was significantly higher than in fetuses with unilateral VM (30.0% vs. 16.7%, P = 0.017). No significant differences were discovered between isolated VM and non-isolated VM, or between mild and moderate VM, or between advanced maternal age (AMA) and non-AMA (all P > 0.05). 28 fetuses with VM were terminated and 214 fetuses were delivered: one presented developmental delay and one presented congenital heart disease. The VM cases with both positive CMA and karyotypic results had a higher rate of termination of pregnancy than those with either a positive CMA or karyotypic result, or both negative testing results (P < 0.001). Conclusion The combination of CMA and karyotyping should be adopted to improve the positive detection rate of chromosomal abnormalities for VM. The total genetic abnormalities detected using both techniques would affect the final pregnancy outcomes. LP/P CNVs at 16p11.2, 17p13, and 22q11.21 were identified as the top three chromosomal hotspots associated with VM, which would enable genetic counselors to provide more precise genetic counseling for VM pregnancies.
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Affiliation(s)
- Fagui Yue
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Xiao Yang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ning Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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Chao C, Qian Y, Lv H, Mei K, Wang M, Liu Y, Wang B, Di D. Whole exome sequencing and proteomics-based investigation of the pathogenesis of coronary artery disease with diffuse long lesion. J Cardiothorac Surg 2024; 19:280. [PMID: 38715006 PMCID: PMC11075290 DOI: 10.1186/s13019-024-02760-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/30/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVES The long-term prognosis of patients with coronary artery disease (CAD) with diffuse long lesion underwent coronary artery bypass graft (CABG) or percutaneous coronary intervention (PCI) remains worse. Here, we aimed to identify distinctive genes involved and offer novel insights into the pathogenesis of diffuse long lesion. MATERIALS AND METHODS Whole exome sequencing was performed on peripheral blood samples from 20 CAD patients with diffuse long lesion (CAD-DLL) and from 10 controls with focal lesion (CAD-FL) through a uniform pipeline. Proteomics analysis was conducted on the serum samples from 10 CAD-DLL patients and from 10 controls with CAD-FL by mass spectrometry. Bioinformatics analysis was performed to elucidate the involved genes, including functional annotation and protein-protein interaction analysis. RESULTS A total of 742 shared variant genes were found in CAD-DLL patients but not in controls. Of these, 46 genes were identified as high-frequency variant genes (≥ 4/20) distinctive genes. According to the consensus variant site, 148 shared variant sites were found in the CAD-DLL group. The lysosome and cellular senescence-related pathway may be the most significant pathway in diffuse long lesion. Following the DNA-protein combined analysis, eight genes were screened whose expression levels were altered at both DNA and protein levels. Among these genes, the MAN2A2 gene, the only one that was highly expressed at the protein level, was associated with metabolic and immune-inflammatory dysregulation. CONCLUSIONS Compared to individuals with CAD-FL, patients with CAD-DLL show additional variants. These findings contribute to the understanding of the mechanism of CAD-DLL and provide potential targets for the diagnosis and treatment of CAD-DLL.
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Affiliation(s)
- Ce Chao
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China
| | - Yongxiang Qian
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China
| | - Hao Lv
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China
| | - Kun Mei
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China
| | - Min Wang
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China
| | - Yang Liu
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China
| | - Bin Wang
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China.
| | - Dongmei Di
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, No.185, Juqian Street, Tianning District, Changzhou, 213003, Jiangsu Province, China.
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Yu Y, Li X, Teng T, He Y, Jiang Y, Liu X, Zhou X, Luo Y, Xie P. Comparative analysis of the nucleus accumbens transcriptional features in multiple depressive animal models. Behav Brain Res 2024; 463:114890. [PMID: 38309372 DOI: 10.1016/j.bbr.2024.114890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
Chronic stress is deemed a significant clinical contributor to depression. The use of animal models of chronic stress can fully reveal the complex pathological mechanisms and their changing trends in the pathogenesis of depression, which is crucial for both disease prevention and therapy. It is also unknown how various forms of stress differ in their impact on animal physiology and behavior. The nucleus accumbens (NAc), an essential brain area for the pathophysiology of depression, and its underlying neural mechanisms remain unclear. Here, we systematically compared transcriptional signatures in the NAc of four chronic stress models in rats: chronic unpredictable mild stress (CUMS), chronic social defeat stress (CSDS), learned helplessness (LH), chronic restraint stress (CRS). The majority of differentially expressed genes (DEGs) were unique to a single depression model, while the rank-rank hypergeometric overlap analysis showed that the CSDS and CRS models had the greatest overlap, and the CRS and CUMS models had the least. Then, we performed pathway analysis of the differential genes and found that the neuroactive ligand-receptor interaction pathway was significantly enriched not only in the LH, CRS and CSDS stress models, but also significantly enriched in stress genes that were also altered in at least two stress models. Finally, we found three hub genes (Dcx, Tnc and Wdfy4) by constructing co-expression networks for stress genes. In summary, our research has the potential to offer fresh insights into the molecular mechanisms underlying depression induced by different types of stress, highlighting both their similarities and differences. It may provide valuable clues for understanding the pathogenesis of depression.
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Affiliation(s)
- Ying Yu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Li
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Teng Teng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuqian He
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuanliang Jiang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xueer Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinyu Zhou
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Yong Luo
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Cheng J, Wang Z, Tang M, Zhang W, Li G, Tan S, Mu C, Hu M, Zhang D, Jia X, Wen Y, Guo H, Xu D, Liu L, Li J, Xia K, Li F, Duan R, Xu Z, Yuan L. KCTD10 regulates brain development by destabilizing brain disorder-associated protein KCTD13. Proc Natl Acad Sci U S A 2024; 121:e2315707121. [PMID: 38489388 PMCID: PMC10963008 DOI: 10.1073/pnas.2315707121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/02/2024] [Indexed: 03/17/2024] Open
Abstract
KCTD10 belongs to the KCTD (potassiumchannel tetramerization domain) family, many members of which are associated with neuropsychiatric disorders. However, the biological function underlying the association with brain disorders remains to be explored. Here, we reveal that Kctd10 is highly expressed in neuronal progenitors and layer V neurons throughout brain development. Kctd10 deficiency triggers abnormal proliferation and differentiation of neuronal progenitors, reduced deep-layer (especially layer V) neurons, increased upper-layer neurons, and lowered brain size. Mechanistically, we screened and identified a unique KCTD10-interacting protein, KCTD13, associated with neurodevelopmental disorders. KCTD10 mediated the ubiquitination-dependent degradation of KCTD13 and KCTD10 ablation resulted in a considerable increase of KCTD13 expression in the developing cortex. KCTD13 overexpression in neuronal progenitors led to reduced proliferation and abnormal cell distribution, mirroring KCTD10 deficiency. Notably, mice with brain-specific Kctd10 knockout exhibited obvious motor deficits. This study uncovers the physiological function of KCTD10 and provides unique insights into the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Jianbo Cheng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Zhen Wang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Manpei Tang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Wen Zhang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Guozhong Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Senwei Tan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Chenjun Mu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Mengyuan Hu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing100101, China
| | - Xiangbin Jia
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Yangxuan Wen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Hui Guo
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Dan Xu
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou350005, China
| | - Liang Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing100053, China
| | - Jiada Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Kun Xia
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Faxiang Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Ranhui Duan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing100101, China
| | - Ling Yuan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
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8
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Cavalli A, Caraffi SG, Rizzi S, Trimarchi G, Napoli M, Frattini D, Spagnoli C, Garavelli L, Fusco C. Heterozygous truncating variant of TAOK1 in a boy with periventricular nodular heterotopia: a case report and literature review of TAOK1-related neurodevelopmental disorders. BMC Med Genomics 2024; 17:68. [PMID: 38443934 PMCID: PMC10916022 DOI: 10.1186/s12920-024-01840-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Thousand and one amino-acid kinase 1 (TAOK1) encodes the MAP3K protein kinase TAO1, which has recently been displayed to be essential for neuronal maturation and cortical differentiation during early brain development. Heterozygous variants in TAOK1 have been reported in children with neurodevelopmental disorders, with or without macrocephaly, hypotonia and mild dysmorphic traits. Literature reports lack evidence of neuronal migration disorders in TAOK1 patients, although studies in animal models suggest this possibility. CASE PRESENTATION We provide a clinical description of a child with a neurodevelopmental disorder due to a novel TAOK1 truncating variant, whose brain magnetic resonance imaging displays periventricular nodular heterotopia. CONCLUSIONS To our knowledge, this is the first report of a neuronal migration disorder in a patient with a TAOK1-related neurodevelopmental disorder, thus supporting the hypothesized pathogenic mechanisms of TAOK1 defects.
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Affiliation(s)
- Anna Cavalli
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy.
| | - Stefano Giuseppe Caraffi
- Medical Genetics Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Susanna Rizzi
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Gabriele Trimarchi
- Medical Genetics Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Manuela Napoli
- Neuroradiology Unit, Arcispedale santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Daniele Frattini
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Carlotta Spagnoli
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Dipartimento Materno-Infantile, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, 42123, Reggio Emilia, Italy
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9
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Nadimpalli Kobren S, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Willett J, Berselli M, Ronchetti W, Sherwood R, Krier J, Kohane IS, Sunyaev SR. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580158. [PMID: 38405764 PMCID: PMC10888768 DOI: 10.1101/2024.02.13.580158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients. The increasing sizes of ultra-rare, "N-of-1" disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.1,2 The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We apply existing and introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We make our gene-level findings and variant-level information across the cohort available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.
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Affiliation(s)
| | | | | | - Daniel Traviglia
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Xinyun Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | | | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Julian Willett
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Michele Berselli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - William Ronchetti
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Richard Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joel Krier
- Department of Genetics, Atrius Health, Boston, MA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | | | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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10
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Nakamura T, Ueda J, Mizuno S, Honda K, Kazuno AA, Yamamoto H, Hara T, Takata A. Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk. CELL GENOMICS 2024; 4:100488. [PMID: 38280381 PMCID: PMC10879036 DOI: 10.1016/j.xgen.2024.100488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 01/29/2024]
Abstract
Whole-genome sequencing (WGS) studies of autism spectrum disorder (ASD) have demonstrated the roles of rare promoter de novo variants (DNVs). However, most promoter DNVs in ASD are not located immediately upstream of known ASD genes. In this study analyzing WGS data of 5,044 ASD probands, 4,095 unaffected siblings, and their parents, we show that promoter DNVs within topologically associating domains (TADs) containing ASD genes are significantly and specifically associated with ASD. An analysis considering TADs as functional units identified specific TADs enriched for promoter DNVs in ASD and indicated that common variants in these regions also confer ASD heritability. Experimental validation using human induced pluripotent stem cells (iPSCs) showed that likely deleterious promoter DNVs in ASD can influence multiple genes within the same TAD, resulting in overall dysregulation of ASD-associated genes. These results highlight the importance of TADs and gene-regulatory mechanisms in better understanding the genetic architecture of ASD.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shota Mizuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - An-A Kazuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hirona Yamamoto
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Organ Anatomy, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
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11
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Kinoshita S, Kojima K, Ohnishi E, Takayama Y, Kikuchi H, Takada S, Nakabayashi K, Kawai T, Hata K. Loss of NSD2 causes dysregulation of synaptic genes and altered H3K36 dimethylation in mice. Front Genet 2024; 15:1308234. [PMID: 38419783 PMCID: PMC10899350 DOI: 10.3389/fgene.2024.1308234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Background: Epigenetic disruptions have been implicated in neurodevelopmental disorders. NSD2 is associated with developmental delay/intellectual disability; however, its role in brain development and function remains unclear. Methods: We performed transcriptomic and epigenetic analyses using Nsd2 knockout mice to better understand the role of NSD2 in the brain. Results and discussion: Transcriptomic analysis revealed that the loss of NSD2 caused dysregulation of genes related to synaptic transmission and formation. By analyzing changes in H3 lysine 36 dimethylation (H3K36me2), NSD2-mediated H3K36me2 mainly marked quiescent state regions and the redistribution of H3K36me2 occurred at transcribed genes and enhancers. By integrating transcriptomic and epigenetic data, we observed that H3K36me2 changes in a subset of dysregulated genes related to synaptic transmission and formation. These results suggest that NSD2 is involved in the regulation of genes important for neural function through H3K36me2. Our findings provide insights into the role of NSD2 and improve our understanding of epigenetic regulation in the brain.
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Affiliation(s)
- Shiori Kinoshita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of NCCHD Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuaki Kojima
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Eriko Ohnishi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuka Takayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiroki Kikuchi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
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12
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Ng JK, Chen Y, Akinwe TM, Heins HB, Mehinovic E, Chang Y, Payne ZL, Manuel JG, Karchin R, Turner TN. Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.02.24302238. [PMID: 38352539 PMCID: PMC10863034 DOI: 10.1101/2024.02.02.24302238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Missense de novo variants (DNVs) and missense somatic variants contribute to neurodevelopmental disorders (NDDs) and cancer, respectively. Proteins with statistical enrichment based on analyses of these variants exhibit convergence in the differing NDD and cancer phenotypes. Herein, the question of why some of the same proteins are identified in both phenotypes is examined through investigation of clustering of missense variation at the protein level. Our hypothesis is that missense variation is present in different protein locations in the two phenotypes leading to the distinct phenotypic outcomes. We tested this hypothesis in 1D protein space using our software CLUMP. Furthermore, we newly developed 3D-CLUMP that uses 3D protein structures to spatially test clustering of missense variation for proteome-wide significance. We examined missense DNVs in 39,883 parent-child sequenced trios with NDDs and missense somatic variants from 10,543 sequenced tumors covering five TCGA cancer types and two COSMIC pan-cancer aggregates of tissue types. There were 57 proteins with proteome-wide significant missense variation clustering in NDDs when compared to cancers and 79 proteins with proteome-wide significant missense clustering in cancers compared to NDDs. While our main objective was to identify differences in patterns of missense variation, we also identified a novel NDD protein BLTP2. Overall, our study is innovative, provides new insights into differential missense variation in NDDs and cancer at the protein-level, and contributes necessary information toward building a framework for thinking about prognostic and therapeutic aspects of these proteins.
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Affiliation(s)
- Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yilin Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Titilope M. Akinwe
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hillary B. Heins
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elvisa Mehinovic
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoonhoo Chang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Human & Statistical Genetics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary L. Payne
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juana G. Manuel
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
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13
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Shim G, Romero-Morales AI, Sripathy SR, Maher BJ. Utilizing hiPSC-derived oligodendrocytes to study myelin pathophysiology in neuropsychiatric and neurodegenerative disorders. Front Cell Neurosci 2024; 17:1322813. [PMID: 38273973 PMCID: PMC10808804 DOI: 10.3389/fncel.2023.1322813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Oligodendrocytes play a crucial role in our central nervous system (CNS) by myelinating axons for faster action potential conduction, protecting axons from degeneration, structuring the position of ion channels, and providing nutrients to neurons. Oligodendrocyte dysfunction and/or dysmyelination can contribute to a range of neurodegenerative diseases and neuropsychiatric disorders such as Multiple Sclerosis (MS), Leukodystrophy (LD), Schizophrenia (SCZ), and Autism Spectrum Disorder (ASD). Common characteristics identified across these disorders were either an inability of oligodendrocytes to remyelinate after degeneration or defects in oligodendrocyte development and maturation. Unfortunately, the causal mechanisms of oligodendrocyte dysfunction are still uncertain, and therapeutic targets remain elusive. Many studies rely on the use of animal models to identify the molecular and cellular mechanisms behind these disorders, however, such studies face species-specific challenges and therefore lack translatability. The use of human induced pluripotent stem cells (hiPSCs) to model neurological diseases is becoming a powerful new tool, improving our understanding of pathophysiology and capacity to explore therapeutic targets. Here, we focus on the application of hiPSC-derived oligodendrocyte model systems to model disorders caused by oligodendrocyte dysregulation.
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Affiliation(s)
- Gina Shim
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Alejandra I. Romero-Morales
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Srinidhi R. Sripathy
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Brady J. Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
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14
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McClellan JM, Zoghbi AW, Buxbaum JD, Cappi C, Crowley JJ, Flint J, Grice DE, Gulsuner S, Iyegbe C, Jain S, Kuo PH, Lattig MC, Passos-Bueno MR, Purushottam M, Stein DJ, Sunshine AB, Susser ES, Walsh CA, Wootton O, King MC. An evolutionary perspective on complex neuropsychiatric disease. Neuron 2024; 112:7-24. [PMID: 38016473 PMCID: PMC10842497 DOI: 10.1016/j.neuron.2023.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Flint
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | | | | | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Anna B Sunshine
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ezra S Susser
- Department of Epidemiology, Mailman School of Public Health, and New York State Psychiatric Institute, Columbia University, New York, NY 10032, USA
| | - Christopher A Walsh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Wootton
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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15
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Liu L, Wang J, Liu X, Wang J, Chen L, Zhu H, Mai J, Hu T, Liu S. Prenatal prevalence and postnatal manifestations of 16p11.2 deletions: A new insights into neurodevelopmental disorders based on clinical investigations combined with multi-omics analysis. Clin Chim Acta 2024; 552:117671. [PMID: 37984529 DOI: 10.1016/j.cca.2023.117671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND The 16p11.2 deletion is one of the most common genetic aetiologies of neurodevelopmental disorders (NDDs). The prenatal phenotype of 16p11.2 deletion and the potential mechanism associated with postnatal clinical manifestations were largely unknow. We revealed the developmental trajectories of 16p11.2 deletion from the prenatal to postnatal periods and to identify key signaling pathways and candidate genes contributing to neurodevelopmental abnormalities. METHODS In this 5-y retrospective cohort study, women with singleton pregnancies who underwent amniocentesis for chromosomal abnormalities were included. Test of copy-number variations (CNVs) involved single nucleotide polymorphism-array and CNV-seq was performed to detected 16p11.2 deletion. For infants born carrying the 16p11.2 deletion, neurological and intellectual evaluations using the Chinese version of the Gesell Development Scale. For patients observed to have vertebral malformations, Sanger sequencing for T-C-A haplotype of TBX6 was performed. For those infants with clinical manifestations, whole-exome sequencing was consecutively performed in trios to rule out single-gene diseases, and transcriptomics combined with untargeted metabolomics were performed. RESULTS The prevalence of 16p11.2 deletion was 0.063% (55/86,035) in the prenatal period. Up to 80% (20/25) of the 16p11.2 deletions were proven de novo by parental confirmation. Approximately half of 16p11.2 deletions (28/55) were detected with prenatal abnormal ultrasound findings. Vertebral malformations were identified as the most distinctive structural malformations and were enriched in fetuses with 16p11.2 deletions compared with controls (90.9‰ [5/55] vs. 8.4‰ [72/85,980]; P < 0.001). All 5 fetuses with vertebral malformations were confirmed to have the TBX6 haplotype of T-C-A. Overall, 47.6% (10/21) infants birthed were diagnosed with NDDs of different degrees. Language impairment was the predominant manifestation (7/10; 70.0%), followed by motor delay (5/10; 50%). Multi-omics analysis indicated that MAPK3 was the central hub of the differentially expressed gene (DEG) network. We firstly reported that histidine-associated metabolism may be the core metabolic pathway related to the 16p11.2 deletion. CONCLUSION We demonstrated the prenatal presentation, incomplete penetrance and variable expressivity of the 16p11.2 deletion. We identified vertebral malformations were the most distinctive prenatal phenotypes, and language impairment was the predominant postnatal manifestation. Most of the 16p11.2 deletion was de novo. Meanwhile, we suggested that MAPK3 and histidine-associated metabolism may contribute to neurodevelopmental abnormalities of 16p11.2 deletion.
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Affiliation(s)
- Lan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Medical College, Tibet University, Lhasa, Tibet 850000, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Chen
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongmei Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingqun Mai
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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16
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Szewczyk LM, Lipiec MA, Liszewska E, Meyza K, Urban-Ciecko J, Kondrakiewicz L, Goncerzewicz A, Rafalko K, Krawczyk TG, Bogaj K, Vainchtein ID, Nakao-Inoue H, Puscian A, Knapska E, Sanders SJ, Jan Nowakowski T, Molofsky AV, Wisniewska MB. Astrocytic β-catenin signaling via TCF7L2 regulates synapse development and social behavior. Mol Psychiatry 2024; 29:57-73. [PMID: 37798419 PMCID: PMC11078762 DOI: 10.1038/s41380-023-02281-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
The Wnt/β-catenin pathway contains multiple high-confidence risk genes that are linked to neurodevelopmental disorders, including autism spectrum disorder. However, its ubiquitous roles across brain cell types and developmental stages have made it challenging to define its impact on neural circuit development and behavior. Here, we show that TCF7L2, which is a key transcriptional effector of the Wnt/β-catenin pathway, plays a cell-autonomous role in postnatal astrocyte maturation and impacts adult social behavior. TCF7L2 was the dominant Wnt effector that was expressed in both mouse and human astrocytes, with a peak during astrocyte maturation. The conditional knockout of Tcf7l2 in postnatal astrocytes led to an enlargement of astrocytes with defective tiling and gap junction coupling. These mice also exhibited an increase in the number of cortical excitatory and inhibitory synapses and a marked increase in social interaction by adulthood. These data reveal an astrocytic role for developmental Wnt/β-catenin signaling in restricting excitatory synapse numbers and regulating adult social behavior.
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Affiliation(s)
- Lukasz Mateusz Szewczyk
- Department of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| | - Marcin Andrzej Lipiec
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Laboratory of Emotions Neurobiology, BRAINCITY-Center of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ewa Liszewska
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Ksenia Meyza
- Laboratory of Emotions Neurobiology, BRAINCITY-Center of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Urban-Ciecko
- Laboratory of Electrophysiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ludwika Kondrakiewicz
- Laboratory of Emotions Neurobiology, BRAINCITY-Center of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Goncerzewicz
- Laboratory of Emotions Neurobiology, BRAINCITY-Center of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Karolina Bogaj
- Laboratory of Electrophysiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ilia Davidovich Vainchtein
- Department of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Johnson & Johnson, Neuroscience Therapeutic Area, San Diego, CA, USA
| | - Hiromi Nakao-Inoue
- Department of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Alicja Puscian
- Laboratory of Emotions Neurobiology, BRAINCITY-Center of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ewelina Knapska
- Laboratory of Emotions Neurobiology, BRAINCITY-Center of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
- New York Genome Center, New York, NY, USA
| | - Tomasz Jan Nowakowski
- Department of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Anna Victoria Molofsky
- Department of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
| | - Marta Barbara Wisniewska
- Laboratory of Molecular Neurobiology, Centre of New Technologies, University of Warsaw, Warsaw, Poland.
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17
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Li K, Xiao J, Ling Z, Luo T, Xiong J, Chen Q, Dong L, Wang Y, Wang X, Jiang Z, Xia L, Yu Z, Hua R, Guo R, Tang D, Lv M, Lian A, Li B, Zhao G, He X, Xia K, Cao Y, Li J. Prioritizing de novo potential non-canonical splicing variants in neurodevelopmental disorders. EBioMedicine 2024; 99:104928. [PMID: 38113761 PMCID: PMC10767160 DOI: 10.1016/j.ebiom.2023.104928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Genomic variants outside of the canonical splicing site (±2) may generate abnormal mRNA splicing, which are defined as non-canonical splicing variants (NCSVs). However, the clinical interpretation of NCSVs in neurodevelopmental disorders (NDDs) is largely unknown. METHODS We investigated the contribution of NCSVs to NDDs from 345,787 de novo variants (DNVs) in 47,574 patients with NDDs. We performed functional enrichment and protein-protein interaction analysis to assess the association between genes carrying prioritised NCSVs and NDDs. Minigene was used to validate the impact of NCSVs on mRNA splicing. FINDINGS We observed significantly more NCSVs (p = 0.02, odds ratio [OR] = 2.05) among patients with NDD than in controls. Both canonical splicing variants (CSVs) and NCSVs contributed to an equal proportion of patients with NDD (0.76% vs. 0.82%). The candidate genes carrying NCSVs were associated with glutamatergic synapse and chromatin remodelling. Minigene successfully validated 59 of 79 (74.68%) NCSVs that led to abnormal splicing in 40 candidate genes, and 9 of the genes (ARID1B, KAT6B, TCF4, SMARCA2, SHANK3, PDHA1, WDR45, SCN2A, SYNGAP1) harboured recurrent NCSVs with the same variant present in more than two unrelated patients with NDD. Moreover, 36 of 59 (61.02%) NCSVs are novel clinically relevant variants, including 34 unreported and 2 clinically conflicting interpretations or of uncertain significance NCSVs in the ClinVar database. INTERPRETATION This study highlights the common pathology and clinical importance of NCSVs in unsolved patients with NDD. FUNDING The present study was funded by grants from the National Natural Science Foundation of China, China Postdoctoral Science Foundation, the Hunan Youth Science and Technology Innovation Talent Project, the Provincial Natural Science Foundation of Hunan, The Scientific Research Program of FuRong laboratory, and the Natural Science Project of the University of Anhui Province.
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Affiliation(s)
- Kuokuo Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Jifang Xiao
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China
| | - Zhengbao Ling
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Luo
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jingyu Xiong
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Chen
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China
| | - Lijie Dong
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China
| | - Zhaowei Jiang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhen Yu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Rong Hua
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Rui Guo
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Dongdong Tang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Aojie Lian
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China
| | - Bin Li
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China
| | - GuiHu Zhao
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China; Anhui Provincial Human Sperm Bank, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Jinchen Li
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China.
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18
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Harris RA, Raveendran M, Warren W, LaDeana HW, Tomlinson C, Graves-Lindsay T, Green RE, Schmidt JK, Colwell JC, Makulec AT, Cole SA, Cheeseman IH, Ross CN, Capuano S, Eichler EE, Levine JE, Rogers J. Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets ( Callithrix jacchus). Genes (Basel) 2023; 14:2185. [PMID: 38137007 PMCID: PMC10742769 DOI: 10.3390/genes14122185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
The common marmoset (Callithrix jacchus) is one of the most widely used nonhuman primate models of human disease. Owing to limitations in sequencing technology, early genome assemblies of this species using short-read sequencing suffered from gaps. In addition, the genetic diversity of the species has not yet been adequately explored. Using long-read genome sequencing and expert annotation, we generated a high-quality genome resource creating a 2.898 Gb marmoset genome in which most of the euchromatin portion is assembled contiguously (contig N50 = 25.23 Mbp, scaffold N50 = 98.2 Mbp). We then performed whole genome sequencing on 84 marmosets sampling the genetic diversity from several marmoset research centers. We identified a total of 19.1 million single nucleotide variants (SNVs), of which 11.9 million can be reliably mapped to orthologous locations in the human genome. We also observed 2.8 million small insertion/deletion variants. This dataset includes an average of 5.4 million SNVs per marmoset individual and a total of 74,088 missense variants in protein-coding genes. Of the 4956 variants orthologous to human ClinVar SNVs (present in the same annotated gene and with the same functional consequence in marmoset and human), 27 have a clinical significance of pathogenic and/or likely pathogenic. This important marmoset genomic resource will help guide genetic analyses of natural variation, the discovery of spontaneous functional variation relevant to human disease models, and the development of genetically engineered marmoset disease models.
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Affiliation(s)
- R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
| | - Wes Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA;
| | - Hillier W. LaDeana
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98104, USA; (H.W.L.); (E.E.E.)
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA; (C.T.); (T.G.-L.)
| | - Tina Graves-Lindsay
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA; (C.T.); (T.G.-L.)
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA;
| | - Jenna K. Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Julia C. Colwell
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Allison T. Makulec
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Shelley A. Cole
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Ian H. Cheeseman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Corinna N. Ross
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98104, USA; (H.W.L.); (E.E.E.)
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jon E. Levine
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
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19
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Li E, Kampmann M. Toward a CRISPR understanding of gene function in human brain development. Cell Stem Cell 2023; 30:1561-1562. [PMID: 38065064 DOI: 10.1016/j.stem.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]
Abstract
Genome-wide association studies pinpoint genetic risk factors for neurodevelopmental disorders (NDDs), but the next challenge is to understand the mechanisms through which these genes affect brain development. Two recent CRISPR screens in human brain organoids1,2 interrogate the function of risk genes for autism spectrum disorder and other NDDs.
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Affiliation(s)
- Emmy Li
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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20
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Gao C, Zhu H, Gong P, Wu C, Xu X, Zhu X. The functions of FOXP transcription factors and their regulation by post-translational modifications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194992. [PMID: 37797785 DOI: 10.1016/j.bbagrm.2023.194992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023]
Abstract
The forkhead box subfamily P (FOXP) of transcription factors, consisting of FOXP1, FOXP2, FOXP3, and FOXP4, is involved in the regulation of multisystemic functioning. Disruption of the transcriptional activity of FOXP proteins leads to neurodevelopmental disorders and immunological diseases, as well as the suppression or promotion of carcinogenesis. The transcriptional activities of FOXP proteins are directly or indirectly regulated by diverse post-translational modifications, including phosphorylation, ubiquitination, SUMOylation, acetylation, O-GlcNAcylation, and methylation. Here, we discuss how post-translational modifications modulate the multiple functions of FOXP proteins and examine the implications for tumorigenesis and cancer therapy.
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Affiliation(s)
- Congwen Gao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China; College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Honglin Zhu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China
| | - Peng Gong
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors & Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China
| | - Chen Wu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China.
| | - Xuefei Zhu
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors & Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China.
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21
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Beard DC, Zhang X, Wu DY, Martin JR, Erickson A, Boua JV, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Palmer CW, Fuhler NA, Lawrence AB, Hill CA, Papouin T, Noguchi KK, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. Cell Rep 2023; 42:113411. [PMID: 37952155 PMCID: PMC10843706 DOI: 10.1016/j.celrep.2023.113411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/06/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Phenotypic heterogeneity in monogenic neurodevelopmental disorders can arise from differential severity of variants underlying disease, but how distinct alleles drive variable disease presentation is not well understood. Here, we investigate missense mutations in DNA methyltransferase 3A (DNMT3A), a DNA methyltransferase associated with overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity. We generate a Dnmt3aP900L/+ mouse mimicking a mutation with mild to moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. P900L mutants exhibit core growth and behavioral phenotypes shared across models but show subtle epigenomic changes, while R878H mutants display extensive disruptions. We identify mutation-specific dysregulated genes that may contribute to variable disease severity. Shared transcriptomic disruption identified across mutations overlaps dysregulation observed in other developmental disorder models and likely drives common phenotypes. Together, our findings define central drivers of DNMT3A disorders and illustrate how variable epigenomic disruption contributes to phenotypic heterogeneity in neurodevelopmental disease.
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Affiliation(s)
- Diana C Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alyssa Erickson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jane Valeriane Boua
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA; Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cory W Palmer
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole A Fuhler
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A Hill
- 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, USA
| | - Kevin K Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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22
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Li SY, Zhao X, Cheng MY, Lu L, Guo JX, Xuan DS, Sun YB, Xing QN, Meng LS, Liao JJ, Cui SH, Zhang LJ, Feng ZQ, Zhang XA. Quantitative Relaxometry Assessment of Brain Microstructural Abnormality of Preschool Children With Autism Spectrum Disorder With Synthetic Magnetic Resonance Imaging. J Comput Assist Tomogr 2023; 47:959-966. [PMID: 37948372 DOI: 10.1097/rct.0000000000001507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
OBJECTIVE This study aimed to perform an assessment of brain microstructure in children with autism aged 2 to 5 years using relaxation times acquired by synthetic magnetic resonance imaging. MATERIALS AND METHODS Thirty-four children with autism spectrum disorder (ASD) (ASD group) and 17 children with global developmental delay (GDD) (GDD group) were enrolled, and synthetic magnetic resonance imaging was performed to obtain T1 and T2 relaxation times. The differences in brain relaxation times between the 2 groups of children were compared, and the correlation between significantly changed T1/T2 and clinical neuropsychological scores in the ASD group was analyzed. RESULTS Compared with the GDD group, shortened T1 relaxation times in the ASD group were distributed in the genu of corpus callosum (GCC) ( P = 0.003), splenium of corpus callosum ( P = 0.002), and right thalamus (TH) ( P = 0.014), whereas shortened T2 relaxation times in the ASD group were distributed in GCC ( P = 0.011), left parietal white matter ( P = 0.035), and bilateral TH (right, P = 0.014; left, P = 0.016). In the ASD group, the T2 of the left parietal white matter is positively correlated with gross motor (developmental quotient [DQ] 2) and personal-social behavior (DQ5), respectively ( r = 0.377, P = 0.028; r = 0.392, P = 0.022); the T2 of the GCC was positively correlated with DQ5 ( r = 0.404, P = 0.018); and the T2 of the left TH is positively correlated with DQ2 and DQ5, respectively ( r = 0.433, P = 0.009; r = 0.377, P = 0.028). All significantly changed relaxation values were not significantly correlated with Childhood Autism Rating Scale scores. CONCLUSIONS The shortened relaxometry times in the brain of children with ASD may be associated with the increased myelin content and decreased water content in the brain of children with ASD in comparison with GDD, contributing the understanding of the pathophysiology of ASD. Therefore, the T1 and T2 relaxometry may be used as promising imaging markers for ASD diagnosis.
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Affiliation(s)
- Shuang-Yu Li
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Xin Zhao
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Mei-Ying Cheng
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Lin Lu
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | | | - De-Sheng Xuan
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Yong-Bing Sun
- Zhengzhou University People's Hospital, Zhengzhou, China
| | - Qing-Na Xing
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Ling-Song Meng
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Jun-Jie Liao
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Shu-Hong Cui
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Ling-Jie Zhang
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Zhan-Qi Feng
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
| | - Xiao-An Zhang
- From the Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou
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23
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Meng X, Yao D, Imaizumi K, Chen X, Kelley KW, Reis N, Thete MV, Arjun McKinney A, Kulkarni S, Panagiotakos G, Bassik MC, Pașca SP. Assembloid CRISPR screens reveal impact of disease genes in human neurodevelopment. Nature 2023; 622:359-366. [PMID: 37758944 PMCID: PMC10567561 DOI: 10.1038/s41586-023-06564-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/22/2023] [Indexed: 09/29/2023]
Abstract
The assembly of cortical circuits involves the generation and migration of interneurons from the ventral to the dorsal forebrain1-3, which has been challenging to study at inaccessible stages of late gestation and early postnatal human development4. Autism spectrum disorder and other neurodevelopmental disorders (NDDs) have been associated with abnormal cortical interneuron development5, but which of these NDD genes affect interneuron generation and migration, and how they mediate these effects remains unknown. We previously developed a platform to study interneuron development and migration in subpallial organoids and forebrain assembloids6. Here we integrate assembloids with CRISPR screening to investigate the involvement of 425 NDD genes in human interneuron development. The first screen aimed at interneuron generation revealed 13 candidate genes, including CSDE1 and SMAD4. We subsequently conducted an interneuron migration screen in more than 1,000 forebrain assembloids that identified 33 candidate genes, including cytoskeleton-related genes and the endoplasmic reticulum-related gene LNPK. We discovered that, during interneuron migration, the endoplasmic reticulum is displaced along the leading neuronal branch before nuclear translocation. LNPK deletion interfered with this endoplasmic reticulum displacement and resulted in abnormal migration. These results highlight the power of this CRISPR-assembloid platform to systematically map NDD genes onto human development and reveal disease mechanisms.
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Affiliation(s)
- Xiangling Meng
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA
| | - David Yao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kent Imaizumi
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA
| | - Xiaoyu Chen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA
| | - Kevin W Kelley
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA
| | - Noah Reis
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA
| | - Mayuri Vijay Thete
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA
| | - Arpana Arjun McKinney
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- Departments of Psychiatry and Neuroscience, Black Family Stem Cell Institute, Seaver Autism Center for Research and Treatment, Alper Center for Neural Development and Regeneration, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shravanti Kulkarni
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA
| | - Georgia Panagiotakos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Departments of Psychiatry and Neuroscience, Black Family Stem Cell Institute, Seaver Autism Center for Research and Treatment, Alper Center for Neural Development and Regeneration, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute and Bio-X, Stanford, CA, USA.
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24
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Shin T, Song JH, Kosicki M, Kenny C, Beck SG, Kelley L, Qian X, Bonacina J, Papandile F, Antony I, Gonzalez D, Scotellaro J, Bushinsky EM, Andersen RE, Maury E, Pennacchio LA, Doan RN, Walsh CA. Rare variation in noncoding regions with evolutionary signatures contributes to autism spectrum disorder risk. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.19.23295780. [PMID: 37790480 PMCID: PMC10543033 DOI: 10.1101/2023.09.19.23295780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Little is known about the role of noncoding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of noncoding regions: Human Accelerated Regions (HARs), which show signatures of positive selection in humans; experimentally validated neural Vista Enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole genome analysis of >16,600 samples and >4900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in a VE near SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved noncoding regions in ASD risk and suggest potential mechanisms of how changes in regulatory regions can modulate social behavior.
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Affiliation(s)
- Taehwan Shin
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Janet H.T. Song
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Michael Kosicki
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor Kenny
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Samantha G. Beck
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Lily Kelley
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Julieta Bonacina
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Frances Papandile
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Irene Antony
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Julia Scotellaro
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Evan M. Bushinsky
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Rebecca E. Andersen
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Eduardo Maury
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Len A. Pennacchio
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan N. Doan
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
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25
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Cuppens T, Kaur M, Kumar AA, Shatto J, Ng ACH, Leclercq M, Reformat MZ, Droit A, Dunham I, Bolduc FV. Developing a cluster-based approach for deciphering complexity in individuals with neurodevelopmental differences. Front Pediatr 2023; 11:1171920. [PMID: 37790694 PMCID: PMC10543689 DOI: 10.3389/fped.2023.1171920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
Objective Individuals with neurodevelopmental disorders such as global developmental delay (GDD) present both genotypic and phenotypic heterogeneity. This diversity has hampered developing of targeted interventions given the relative rarity of each individual genetic etiology. Novel approaches to clinical trials where distinct, but related diseases can be treated by a common drug, known as basket trials, which have shown benefits in oncology but have yet to be used in GDD. Nonetheless, it remains unclear how individuals with GDD could be clustered. Here, we assess two different approaches: agglomerative and divisive clustering. Methods Using the largest cohort of individuals with GDD, which is the Deciphering Developmental Disorders (DDD), characterized using a systematic approach, we extracted genotypic and phenotypic information from 6,588 individuals with GDD. We then used a k-means clustering (divisive) and hierarchical agglomerative clustering (HAC) to identify subgroups of individuals. Next, we extracted gene network and molecular function information with regard to the clusters identified by each approach. Results HAC based on phenotypes identified in individuals with GDD revealed 16 clusters, each presenting with one dominant phenotype displayed by most individuals in the cluster, along with other minor phenotypes. Among the most common phenotypes reported were delayed speech, absent speech, and seizure. Interestingly, each phenotypic cluster molecularly included several (3-12) gene sub-networks of more closely related genes with diverse molecular function. k-means clustering also segregated individuals harboring those phenotypes, but the genetic pathways identified were different from the ones identified from HAC. Conclusion Our study illustrates how divisive (k-means) and agglomerative clustering can be used in order to group individuals with GDD for future basket trials. Moreover, the result of our analysis suggests that phenotypic clusters should be subdivided into molecular sub-networks for an increased likelihood of successful treatment. Finally, a combination of both agglomerative and divisive clustering may be required for developing of a comprehensive treatment.
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Affiliation(s)
- Tania Cuppens
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Manpreet Kaur
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Ajay A. Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julie Shatto
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Andy Cheuk-Him Ng
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Mickael Leclercq
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Marek Z. Reformat
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - François V. Bolduc
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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26
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LaPolice TM, Huang YF. An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data. BMC Bioinformatics 2023; 24:347. [PMID: 37723435 PMCID: PMC10506225 DOI: 10.1186/s12859-023-05481-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/13/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. While the existing methods are highly predictive of essential genes of long length, they have limited power in pinpointing short essential genes due to the sparsity of polymorphisms in the human genome. RESULTS Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. Compared with previous methods, DeepLOF shows unmatched performance in predicting ClinGen haploinsufficient genes, mouse essential genes, and essential genes in human cell lines. Notably, at a false positive rate of 5%, DeepLOF detects 50% more ClinGen haploinsufficient genes than previous methods. Furthermore, DeepLOF discovers 109 novel essential genes that are too short to be identified by previous methods. CONCLUSION The predictive power of DeepLOF shows that it is a compelling computational method to aid in the discovery of essential genes.
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Affiliation(s)
- Troy M LaPolice
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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27
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Turner TN. Acorn: an R package for de novo variant analysis. BMC Bioinformatics 2023; 24:330. [PMID: 37660114 PMCID: PMC10475174 DOI: 10.1186/s12859-023-05457-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND The study of de novo variation is important for assessing biological characteristics of new variation and for studies related to human phenotypes. Software programs exist to call de novo variants and programs also exist to test the burden of these variants in genomic regions; however, I am unaware of a program that fits in between these two aspects of de novo variant assessment. This intermediate space is important for assessing the quality of de novo variants and to understand the characteristics of the callsets. For this reason, I developed an R package called acorn. RESULTS Acorn is an R package that examines various features of de novo variants including subsetting the data by individual(s), variant type, or genomic region; calculating features including variant change counts, variant lengths, and presence/absence at CpG sites; and characteristics of parental age in relation to de novo variant counts. CONCLUSIONS Acorn is an R package that fills a critical gap in assessing de novo variants and will be of benefit to many investigators studying de novo variation.
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Affiliation(s)
- Tychele N Turner
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.
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28
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Cuppens T, Shatto J, Mangnier L, Kumar AA, Ng ACH, Kaur M, Bui TA, Leclercq M, Droit A, Dunham I, Bolduc FV. Sex difference contributes to phenotypic diversity in individuals with neurodevelopmental disorders. Front Pediatr 2023; 11:1172154. [PMID: 37609366 PMCID: PMC10441218 DOI: 10.3389/fped.2023.1172154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
Objective Gain a better understanding of sex-specific differences in individuals with global developmental delay (GDD), with a focus on phenotypes and genotypes. Methods Using the Deciphering Developmental Disorders (DDD) dataset, we extracted phenotypic information from 6,588 individuals with GDD and then identified statistically significant variations in phenotypes and genotypes based on sex. We compared genes with pathogenic variants between sex and then performed gene network and molecular function enrichment analysis and gene expression profiling between sex. Finally, we contrasted individuals with autism as an associated condition. Results We identified significantly differentially expressed phenotypes in males vs. females individuals with GDD. Autism and macrocephaly were significantly more common in males whereas microcephaly and stereotypies were more common in females. Importantly, 66% of GDD genes with pathogenic variants overlapped between both sexes. In the cohort, males presented with only slightly increased X-linked genes (9% vs. 8%, respectively). Individuals from both sexes harbored a similar number of pathogenic variants overall (3) but females presented with a significantly higher load for GDD genes with high intolerance to loss of function. Sex difference in gene expression correlated with genes identified in a sex specific manner. While we identified sex-specific GDD gene mutations, their pathways overlapped. Interestingly, individuals with GDD but also co-morbid autism phenotypes, we observed distinct mutation load, pathways and phenotypic presentation. Conclusion Our study shows for the first time that males and females with GDD present with significantly different phenotypes. Moreover, while most GDD genes overlapped, some genes were found uniquely in each sex. Surprisingly they shared similar molecular functions. Sorting genes by predicted tolerance to loss of function (pLI) led to identifying an increased mutation load in females with GDD, suggesting potentially a tolerance to GDD genes of higher pLI compared to overall GDD genes. Finally, we show that considering associated conditions (for instance autism) may influence the genomic underpinning found in individuals with GDD and highlight the importance of comprehensive phenotyping.
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Affiliation(s)
- Tania Cuppens
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Julie Shatto
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Loïc Mangnier
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Ajay A. Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Andy Cheuk-Him Ng
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Manpreet Kaur
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Truong An Bui
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Mickael Leclercq
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec-Université Laval, Département de Médecine Moléculaire de L'Université Laval, Québec, QC, Canada
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Francois V. Bolduc
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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29
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Zhong G, Choi YA, Shen Y. VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Commun Biol 2023; 6:774. [PMID: 37491581 PMCID: PMC10368729 DOI: 10.1038/s42003-023-05155-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
Rare or de novo variants have substantial contribution to human diseases, but the statistical power to identify risk genes by rare variants is generally low due to rarity of genotype data. Previous studies have shown that risk genes usually have high expression in relevant cell types, although for many conditions the identity of these cell types are largely unknown. Recent efforts in single cell atlas in human and model organisms produced large amount of gene expression data. Here we present VBASS, a Bayesian method that integrates single-cell expression and de novo variant (DNV) data to improve power of disease risk gene discovery. VBASS models disease risk prior as a function of expression profiles, approximated by deep neural networks. It learns the weights of neural networks and parameters of Gamma-Poisson likelihood models of DNV counts jointly from expression and genetics data. On simulated data, VBASS shows proper error rate control and better power than state-of-the-art methods. We applied VBASS to published datasets and identified more candidate risk genes with supports from literature or data from independent cohorts. VBASS can be generalized to integrate other types of functional genomics data in statistical genetics analysis.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Yoolim A Choi
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
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30
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Lax E, Do Carmo S, Enuka Y, Sapozhnikov DM, Welikovitch LA, Mahmood N, Rabbani SA, Wang L, Britt JP, Hancock WW, Yarden Y, Szyf M. Methyl-CpG binding domain 2 (Mbd2) is an epigenetic regulator of autism-risk genes and cognition. Transl Psychiatry 2023; 13:259. [PMID: 37443311 PMCID: PMC10344909 DOI: 10.1038/s41398-023-02561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The Methyl-CpG-Binding Domain Protein family has been implicated in neurodevelopmental disorders. The Methyl-CpG-binding domain 2 (Mbd2) binds methylated DNA and was shown to play an important role in cancer and immunity. Some evidence linked this protein to neurodevelopment. However, its exact role in neurodevelopment and brain function is mostly unknown. Here we show that Mbd2-deficiency in mice (Mbd2-/-) results in deficits in cognitive, social and emotional functions. Mbd2 binds regulatory DNA regions of neuronal genes in the hippocampus and loss of Mbd2 alters the expression of hundreds of genes with a robust down-regulation of neuronal gene pathways. Further, a genome-wide DNA methylation analysis found an altered DNA methylation pattern in regulatory DNA regions of neuronal genes in Mbd2-/- mice. Differentially expressed genes significantly overlap with gene-expression changes observed in brains of Autism Spectrum Disorder (ASD) individuals. Notably, downregulated genes are significantly enriched for human ortholog ASD risk genes. Observed hippocampal morphological abnormalities were similar to those found in individuals with ASD and ASD rodent models. Hippocampal Mbd2 knockdown partially recapitulates the behavioral phenotypes observed in Mbd2-/- mice. These findings suggest that Mbd2 is a novel epigenetic regulator of genes that are associated with ASD in humans. Mbd2 loss causes behavioral alterations that resemble those found in ASD individuals.
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Affiliation(s)
- Elad Lax
- Department of Molecular Biology, Ariel University, Ariel, Israel.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
| | - Sonia Do Carmo
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Yehoshua Enuka
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Lindsay A Welikovitch
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Niaz Mahmood
- Department of Medicine, McGill University Health Center, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Center, Montreal, QC, Canada
| | - Liqing Wang
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, and Biesecker Center for Pediatric Liver Diseases, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan P Britt
- Department of Psychology, McGill University, Montreal, QC, Canada
| | - Wayne W Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, and Biesecker Center for Pediatric Liver Diseases, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
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31
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Rolland T, Cliquet F, Anney RJL, Moreau C, Traut N, Mathieu A, Huguet G, Duan J, Warrier V, Portalier S, Dry L, Leblond CS, Douard E, Amsellem F, Malesys S, Maruani A, Toro R, Børglum AD, Grove J, Baron-Cohen S, Packer A, Chung WK, Jacquemont S, Delorme R, Bourgeron T. Phenotypic effects of genetic variants associated with autism. Nat Med 2023; 29:1671-1680. [PMID: 37365347 PMCID: PMC10353945 DOI: 10.1038/s41591-023-02408-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/19/2023] [Indexed: 06/28/2023]
Abstract
While over 100 genes have been associated with autism, little is known about the prevalence of variants affecting them in individuals without a diagnosis of autism. Nor do we fully appreciate the phenotypic diversity beyond the formal autism diagnosis. Based on data from more than 13,000 individuals with autism and 210,000 undiagnosed individuals, we estimated the odds ratios for autism associated to rare loss-of-function (LoF) variants in 185 genes associated with autism, alongside 2,492 genes displaying intolerance to LoF variants. In contrast to autism-centric approaches, we investigated the correlates of these variants in individuals without a diagnosis of autism. We show that these variants are associated with a small but significant decrease in fluid intelligence, qualification level and income and an increase in metrics related to material deprivation. These effects were larger for autism-associated genes than in other LoF-intolerant genes. Using brain imaging data from 21,040 individuals from the UK Biobank, we could not detect significant differences in the overall brain anatomy between LoF carriers and non-carriers. Our results highlight the importance of studying the effect of the genetic variants beyond categorical diagnosis and the need for more research to understand the association between these variants and sociodemographic factors, to best support individuals carrying these variants.
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Affiliation(s)
- Thomas Rolland
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
| | - Freddy Cliquet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Richard J L Anney
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Clara Moreau
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Nicolas Traut
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
| | - Jinjie Duan
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Swan Portalier
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Louise Dry
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Claire S Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Frédérique Amsellem
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Simon Malesys
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Anna Maruani
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Roberto Toro
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | | | - Wendy K Chung
- Simons Foundation, New York, NY, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
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32
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Liu X, Xu W, Leng F, Zhang P, Guo R, Zhang Y, Hao C, Ni X, Li W. NeuroCNVscore: a tissue-specific framework to prioritise the pathogenicity of CNVs in neurodevelopmental disorders. BMJ Paediatr Open 2023; 7:e001966. [PMID: 37407247 DOI: 10.1136/bmjpo-2023-001966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) are associated with altered development of the brain especially in childhood. Copy number variants (CNVs) play a crucial role in the genetic aetiology of NDDs by disturbing gene expression directly at linear sequence or remotely at three-dimensional genome level in a tissue-specific manner. Despite the substantial increase in NDD studies employing whole-genome sequencing, there is no specific tool for prioritising the pathogenicity of CNVs in the context of NDDs. METHODS Using an XGBoost classifier, we integrated 189 features that represent genomic sequences, gene information and functional/genomic segments for evaluating genome-wide CNVs in a neuro/brain-specific manner, to develop a new tool, neuroCNVscore. We used Human Phenotype Ontology to construct an independent NDD-related set. RESULTS Our neuroCNVscore framework (https://github.com/lxsbch/neuroCNVscore) achieved high predictive performance (precision recall=0.82; area under curve=0.85) and outperformed an existing reference method SVScore. Notably, the predicted pathogenic CNVs showed enrichment in known genes associated with autism. CONCLUSIONS NeuroCNVscore prioritises functional, deleterious and pathogenic CNVs in NDDs at whole genome-wide level, which is important for genetic studies and clinical genomic screening of NDDs as well as for providing novel biological insights into NDDs.
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Affiliation(s)
- Xuanshi Liu
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Wenjian Xu
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Fei Leng
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Peng Zhang
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Ruolan Guo
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Yue Zhang
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Chanjuan Hao
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Xin Ni
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- National Centre for Children's Health, Beijing, China
| | - Wei Li
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
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33
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Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel C, Ellis JL, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann S, van der Schoot V, Brunet T, Bußmann C, Mignot C, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, Wang T. Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.13.23290941. [PMID: 37398376 PMCID: PMC10312857 DOI: 10.1101/2023.06.13.23290941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Purpose De novo variants in CUL3 (Cullin-3 ubiquitin ligase) have been strongly associated with neurodevelopmental disorders (NDDs), but no large case series have been reported so far. Here we aimed to collect sporadic cases carrying rare variants in CUL3, describe the genotype-phenotype correlation, and investigate the underlying pathogenic mechanism. Methods Genetic data and detailed clinical records were collected via multi-center collaboration. Dysmorphic facial features were analyzed using GestaltMatcher. Variant effects on CUL3 protein stability were assessed using patient-derived T-cells. Results We assembled a cohort of 35 individuals with heterozygous CUL3 variants presenting a syndromic NDD characterized by intellectual disability with or without autistic features. Of these, 33 have loss-of-function (LoF) and two have missense variants. CUL3 LoF variants in patients may affect protein stability leading to perturbations in protein homeostasis, as evidenced by decreased ubiquitin-protein conjugates in vitro . Specifically, we show that cyclin E1 (CCNE1) and 4E-BP1 (EIF4EBP1), two prominent substrates of CUL3, fail to be targeted for proteasomal degradation in patient-derived cells. Conclusion Our study further refines the clinical and mutational spectrum of CUL3 -associated NDDs, expands the spectrum of cullin RING E3 ligase-associated neuropsychiatric disorders, and suggests haploinsufficiency via LoF variants is the predominant pathogenic mechanism.
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34
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Wojcik MH, Srivastava S, Agrawal PB, Balci TB, Callewaert B, Calvo PL, Carli D, Caudle M, Colaiacovo S, Cross L, Demetriou K, Drazba K, Dutra-Clarke M, Edwards M, Genetti CA, Grange DK, Hickey SE, Isidor B, Küry S, Lachman HM, Lavillaureix A, Lyons MJ, Marcelis C, Marco EJ, Martinez-Agosto JA, Nowak C, Pizzol A, Planes M, Prijoles EJ, Riberi E, Rush ET, Russell BE, Sachdev R, Schmalz B, Shears D, Stevenson DA, Wilson K, Jansen S, de Vries BBA, Curry CJ. Jansen-de Vries syndrome: Expansion of the PPM1D clinical and phenotypic spectrum in 34 families. Am J Med Genet A 2023. [PMID: 37183572 DOI: 10.1002/ajmg.a.63226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Jansen-de Vries syndrome (JdVS) is a neurodevelopmental condition attributed to pathogenic variants in Exons 5 and 6 of PPM1D. As the full phenotypic spectrum and natural history remain to be defined, we describe a large cohort of children and adults with JdVS. This is a retrospective cohort study of 37 individuals from 34 families with disease-causing variants in PPM1D leading to JdVS. Clinical data were provided by treating physicians and/or families. Of the 37 individuals, 27 were male and 10 female, with median age 8.75 years (range 8 months to 62 years). Four families document autosomal dominant transmission, and 32/34 probands were diagnosed via exome sequencing. The facial gestalt, including a broad forehead and broad mouth with a thin and tented upper lip, was most recognizable between 18 and 48 months of age. Common manifestations included global developmental delay (35/36, 97%), hypotonia (25/34, 74%), short stature (14/33, 42%), constipation (22/31, 71%), and cyclic vomiting (6/35, 17%). Distinctive personality traits include a hypersocial affect (21/31, 68%) and moderate-to-severe anxiety (18/28, 64%). In conclusion, JdVS is a clinically recognizable neurodevelopmental syndrome with a characteristic personality and distinctive facial features. The association of pathogenic variants in PPM1D with cyclic vomiting bears not only medical attention but also further pathogenic and mechanistic evaluation.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pankaj B Agrawal
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Neonatology, Department of Pediatrics, Miller School of Medicine, University of Miami and Holtz Children's Hospital, Jackson Health System, Miami, Florida, USA
| | - Tugce B Balci
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Bert Callewaert
- Center for Medical Genetics, Pediatrics Department, Ghent University Hospital, Ghent, Belgium
| | - Pier Luigi Calvo
- Pediatric Gastroenterology Unit, Regina Margherita Children's Hospital, Azienda Ospedaliera-Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Torino, Italy
| | - Michelle Caudle
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Samantha Colaiacovo
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Laura Cross
- Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Kalliope Demetriou
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Katy Drazba
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Marina Dutra-Clarke
- Division of Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Matthew Edwards
- Paediatrics, School of Medicine, Western Sydney University, Hunter Genetics, Newcastle, New South Wales, Australia
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Bertrand Isidor
- Department of Medical Genetics, Nantes Hospital, Nantes, France
| | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, Nantes, France
| | - Herbert M Lachman
- Departments of Behavioral Science, Medicine, and Psychiatry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alinoe Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, CHU Rennes, Hôpital Sud, Rennes, France
| | | | - Carlo Marcelis
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elysa J Marco
- Cortica Healthcare, Marin Center, San Rafael, California, USA
| | - Julian A Martinez-Agosto
- Division of Genetics, Departments of Pediatrics and Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Catherine Nowak
- Division of Genetics and Genomics, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Antonio Pizzol
- Pediatric Gastroenterology Unit, Regina Margherita Children's Hospital, Azienda Ospedaliera-Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Marc Planes
- Service de Génétique Clinique, University Hospital Morvan, Brest, France
| | | | - Evelise Riberi
- Department of Public Health and Pediatrics, University of Torino, Torino, Italy
| | - Eric T Rush
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, USA
- Division of Genetics, Children's Mercy Kansas City, Kansas City, Missouri, USA
- Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, Missouri, USA
| | - Bianca E Russell
- Division of Genetics, Departments of Pediatrics and Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Betsy Schmalz
- Department of Pediatrics, The Ohio State University College of Medicine, Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David A Stevenson
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sandra Jansen
- Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California San Francisco/Fresno, Fresno, California, USA
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35
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Galgani A, Bartolini E, D'Amora M, Faraguna U, Giorgi FS. The Central Noradrenergic System in Neurodevelopmental Disorders: Merging Experimental and Clinical Evidence. Int J Mol Sci 2023; 24:ijms24065805. [PMID: 36982879 PMCID: PMC10055776 DOI: 10.3390/ijms24065805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The aim of this article is to highlight the potential role of the locus-coeruleus-noradrenergic (LC-NA) system in neurodevelopmental disorders (NdDs). The LC is the main brain noradrenergic nucleus, key in the regulation of arousal, attention, and stress response, and its early maturation and sensitivity to perinatal damage make it an interesting target for translational research. Clinical data shows the involvement of the LC-NA system in several NdDs, suggesting a pathogenetic role in the development of such disorders. In this context, a new neuroimaging tool, LC Magnetic Resonance Imaging (MRI), has been developed to visualize the LC in vivo and assess its integrity, which could be a valuable tool for exploring morphological alterations in NdD in vivo in humans. New animal models may be used to test the contribution of the LC-NA system to the pathogenic pathways of NdD and to evaluate the efficacy of NA-targeting drugs. In this narrative review, we provide an overview of how the LC-NA system may represent a common pathophysiological and pathogenic mechanism in NdD and a reliable target for symptomatic and disease-modifying drugs. Further research is needed to fully understand the interplay between the LC-NA system and NdD.
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Affiliation(s)
- Alessandro Galgani
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Emanuele Bartolini
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy
- Tuscany PhD Programme in Neurosciences, 50121 Florence, Italy
| | - Marta D'Amora
- Department of Biology, University of Pisa, 56125 Pisa, Italy
- Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Ugo Faraguna
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy
| | - Filippo Sean Giorgi
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
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36
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Chow JC, Hormozdiari F. Prediction of Neurodevelopmental Disorders Based on De Novo Coding Variation. J Autism Dev Disord 2023; 53:963-976. [PMID: 35596027 PMCID: PMC9986216 DOI: 10.1007/s10803-022-05586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/27/2022]
Abstract
The early detection of neurodevelopmental disorders (NDDs) can significantly improve patient outcomes. The differential burden of non-synonymous de novo mutation among NDD cases and controls indicates that de novo coding variation can be used to identify a subset of samples that will likely display an NDD phenotype. Thus, we have developed an approach for the accurate prediction of NDDs with very low false positive rate (FPR) using de novo coding variation for a small subset of cases. We use a shallow neural network that integrates de novo likely gene-disruptive and missense variants, measures of gene constraint, and conservation information to predict a small subset of NDD cases at very low FPR and prioritizes NDD risk genes for future clinical study.
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Affiliation(s)
- Julie C Chow
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
| | - Fereydoun Hormozdiari
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, University of California, Davis, 95817, USA.
- Biochemistry and Molecular Medicine, University of California, Davis, 95616, USA.
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37
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Pérez-Cano L, Azidane Chenlo S, Sabido-Vera R, Sirci F, Durham L, Guney E. Translating precision medicine for autism spectrum disorder: A pressing need. Drug Discov Today 2023; 28:103486. [PMID: 36623795 DOI: 10.1016/j.drudis.2023.103486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/01/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Autism spectrum disorder (ASD) is a heterogenous group of neurodevelopmental disorders (NDDs) with a high unmet medical need. Currently, ASD is diagnosed according to behavior-based criteria that overlook clinical and genomic heterogeneity, thus repeatedly resulting in failed clinical trials. Here, we summarize the scientific evidence pointing to the pressing need to create a precision medicine framework for ASD and other NDDs. We discuss the role of omics and systems biology to characterize more homogeneous disease subtypes with different underlying pathophysiological mechanisms and to determine corresponding tailored treatments. Finally, we provide recent initiatives towards tackling the complexity in NDDs for precision medicine and cost-effective drug discovery.
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Affiliation(s)
- Laura Pérez-Cano
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Sara Azidane Chenlo
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Rubén Sabido-Vera
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Francesco Sirci
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain
| | - Lynn Durham
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; Drug Development Unit (DDU), STALICLA SA, Avenue de Sécheron 15, 1202 Geneva, Switzerland.
| | - Emre Guney
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain.
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38
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Beard DC, Zhang X, Wu DY, Martin JR, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Lawrence AB, Hill CA, Papouin T, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530041. [PMID: 36909558 PMCID: PMC10002657 DOI: 10.1101/2023.02.27.530041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Phenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.
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Affiliation(s)
- Diana C. Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y. Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R. Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G. Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B. McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B. Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A. Hill
- 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, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R. Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D. Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E. Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W. Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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39
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Rotaru DC, Wallaard I, de Vries M, van der Bie J, Elgersma Y. UBE3A expression during early postnatal brain development is required for proper dorsomedial striatal maturation. JCI Insight 2023; 8:e166073. [PMID: 36810252 PMCID: PMC9977510 DOI: 10.1172/jci.insight.166073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/05/2023] [Indexed: 02/23/2023] Open
Abstract
Angelman syndrome (AS) is a severe neurodevelopmental disorder (NDD) caused by loss of functional ubiquitin protein ligase E3A (UBE3A). Previous studies showed that UBE3A plays an important role in the first postnatal weeks of mouse brain development, but its precise role is unknown. Since impaired striatal maturation has been implicated in several mouse models for NDDs, we studied the importance of UBE3A in striatal maturation. We used inducible Ube3a mouse models to investigate the maturation of medium spiny neurons (MSNs) from dorsomedial striatum. MSNs of mutant mice matured properly till postnatal day 15 (P15) but remained hyperexcitable with fewer excitatory synaptic events at later ages, indicative of stalled striatal maturation in Ube3a mice. Reinstatement of UBE3A expression at P21 fully restored MSN excitability but only partially restored synaptic transmission and the operant conditioning behavioral phenotype. Gene reinstatement at P70 failed to rescue both electrophysiological and behavioral phenotypes. In contrast, deletion of Ube3a after normal brain development did not result in these electrophysiological and behavioral phenotypes. This study emphasizes the role of UBE3A in striatal maturation and the importance of early postnatal reinstatement of UBE3A expression to obtain a full rescue of behavioral phenotypes associated with striatal function in AS.
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Affiliation(s)
- Diana C. Rotaru
- Department of Clinical Genetics and
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, Netherlands
| | - Ilse Wallaard
- Department of Clinical Genetics and
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, Netherlands
| | - Maud de Vries
- Department of Clinical Genetics and
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, Netherlands
| | - Julia van der Bie
- Department of Clinical Genetics and
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, Netherlands
| | - Ype Elgersma
- Department of Clinical Genetics and
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, Netherlands
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40
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Hu H, Long Y, Song G, Chen S, Xu Z, Li Q, Wu Z. Dysfunction of Prkcaa Links Social Behavior Defects with Disturbed Circadian Rhythm in Zebrafish. Int J Mol Sci 2023; 24:ijms24043849. [PMID: 36835261 PMCID: PMC9961154 DOI: 10.3390/ijms24043849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Protein kinase Cα (PKCα/PRKCA) is a crucial regulator of circadian rhythm and is associated with human mental illnesses such as autism spectrum disorders and schizophrenia. However, the roles of PRKCA in modulating animal social behavior and the underlying mechanisms remain to be explored. Here we report the generation and characterization of prkcaa-deficient zebrafish (Danio rerio). The results of behavioral tests indicate that a deficiency in Prkcaa led to anxiety-like behavior and impaired social preference in zebrafish. RNA-sequencing analyses revealed the significant effects of the prkcaa mutation on the expression of the morning-preferring circadian genes. The representatives are the immediate early genes, including egr2a, egr4, fosaa, fosab and npas4a. The downregulation of these genes at night was attenuated by Prkcaa dysfunction. Consistently, the mutants demonstrated reversed day-night locomotor rhythm, which are more active at night than in the morning. Our data show the roles of PRKCA in regulating animal social interactions and link the social behavior defects with a disturbed circadian rhythm.
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Affiliation(s)
- Han Hu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Research Center of Fishery Resources and Environment, Southwest University, Chongqing 400715, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence: (Y.L.); (Z.W.); Tel.: +86-27-6878-0100 (Y.L.); +86-23-6836-6018 (Z.W.)
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shaoxiong Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Zhicheng Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Research Center of Fishery Resources and Environment, Southwest University, Chongqing 400715, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhengli Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Research Center of Fishery Resources and Environment, Southwest University, Chongqing 400715, China
- Correspondence: (Y.L.); (Z.W.); Tel.: +86-27-6878-0100 (Y.L.); +86-23-6836-6018 (Z.W.)
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41
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Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S, Gleeson JG. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet 2023; 55:209-220. [PMID: 36635388 PMCID: PMC9961399 DOI: 10.1038/s41588-022-01276-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/30/2022] [Indexed: 01/14/2023]
Abstract
Malformations of cortical development (MCD) are neurological conditions involving focal disruptions of cortical architecture and cellular organization that arise during embryogenesis, largely from somatic mosaic mutations, and cause intractable epilepsy. Identifying the genetic causes of MCD has been a challenge, as mutations remain at low allelic fractions in brain tissue resected to treat condition-related epilepsy. Here we report a genetic landscape from 283 brain resections, identifying 69 mutated genes through intensive profiling of somatic mutations, combining whole-exome and targeted-amplicon sequencing with functional validation including in utero electroporation of mice and single-nucleus RNA sequencing. Genotype-phenotype correlation analysis elucidated specific MCD gene sets associated with distinct pathophysiological and clinical phenotypes. The unique single-cell level spatiotemporal expression patterns of mutated genes in control and patient brains indicate critical roles in excitatory neurogenic pools during brain development and in promoting neuronal hyperexcitability after birth.
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Affiliation(s)
- Changuk Chung
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Catharina Donkels
- Department of Neurosurgery, Experimental Epilepsy Research, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Westley Phillips
- Department of Neurosurgery, University of California at Los Angeles, Los Angeles, CA, USA
| | - Zhen Li
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Ashley P L Marsh
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martin W Breuss
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Aurora, Aurora, CO, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Camila Araújo Bernardino Garcia
- Laboratory of Pediatric Neurosurgery and Developmental Neuropathology, Department of Surgery and Anatomy, University of São Paulo, Ribeirão Preto, Brazil
| | - Renee D George
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jing Gu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Mingchu Xu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Kiely N James
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Anna S Nidhiry
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sami Khoury
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Gabrielle Howe
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Emily Riley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Xin Xu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Brett Copeland
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Andreas Schulze-Bonhage
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carola A Haas
- Department of Neurosurgery, Experimental Epilepsy Research, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Horst Urbach
- Department of Neuroradiology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Marco Prinz
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - David D Limbrick
- Department of Neurology, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Christina A Gurnett
- Department of Neurology, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Matthew D Smyth
- Department of Neurosurgery, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Shifteh Sattar
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - Mark Nespeca
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - David D Gonda
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - Katsumi Imai
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Hsin-Hung Chen
- Division of Pediatric Neurosurgery, The Neurological Institute, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Jin-Wu Tsai
- Institute of Brain Science, Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Valerio Conti
- Pediatric Neurology Unit and Laboratories, IRCCS Meyer Children's Hospital University of Florence, Firenze, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, IRCCS Meyer Children's Hospital University of Florence, Firenze, Italy
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, Department of Neurology, New York University Langone Health, New York, NY, USA
| | - Wilson A Silva
- Department of Genetics, Center for Cell-Based Therapy, Center for Integrative Systems Biology, University of São Paulo, Ribeirão Preto, Brazil
| | - Helio R Machado
- Laboratory of Pediatric Neurosurgery and Developmental Neuropathology, Department of Surgery and Anatomy, University of São Paulo, Ribeirão Preto, Brazil
| | - Gary W Mathern
- Department of Neurosurgery, University of California at Los Angeles, Los Angeles, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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42
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Rapanelli M, Wang W, Hurley E, Feltri ML, Pittenger C, Frick LR, Yan Z. Cholinergic neurons in the basal forebrain are involved in behavioral abnormalities associated with Cul3 deficiency: Role of prefrontal cortex projections in cognitive deficits. Transl Psychiatry 2023; 13:22. [PMID: 36693858 PMCID: PMC9873627 DOI: 10.1038/s41398-023-02306-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
Loss-of-function mutations of the gene Cul3 have been identified as a risk factor for autism-spectrum disorder (ASD), but the pathogenic mechanisms are not well understood. Conditional Cul3 ablation in cholinergic neurons of mice (ChatCRECul3F/+) recapitulated ASD-like social and sensory gating phenotypes and caused significant cognitive impairments, with diminished activity of cholinergic neurons in the basal forebrain (BF). Chemogenetic inhibition of BF cholinergic neurons in healthy mice induced similar social and cognitive deficits. Conversely, chemogenetic stimulation of BF cholinergic neurons in ChatCRECul3F/+ mice reversed abnormalities in sensory gating and cognition. Cortical hypofunction was also found after ChAT-specific Cul3 ablation and stimulation of cholinergic projections from the BF to the prefrontal cortex (PFC) mitigated cognitive deficits. Overall, we demonstrate that cholinergic dysfunction due to Cul3 deficiency is involved in ASD-like behavioral abnormalities, and that BF cholinergic neurons are particularly critical for cognitive component through their projections to the PFC.
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Affiliation(s)
- Maximiliano Rapanelli
- Department of Physiology and Biophysics, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
| | - Wei Wang
- Department of Physiology and Biophysics, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
| | - Edward Hurley
- Department of Neurology, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
- Institute for Myelin and Glia Exploration, University at Buffalo, The State University of New York, Buffalo, USA
| | - Maria Laura Feltri
- Department of Neurology, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
- Institute for Myelin and Glia Exploration, University at Buffalo, The State University of New York, Buffalo, USA
- Department of Biochemistry, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
- Neuroscience Graduate Program. Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
| | - Christopher Pittenger
- Departments of Psychiatry and Psychology, Yale Child Study Center, and Interdepartmental Neuroscience Program, Yale University School of Medicine, Buffalo, USA
| | - Luciana Romina Frick
- Department of Neurology, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Neuroscience Graduate Program. Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Department of Medicine, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Clinical and Translational Research Center, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
| | - Zhen Yan
- Department of Physiology and Biophysics, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Neuroscience Graduate Program. Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
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43
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Is bRaQCing bad? New roles for ribosome associated quality control factors in stress granule regulation. Biochem Soc Trans 2022; 50:1715-1724. [DOI: 10.1042/bst20220549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
Maintenance of proteostasis is of utmost importance to cellular viability and relies on the coordination of many post-transcriptional processes to respond to stressful stimuli. Stress granules (SGs) are RNA–protein condensates that form after translation initiation is inhibited, such as during the integrated stress response (ISR), and may facilitate cellular adaptation to stress. The ribosome-associated quality control (RQC) pathway is a critical translation monitoring system that recognizes aberrant mRNAs encoding potentially toxic nascent peptides to target them for degradation. Both SG regulation and the RQC pathway are directly associated with translation regulation, thus it is of no surprise recent developments have demonstrated a connection between them. VCP's function in the stress activated RQC pathway, ribosome collisions activating the ISR, and the regulation of the 40S ribosomal subunit by canonical SG proteins during the RQC all connect SGs to the RQC pathway. Because mutations in genes that are involved in both SG and RQC regulation are associated with degenerative and neurological diseases, understanding the coordination and interregulation of SGs and RQC may shed light on disease mechanisms. This minireview will highlight recent advances in understanding how SGs and the RQC pathway interact in health and disease contexts.
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Ng JK, Vats P, Fritz-Waters E, Sarkar S, Sams EI, Padhi EM, Payne ZL, Leonard S, West MA, Prince C, Trani L, Jansen M, Vacek G, Samadi M, Harkins TT, Pohl C, Turner TN. de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project. Hum Mutat 2022; 43:1979-1993. [PMID: 36054329 PMCID: PMC9771978 DOI: 10.1002/humu.24455] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 01/25/2023]
Abstract
Detection of de novo variants (DNVs) is critical for studies of disease-related variation and mutation rates. To accelerate DNV calling, we developed a graphics processing units-based workflow. We applied our workflow to whole-genome sequencing data from three parent-child sequenced cohorts including the Simons Simplex Collection (SSC), Simons Foundation Powering Autism Research (SPARK), and the 1000 Genomes Project (1000G) that were sequenced using DNA from blood, saliva, and lymphoblastoid cell lines (LCLs), respectively. The SSC and SPARK DNV callsets were within expectations for number of DNVs, percent at CpG sites, phasing to the paternal chromosome of origin, and average allele balance. However, the 1000G DNV callset was not within expectations and contained excessive DNVs that are likely cell line artifacts. Mutation signature analysis revealed 30% of 1000G DNV signatures matched B-cell lymphoma. Furthermore, we found variants in DNA repair genes and at Clinvar pathogenic or likely-pathogenic sites and significant excess of protein-coding DNVs in IGLL5; a gene known to be involved in B-cell lymphomas. Our study provides a new rapid DNV caller for the field and elucidates important implications of using sequencing data from LCLs for reference building and disease-related projects.
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Affiliation(s)
- Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
| | - Elyn Fritz-Waters
- Research Infrastructure Services, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Stephanie Sarkar
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eleanor I. Sams
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Evin M. Padhi
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zachary L. Payne
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shawn Leonard
- Research Infrastructure Services, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Marc A. West
- NVIDIA Corporation, Santa Clara, California, USA
| | - Chandler Prince
- Research Infrastructure Services, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lee Trani
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Marshall Jansen
- Research Infrastructure Services, Washington University School of Medicine, St. Louis, Missouri, USA
| | - George Vacek
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | - Craig Pohl
- Research Infrastructure Services, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
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45
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Geng Y, Zhang T, Alonzo IG, Godar SC, Yates C, Pluimer BR, Harrison DL, Nath AK, Yeh JRJ, Drummond IA, Bortolato M, Peterson RT. Top2a promotes the development of social behavior via PRC2 and H3K27me3. SCIENCE ADVANCES 2022; 8:eabm7069. [PMID: 36417527 PMCID: PMC9683714 DOI: 10.1126/sciadv.abm7069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Little is understood about the embryonic development of sociality. We screened 1120 known drugs and found that embryonic inhibition of topoisomerase IIα (Top2a) resulted in lasting social deficits in zebrafish. In mice, prenatal Top2 inhibition caused defects in social interaction and communication, which are behaviors that relate to core symptoms of autism. Mutation of Top2a in zebrafish caused down-regulation of a set of genes highly enriched for genes associated with autism in humans. Both the Top2a-regulated and autism-associated gene sets have binding sites for polycomb repressive complex 2 (PRC2), a regulatory complex responsible for H3K27 trimethylation (H3K27me3). Moreover, both gene sets are highly enriched for H3K27me3. Inhibition of the PRC2 component Ezh2 rescued social deficits caused by Top2 inhibition. Therefore, Top2a is a key component of an evolutionarily conserved pathway that promotes the development of social behavior through PRC2 and H3K27me3.
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Affiliation(s)
- Yijie Geng
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Tejia Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Ivy G. Alonzo
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Sean C. Godar
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Christopher Yates
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Brock R. Pluimer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Devin L. Harrison
- The Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Anjali K. Nath
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
- Metabolism Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Iain A. Drummond
- Davis Center for Aging and Regeneration, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Marco Bortolato
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Randall T. Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
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46
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Wang T, Kim CN, Bakken TE, Gillentine MA, Henning B, Mao Y, Gilissen C, Nowakowski TJ, Eichler EE. Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders. Proc Natl Acad Sci U S A 2022; 119:e2203491119. [PMID: 36350923 PMCID: PMC9674258 DOI: 10.1073/pnas.2203491119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/28/2022] [Indexed: 08/15/2023] Open
Abstract
Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here, we analyzed de novo variants (DNVs) from 15,560 ASD (6,557 from SPARK) and 31,052 DD trios independently and also combined as broader neurodevelopmental disorders (NDDs) using three models. We identify 615 NDD candidate genes (false discovery rate [FDR] < 0.05) supported by ≥1 models, including 138 reaching Bonferroni exome-wide significance (P < 3.64e-7) in all models. The genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes that show mutational bias, including enrichments for missense (n = 41) or truncating (n = 12) DNVs. We also find 10 genes with evidence of male- or female-bias enrichment, including 4 X chromosome genes with significant female burden (DDX3X, MECP2, WDR45, and HDAC8). This large-scale integrative analysis identifies candidates and functional subsets of NDD genes.
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Affiliation(s)
- Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
- Neuroscience Research Institute, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, 100191, China
| | - Chang N. Kim
- Department of Anatomy, University of California, San Francisco, CA 94143
| | | | - Madelyn A. Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
| | - Barbara Henning
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
| | - Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | | | - Tomasz J. Nowakowski
- Department of Anatomy, University of California, San Francisco, CA 94143
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
- HHMI, University of Washington, Seattle, WA 98195
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47
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Gillentine MA, Wang T, Eichler EE. Estimating the Prevalence of De Novo Monogenic Neurodevelopmental Disorders from Large Cohort Studies. Biomedicines 2022; 10:2865. [PMID: 36359385 PMCID: PMC9687899 DOI: 10.3390/biomedicines10112865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 11/26/2023] Open
Abstract
Rare diseases impact up to 400 million individuals globally. Of the thousands of known rare diseases, many are rare neurodevelopmental disorders (RNDDs) impacting children. RNDDs have proven to be difficult to assess epidemiologically for several reasons. The rarity of them makes it difficult to observe them in the population, there is clinical overlap among many disorders, making it difficult to assess the prevalence without genetic testing, and data have yet to be available to have accurate counts of cases. Here, we utilized large sequencing cohorts of individuals with rare, de novo monogenic disorders to estimate the prevalence of variation in over 11,000 genes among cohorts with developmental delay, autism spectrum disorder, and/or epilepsy. We found that the prevalence of many RNDDs is positively correlated to the previously estimated incidence. We identified the most often mutated genes among neurodevelopmental disorders broadly, as well as developmental delay and autism spectrum disorder independently. Finally, we assessed if social media group member numbers may be a valuable way to estimate prevalence. These data are critical for individuals and families impacted by these RNDDs, clinicians and geneticists in their understanding of how common diseases are, and for researchers to potentially prioritize research into particular genes or gene sets.
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Affiliation(s)
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory for Neuroscience, Neuroscience Research Institute, Peking University, Ministry of Education of China & National Health Commission of China, Beijing 100191, China
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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48
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Mew M, Caldwell KA, Caldwell GA. From bugs to bedside: functional annotation of human genetic variation for neurological disorders using invertebrate models. Hum Mol Genet 2022; 31:R37-R46. [PMID: 35994032 PMCID: PMC9585664 DOI: 10.1093/hmg/ddac203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 02/02/2023] Open
Abstract
The exponential accumulation of DNA sequencing data has opened new avenues for discovering the causative roles of single-nucleotide polymorphisms (SNPs) in neurological diseases. The opportunities emerging from this are staggering, yet only as good as our abilities to glean insights from this surplus of information. Whereas computational biology continues to improve with respect to predictions and molecular modeling, the differences between in silico and in vivo analysis remain substantial. Invertebrate in vivo model systems represent technically advanced, experimentally mature, high-throughput, efficient and cost-effective resources for investigating a disease. With a decades-long track record of enabling investigators to discern function from DNA, fly (Drosophila) and worm (Caenorhabditis elegans) models have never been better poised to serve as living engines of discovery. Both of these animals have already proven useful in the classification of genetic variants as either pathogenic or benign across a range of neurodevelopmental and neurodegenerative disorders-including autism spectrum disorders, ciliopathies, amyotrophic lateral sclerosis, Alzheimer's and Parkinson's disease. Pathogenic SNPs typically display distinctive phenotypes in functional assays when compared with null alleles and frequently lead to protein products with gain-of-function or partial loss-of-function properties that contribute to neurological disease pathogenesis. The utility of invertebrates is logically limited by overt differences in anatomical and physiological characteristics, and also the evolutionary distance in genome structure. Nevertheless, functional annotation of disease-SNPs using invertebrate models can expedite the process of assigning cellular and organismal consequences to mutations, ascertain insights into mechanisms of action, and accelerate therapeutic target discovery and drug development for neurological conditions.
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Affiliation(s)
- Melanie Mew
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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49
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Tai DJC, Razaz P, Erdin S, Gao D, Wang J, Nuttle X, de Esch CE, Collins RL, Currall BB, O'Keefe K, Burt ND, Yadav R, Wang L, Mohajeri K, Aneichyk T, Ragavendran A, Stortchevoi A, Morini E, Ma W, Lucente D, Hastie A, Kelleher RJ, Perlis RH, Talkowski ME, Gusella JF. Tissue- and cell-type-specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models. Am J Hum Genet 2022; 109:1789-1813. [PMID: 36152629 PMCID: PMC9606388 DOI: 10.1016/j.ajhg.2022.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
Chromosome 16p11.2 reciprocal genomic disorder, resulting from recurrent copy-number variants (CNVs), involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia, but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, and white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue-, cell-type-, and dosage-specific, although more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2,163 differentially expressed genes), and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated, loss-of-function constraint, and fragile X messenger ribonucleoprotein target gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, and single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Changes both in neuronal ratios and in gene expression in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption that might contribute to changes in neurodevelopmental and cognitive function in 16p11.2 carriers. Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes and that this disruption has relative impacts that are context specific.
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Affiliation(s)
- Derek J C Tai
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Parisa Razaz
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Serkan Erdin
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dadi Gao
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer Wang
- Center for Quantitative Health, Division of Clinical Research, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Xander Nuttle
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Celine E de Esch
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan L Collins
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn O'Keefe
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicholas D Burt
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rachita Yadav
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lily Wang
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiana Mohajeri
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tatsiana Aneichyk
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elisabetta Morini
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Weiyuan Ma
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Raymond J Kelleher
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Roy H Perlis
- Center for Quantitative Health, Division of Clinical Research, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael E Talkowski
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
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Mahjani B, Birnbaum R, Buxbaum Grice A, Cappi C, Jung S, Avila MN, Reichenberg A, Sandin S, Hultman CM, Buxbaum JD, Grice DE. Phenotypic Impact of Rare Potentially Damaging Copy Number Variation in Obsessive-Compulsive Disorder and Chronic Tic Disorders. Genes (Basel) 2022; 13:1796. [PMID: 36292681 PMCID: PMC9601402 DOI: 10.3390/genes13101796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Recent studies report an important-and previously underestimated-role of rare variation in risk of obsessive-compulsive disorder (OCD) and chronic tic disorders (CTD). Using data from a large epidemiological study, we evaluate the distribution of potentially damaging copy number variation (pdCNV) in OCD and CTD, examining associations between pdCNV and the phenotypes of probands, including a consideration of early- vs. late-diagnoses. METHOD The Obsessive-Compulsive Inventory-Revised (OCI-R) questionnaire was used to ascertain psychometric profiles of OCD probands. CNV were identified genome-wide using chromosomal microarray data. RESULTS For 993 OCD cases, 86 (9%) were identified as pdCNV carriers. The most frequent pdCNV found was at the 16p13.11 region. There was no significant association between pdCNV and the OCI-R total score. However, pdCNV was associated with Obsessing and Checking subscores. There was no significant difference in pdCNV frequency between early- vs. late-diagnosed OCD probands. Of the 217 CTD cases, 18 (8%) were identified as pdCNV carriers. CTD probands with pdCNV were significantly more likely to have co-occurring autism spectrum disorder (ASD). CONCLUSIONS pdCNV represents part of the risk architecture for OCD and CTD. If replicated, our findings suggest pdCNV impact some OCD symptoms. Genes within the 16p13.11 region are potential OCD risk genes.
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Affiliation(s)
- Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Tics, OCD and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariela Buxbaum Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seulgi Jung
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Natividad Avila
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dorothy E. Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Tics, OCD and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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