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Berger H, Gerstner S, Horstmann MF, Pauli S, Borchers A. Fbrsl1 is required for heart development in Xenopus laevis and de novo variants in FBRSL1 can cause human heart defects. Dis Model Mech 2024; 17:dmm050507. [PMID: 38501224 PMCID: PMC11128277 DOI: 10.1242/dmm.050507] [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: 09/29/2023] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
De novo truncating variants in fibrosin-like 1 (FBRSL1), a member of the AUTS2 gene family, cause a disability syndrome, including organ malformations such as heart defects. Here, we use Xenopus laevis to investigate whether Fbrsl1 plays a role in heart development. Xenopus laevis fbrsl1 is expressed in tissues relevant for heart development, and morpholino-mediated knockdown of Fbrsl1 results in severely hypoplastic hearts. Our data suggest that Fbrsl1 is required for the development of the first heart field, which contributes to the ventricle and the atria, but not for the second heart field, which gives rise to the outflow tract. The morphant heart phenotype could be rescued using a human N-terminal FBRSL1 isoform that contains an alternative exon, but lacks the AUTS2 domain. N-terminal isoforms carrying patient variants failed to rescue. Interestingly, a long human FBRSL1 isoform, harboring the AUTS2 domain, also did not rescue the morphant heart defects. Thus, our data suggest that different FBRSL1 isoforms may have distinct functions and that only the short N-terminal isoform, appears to be critical for heart development.
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Affiliation(s)
- Hanna Berger
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Sarah Gerstner
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Marc-Frederik Horstmann
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
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Hill MD, Gill SS, Le-Niculescu H, MacKie O, Bhagar R, Roseberry K, Murray OK, Dainton HD, Wolf SK, Shekhar A, Kurian SM, Niculescu AB. Precision medicine for psychotic disorders: objective assessment, risk prediction, and pharmacogenomics. Mol Psychiatry 2024; 29:1528-1549. [PMID: 38326562 DOI: 10.1038/s41380-024-02433-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/16/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Psychosis occurs inside the brain, but may have external manifestations (peripheral molecular biomarkers, behaviors) that can be objectively and quantitatively measured. Blood biomarkers that track core psychotic manifestations such as hallucinations and delusions could provide a window into the biology of psychosis, as well as help with diagnosis and treatment. We endeavored to identify objective blood gene expression biomarkers for hallucinations and delusions, using a stepwise discovery, prioritization, validation, and testing in independent cohorts design. We were successful in identifying biomarkers that were predictive of high hallucinations and of high delusions states, and of future psychiatric hospitalizations related to them, more so when personalized by gender and diagnosis. Top biomarkers for hallucinations that survived discovery, prioritization, validation and testing include PPP3CB, DLG1, ENPP2, ZEB2, and RTN4. Top biomarkers for delusions include AUTS2, MACROD2, NR4A2, PDE4D, PDP1, and RORA. The top biological pathways uncovered by our work are glutamatergic synapse for hallucinations, as well as Rap1 signaling for delusions. Some of the biomarkers are targets of existing drugs, of potential utility in pharmacogenomics approaches (matching patients to medications, monitoring response to treatment). The top biomarkers gene expression signatures through bioinformatic analyses suggested a prioritization of existing medications such as clozapine and risperidone, as well as of lithium, fluoxetine, valproate, and the nutraceuticals omega-3 fatty acids and magnesium. Finally, we provide an example of how a personalized laboratory report for doctors would look. Overall, our work provides advances for the improved diagnosis and treatment for schizophrenia and other psychotic disorders.
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Affiliation(s)
- M D Hill
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
- Indianapolis VA Medical Center, Indianapolis, IN, USA
| | - S S Gill
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - H Le-Niculescu
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - O MacKie
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
- Indianapolis VA Medical Center, Indianapolis, IN, USA
| | - R Bhagar
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - K Roseberry
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - O K Murray
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - H D Dainton
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Neurology, Medical University of South Carolina, Charleston, SC, USA
| | - S K Wolf
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Neurology, Ohio State University Medical Center, Columbus, OH, USA
| | - A Shekhar
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
- Office of the Dean, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - A B Niculescu
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA.
- Indianapolis VA Medical Center, Indianapolis, IN, USA.
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
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3
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Ye S, Lyu Y, Chen L, Wang Y, He Y, Li Q, Tian L, Liu F, Wang X, Ai F. Construction of a molecular inflammatory predictive model with histone modification-related genes and identification of CAMK2D as a potential response signature to infliximab in ulcerative colitis. Front Immunol 2024; 14:1282136. [PMID: 38274809 PMCID: PMC10808628 DOI: 10.3389/fimmu.2023.1282136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Background Ulcerative colitis (UC) is a lifelong inflammatory disease affecting the rectum and colon with numerous treatment options that require an individualized treatment plan. Histone modifications regulate chromosome structure and gene expression, resulting in effects on inflammatory and immune responses. However, the relationship between histone modification-related genes and UC remains unclear. Methods Transcriptomic data from GSE59071 and GSE66407 were obtained from the Gene Expression Omnibus (GEO), encompassing colonic biopsy expression profiles of UC patients in inflamed and non-inflamed status. Differentially expressed gene (DEG) analyses, functional enrichment analyses, weighted gene co-expression network analysis (WGCNA), and random forest were performed to identify histone modification-related core genes associated with UC inflammation. Features were screened through the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), establishing a molecular inflammatory predictive model using logistic regression. The model was validated in the GSE107499 dataset, and the performance of the features was assessed using receiver operating characteristic (ROC) and calibration curves. Immunohistochemistry (IHC) staining of colonic biopsy tissues from UC patients treated with infliximab was used to further confirm the clinical application value. Univariate logistic regression on GSE14580 highlighted features linked to infliximab response. Results A total of 253 histone modification-related DEGs were identified between inflammatory and non-inflammatory patients with UC. Seven key genes (IL-1β, MSL3, HDAC7, IRF4, CAMK2D, AUTS2, and PADI2) were selected using WGCNA and random forest. Through univariate logistic regression, three core genes (CAMK2D, AUTS2, and IL-1β) were further incorporated to construct the molecular inflammatory predictive model. The area under the curve (AUC) of the model was 0.943 in the independent validation dataset. A significant association between CAMK2D protein expression and infliximab response was observed, which was validated in another independent verification set of GSE14580 from the GEO database. Conclusion The molecular inflammatory predictive model based on CAMK2D, AUTS2, and IL-1β could reliably distinguish the mucosal inflammatory status of UC patients. We further revealed that CAMK2D was a predictive marker of infliximab response. These findings are expected to provide a new evidence base for personalized treatment and management strategies for UC patients.
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Affiliation(s)
- Shuyu Ye
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yongqing Lyu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Libin Chen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yiwei Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yue He
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Quansi Li
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Li Tian
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Fen Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Feiyan Ai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
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Newman J, Tong X, Tan A, Yeasky T, De Paiva VN, Presicce P, Kannan PS, Williams K, Damianos A, Tamase Newsam M, Benny MK, Wu S, Young KC, Miller LA, Kallapur SG, Chougnet CA, Jobe AH, Brambilla R, Schmidt AF. Chorioamnionitis accelerates granule cell and oligodendrocyte maturation in the cerebellum of preterm nonhuman primates. J Neuroinflammation 2024; 21:16. [PMID: 38200558 PMCID: PMC10777625 DOI: 10.1186/s12974-024-03012-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Preterm birth is often associated with chorioamnionitis and leads to increased risk of neurodevelopmental disorders, such as autism. Preterm birth can lead to cerebellar underdevelopment, but the mechanisms of disrupted cerebellar development in preterm infants are not well understood. The cerebellum is consistently affected in people with autism spectrum disorders, showing reduction of Purkinje cells, decreased cerebellar grey matter, and altered connectivity. METHODS Preterm rhesus macaque fetuses were exposed to intra-amniotic LPS (1 mg, E. coli O55:B5) at 127 days (80%) gestation and delivered by c-section 5 days after injections. Maternal and fetal plasma were sampled for cytokine measurements. Chorio-decidua was analyzed for immune cell populations by flow cytometry. Fetal cerebellum was sampled for histology and molecular analysis by single-nuclei RNA-sequencing (snRNA-seq) on a 10× chromium platform. snRNA-seq data were analyzed for differences in cell populations, cell-type specific gene expression, and inferred cellular communications. RESULTS We leveraged snRNA-seq of the cerebellum in a clinically relevant rhesus macaque model of chorioamnionitis and preterm birth, to show that chorioamnionitis leads to Purkinje cell loss and disrupted maturation of granule cells and oligodendrocytes in the fetal cerebellum at late gestation. Purkinje cell loss is accompanied by decreased sonic hedgehog signaling from Purkinje cells to granule cells, which show an accelerated maturation, and to oligodendrocytes, which show accelerated maturation from pre-oligodendrocytes into myelinating oligodendrocytes. CONCLUSION These findings suggest a role of chorioamnionitis on disrupted cerebellar maturation associated with preterm birth and on the pathogenesis of neurodevelopmental disorders among preterm infants.
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Affiliation(s)
- Josef Newman
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Xiaoying Tong
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - April Tan
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Toni Yeasky
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Vanessa Nunes De Paiva
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Pietro Presicce
- Division of Neonatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, USA
| | - Paranthaman S Kannan
- Division of Neonatology and Pulmonary Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Kevin Williams
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Andreas Damianos
- Division of Neonatology and Pulmonary Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Marione Tamase Newsam
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Merline K Benny
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Shu Wu
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Karen C Young
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA
| | - Lisa A Miller
- California National Primate Research Center, University of California, Davis, USA
| | - Suhas G Kallapur
- Division of Neonatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, USA
| | - Claire A Chougnet
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Alan H Jobe
- Division of Neonatology and Pulmonary Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Roberta Brambilla
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, USA
| | - Augusto F Schmidt
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine/Holtz Children's Hospital, Jackson Health System, Miami, USA.
- Batchelor Children's Research Institute, 1580 NW 10Th Ave, Room 348, Miami, FL, 33146, USA.
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5
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, 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
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, 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
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, 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
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, 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
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, 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
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, 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
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, 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
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, 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
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, 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
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Liu Y, Wu Z, Feng Y, Gao J, Wang B, Lian C, Diao B. Integration analysis of single-cell and spatial transcriptomics reveal the cellular heterogeneity landscape in glioblastoma and establish a polygenic risk model. Front Oncol 2023; 13:1109037. [PMID: 37397378 PMCID: PMC10308022 DOI: 10.3389/fonc.2023.1109037] [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: 11/27/2022] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Background Glioblastoma (GBM) is adults' most common and fatally malignant brain tumor. The heterogeneity is the leading cause of treatment failure. However, the relationship between cellular heterogeneity, tumor microenvironment, and GBM progression is still elusive. Methods Integrated analysis of single-cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing (stRNA-seq) of GBM were conducted to analyze the spatial tumor microenvironment. We investigated the subpopulation heterogeneity of malignant cells through gene set enrichment analyses, cell communications analyses, and pseudotime analyses. Significantly changed genes of the pseudotime analysis were screened to create a tumor progress-related gene risk score (TPRGRS) using Cox regression algorithms in the bulkRNA-sequencing(bulkRNA-seq) dataset. We combined the TPRGRS and clinical characteristics to predict the prognosis of patients with GBM. Furthermore, functional analysis was applied to uncover the underlying mechanisms of the TPRGRS. Results GBM cells were accurately charted to their spatial locations and uncovered their spatial colocalization. The malignant cells were divided into five clusters with transcriptional and functional heterogeneity, including unclassified malignant cells and astrocyte-like, mesenchymal-like, oligodendrocytes-progenitor-like, and neural-progenitor-like malignant cells. Cell-cell communications analysis in scRNA-seq and stRNA-seq identified ligand-receptor pairs of the CXCL, EGF, FGF, and MIF signaling pathways as bridges implying that tumor microenvironment may cause malignant cells' transcriptomic adaptability and disease progression. Pseudotime analysis showed the differentiation trajectory of GBM cells from proneural to mesenchymal transition and identified genes or pathways that affect cell differentiation. TPRGRS could successfully divide patients with GBM in three datasets into high- and low-risk groups, which was proved to be a prognostic factor independent of routine clinicopathological characteristics. Functional analysis revealed the TPRGRS associated with growth factor binding, cytokine activity, signaling receptor activator activity functions, and oncogenic pathways. Further analysis revealed the association of the TPRGRS with gene mutations and immunity in GBM. Finally, the external datasets and qRT-PCR verified high expressions of the TPRGRS mRNAs in GBM cells. Conclusion Our study provides novel insights into heterogeneity in GBM based on scRNA-seq and stRNA-seq data. Moreover, our study proposed a malignant cell transition-based TPRGRS through integrated analysis of bulkRNA-seq and scRNA-seq data, combined with the routine clinicopathological evaluation of tumors, which may provide more personalized drug regimens for GBM patients.
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Affiliation(s)
- Yaxuan Liu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
- Department of Basic Medicine, General Hospital of Central Theatre Command, Wuhan, Hubei, China
| | - Zhenyu Wu
- Department of Urology, The First People’s Hospital of Foshan, Foshan, Guangdong, China
| | - Yueyuan Feng
- Cancer Hospital, The First People's Hospital of Foshan, Foshan, Foshan, Guangdong, China
| | - Jiawei Gao
- College of Medicine, JiShou University, Xiangxi, Hunan, China
| | - Bo Wang
- College of Medicine, JiShou University, Xiangxi, Hunan, China
| | - Changlin Lian
- Cancer Hospital, The First People's Hospital of Foshan, Foshan, Foshan, Guangdong, China
| | - Bo Diao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
- Department of Basic Medicine, General Hospital of Central Theatre Command, Wuhan, Hubei, China
- Department of Neurosurgery, Wuhan General Hospital of Guangzhou Command and Hubei Key Laboratory of Central Nervous System Tumor and Intervention, Wuhan, Hubei, China
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7
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Liu M, Chen Y, Sun M, Du Y, Bai Y, Lei G, Zhang C, Zhang M, Zhang Y, Xi C, Ma Y, Wang G. Auts2 regulated autism-like behavior, glucose metabolism and oxidative stress in mice. Exp Neurol 2023; 361:114298. [PMID: 36525998 DOI: 10.1016/j.expneurol.2022.114298] [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: 10/17/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by abnormal social behavior and communication. The autism susceptibility candidate 2 (AUTS2) gene has been associated with multiple neurological diseases, including ASD. Glucose metabolism plays an important role in social behaviors associated with ASD, but the potential role of AUTS2 in glucose metabolism has not been studied. Here, we generated Auts2flox/flox; Emx1Cre+ conditional knockout mice with Auts2 deletion specifically in Exm1-positive neurons in the brain (Auts2-cKO mice) to evaluate the effects of Auts2 knockdown on social behaviors and metabolic pathways. Auts2-cKO mice exhibited ASD-like behaviors, including impaired social interactions and repetitive grooming behaviors. At the molecular level, we found that Auts2 knockdown reduced brain glucose uptake and inhibited the pentose phosphate pathway. Auts2 knockdown also resulted in signs of oxidative stress, and we documented increased levels of reactive oxygen species and malondialdehyde as well as decreased levels of antioxidant molecules, including glutathione and superoxide dismutases in Auts2-cKO mouse brains compared to controls. Finally, Auts2 knockdown significantly disrupted mitochondrial homeostasis and inhibited activity of the SIRT1-SIRT3 axis. Taken together, our findings indicate that loss of AUTS2 expression in Emx1-expressing cells induces multiple changes in metabolic pathways that have been linked to the pathology of ASD. Further characterization of the role of AUTS2 in Emx1-expressing cells in regulating the metabolism of brain neurons may identify opportunities to treat ASD and AUTS2-deficiency disorders with metabolism-targeted therapies.
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Affiliation(s)
- Min Liu
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yimeng Chen
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Miao Sun
- Department of Anesthesiology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou 121000, China
| | - Yingjie Du
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yafan Bai
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Guiyu Lei
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Congya Zhang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Mingru Zhang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yue Zhang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Chunhua Xi
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yulong Ma
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China.
| | - Guyan Wang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.
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8
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A Systematic Review of the Human Accelerated Regions in Schizophrenia and Related Disorders: Where the Evolutionary and Neurodevelopmental Hypotheses Converge. Int J Mol Sci 2023; 24:ijms24043597. [PMID: 36835010 PMCID: PMC9962562 DOI: 10.3390/ijms24043597] [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: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Schizophrenia is a psychiatric disorder that results from genetic and environmental factors interacting and disrupting neurodevelopmental trajectories. Human Accelerated Regions (HARs) are evolutionarily conserved genomic regions that have accumulated human-specific sequence changes. Thus, studies on the impact of HARs in the context of neurodevelopment, as well as with respect to adult brain phenotypes, have increased considerably in the last few years. Through a systematic approach, we aim to offer a comprehensive review of HARs' role in terms of human brain development, configuration, and cognitive abilities, as well as whether HARs modulate the susceptibility to neurodevelopmental psychiatric disorders such as schizophrenia. First, the evidence in this review highlights HARs' molecular functions in the context of the neurodevelopmental regulatory genetic machinery. Second, brain phenotypic analyses indicate that HAR genes' expression spatially correlates with the regions that suffered human-specific cortical expansion, as well as with the regional interactions for synergistic information processing. Lastly, studies based on candidate HAR genes and the global "HARome" variability describe the involvement of these regions in the genetic background of schizophrenia, but also in other neurodevelopmental psychiatric disorders. Overall, the data considered in this review emphasise the crucial role of HARs in human-specific neurodevelopment processes and encourage future research on this evolutionary marker for a better understanding of the genetic basis of schizophrenia and other neurodevelopmental-related psychiatric disorders. Accordingly, HARs emerge as interesting genomic regions that require further study in order to bridge the neurodevelopmental and evolutionary hypotheses in schizophrenia and other related disorders and phenotypes.
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9
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Pang W, Wang M, Bi Q, Li H, Zhou Q, Ye X, Xiang W, Xiao L. Activity-Dependent Differential Regulation of Auts2 Isoforms In Vitro and In Vivo. Mol Neurobiol 2023; 60:2973-2985. [PMID: 36754912 DOI: 10.1007/s12035-023-03241-x] [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: 07/11/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder of unknown cause, although one hypothesis suggests a potential imbalance between excitation and inhibition that leads to changes in neuronal activity and a disturbance in the brain network. However, the mechanisms through which neuronal activity contributes to the development of ASD remain largely unexplained. In this study, we described that neuronal activity at the transcriptional and translational levels regulated the expression of Auts2 isoforms. The prolonged stimulation of cultured cortical neurons significantly reduced the auts2 transcripts, accompanied by the decrease of FL-Auts2 protein, as well as one of the short isoforms (S-Auts2 var.1). Blocking neuronal activity increased the number of auts2 transcripts but not protein levels. Furthermore, blocking the NMDA receptors during stimulation could partially restore the FL-Auts2 and S-Auts2 var.1 at protein level, but not at mRNA level. Finally, Auts2 expression in the hippocampus was reduced in mice exposed to an enriched environment, a behavior paradigm designed to increase the brain activity through abundant sensory and social stimulations. Thus, our study revealed a novel regulatory effect of neuronal activity on the transcription and translation of ASD-risk gene auts2.
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Affiliation(s)
- Wenbin Pang
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
- School of Pediatrics, Hainan Medical University, Haikou, China
| | - Meijuan Wang
- School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
| | - Qingshang Bi
- School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
| | - Hongai Li
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China
- School of Pediatrics, Hainan Medical University, Haikou, China
| | - Qionglin Zhou
- School of Pediatrics, Hainan Medical University, Haikou, China
| | - Xiaoshan Ye
- School of Pediatrics, Hainan Medical University, Haikou, China
| | - Wei Xiang
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China.
- School of Pediatrics, Hainan Medical University, Haikou, China.
- National Health Commission (NHC) Key Laboratory of Control of Tropical Diseases, Hainan Medical University, Haikou, China.
| | - Le Xiao
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, China.
- School of Pediatrics, Hainan Medical University, Haikou, China.
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10
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Geng Z, Wang Q, Miao W, Wolf T, Chavez J, Giddings E, Hobbs R, DeGraff DJ, Wang Y, Stafford J, Gao Z. AUTS2 Controls Neuronal Lineage Choice Through a Novel PRC1-Independent Complex and BMP Inhibition. Stem Cell Rev Rep 2023; 19:531-549. [PMID: 36258139 PMCID: PMC9905272 DOI: 10.1007/s12015-022-10459-0] [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] [Accepted: 09/28/2022] [Indexed: 02/07/2023]
Abstract
Despite a prominent risk factor for Neurodevelopmental disorders (NDD), it remains unclear how Autism Susceptibility Candidate 2 (AUTS2) controls the neurodevelopmental program. Our studies investigated the role of AUTS2 in neuronal differentiation and discovered that AUTS2, together with WDR68 and SKI, forms a novel protein complex (AWS) specifically in neuronal progenitors and promotes neuronal differentiation through inhibiting BMP signaling. Genomic and biochemical analyses demonstrated that the AWS complex achieves this effect by recruiting the CUL4 E3 ubiquitin ligase complex to mediate poly-ubiquitination and subsequent proteasomal degradation of phosphorylated SMAD1/5/9. Furthermore, using primary cortical neurons, we observed aberrant BMP signaling and dysregulated expression of neuronal genes upon manipulating the AWS complex, indicating that the AWS-CUL4-BMP axis plays a role in regulating neuronal lineage specification in vivo. Thus, our findings uncover a sophisticated cellular signaling network mobilized by a prominent NDD risk factor, presenting multiple potential therapeutic targets for NDD.
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Affiliation(s)
- Zhuangzhuang Geng
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Qiang Wang
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Weili Miao
- Department of Chemistry, University of California at Riverside, Riverside, CA, 92521, USA
| | - Trevor Wolf
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Jessenia Chavez
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Emily Giddings
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Ryan Hobbs
- Department of Dermatology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Penn State College of Medicine, Hershey, PA, 17033, USA
- Penn State Hershey Cancer Institute, Hershey, PA, 17033, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California at Riverside, Riverside, CA, 92521, USA
| | - James Stafford
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Zhonghua Gao
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.
- Penn State Hershey Cancer Institute, Hershey, PA, 17033, USA.
- The Stem Cell and Regenerative Biology Program, Penn State College of Medicine, Hershey, PA, 17033, USA.
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11
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Hillis DA, Garland T. Multiple solutions at the genomic level in response to selective breeding for high locomotor activity. Genetics 2023; 223:iyac165. [PMID: 36305689 PMCID: PMC9836024 DOI: 10.1093/genetics/iyac165] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 01/19/2023] Open
Abstract
Replicate lines under uniform selection often evolve in different ways. Previously, analyses using whole-genome sequence data for individual mice (Mus musculus) from 4 replicate High Runner lines and 4 nonselected control lines demonstrated genomic regions that have responded consistently to selection for voluntary wheel-running behavior. Here, we ask whether the High Runner lines have evolved differently from each other, even though they reached selection limits at similar levels. We focus on 1 High Runner line (HR3) that became fixed for a mutation at a gene of major effect (Myh4Minimsc) that, in the homozygous condition, causes a 50% reduction in hindlimb muscle mass and many pleiotropic effects. We excluded HR3 from SNP analyses and identified 19 regions not consistently identified in analyses with all 4 lines. Repeating analyses while dropping each of the other High Runner lines identified 12, 8, and 6 such regions. (Of these 45 regions, 37 were unique.) These results suggest that each High Runner line indeed responded to selection somewhat uniquely, but also that HR3 is the most distinct. We then applied 2 additional analytical approaches when dropping HR3 only (based on haplotypes and nonstatistical tests involving fixation patterns). All 3 approaches identified 7 new regions (as compared with analyses using all 4 High Runner lines) that include genes associated with activity levels, dopamine signaling, hippocampus morphology, heart size, and body size, all of which differ between High Runner and control lines. Our results illustrate how multiple solutions and "private" alleles can obscure general signatures of selection involving "public" alleles.
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Affiliation(s)
- David A Hillis
- Genetics, Genomics, and Bioinformatics Graduate Program, University of California, Riverside, CA 92521, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
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12
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Tong C, Avilés L, Rayor LS, Mikheyev AS, Linksvayer TA. Genomic signatures of recent convergent transitions to social life in spiders. Nat Commun 2022; 13:6967. [PMID: 36414623 PMCID: PMC9681848 DOI: 10.1038/s41467-022-34446-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.
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Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Leticia Avilés
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Linda S Rayor
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander S Mikheyev
- Evolutionary Genomics Group, Research School of Biology, Australian National University, Canberra, 0200, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
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13
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Kang H, Cabrera JR, Zee BM, Kang HA, Jobe JM, Hegarty MB, Barry AE, Glotov A, Schwartz YB, Kuroda MI. Variant Polycomb complexes in Drosophila consistent with ancient functional diversity. SCIENCE ADVANCES 2022; 8:eadd0103. [PMID: 36070387 PMCID: PMC9451159 DOI: 10.1126/sciadv.add0103] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Polycomb group (PcG) mutants were first identified in Drosophila on the basis of their failure to maintain proper Hox gene repression during development. The proteins encoded by the corresponding fly genes mainly assemble into one of two discrete Polycomb repressive complexes: PRC1 or PRC2. However, biochemical analyses in mammals have revealed alternative forms of PRC2 and multiple distinct types of noncanonical or variant PRC1. Through a series of proteomic analyses, we identify analogous PRC2 and variant PRC1 complexes in Drosophila, as well as a broader repertoire of interactions implicated in early development. Our data provide strong support for the ancient diversity of PcG complexes and a framework for future analysis in a longstanding and versatile genetic system.
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Affiliation(s)
- Hyuckjoon Kang
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Janel R. Cabrera
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Biology Department, Emmanuel College, Boston, MA 02115, USA
| | - Barry M. Zee
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Heather A. Kang
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Alexander Glotov
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Yuri B. Schwartz
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Mitzi I. Kuroda
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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14
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Flanagan K, Baradaran-Heravi A, Yin Q, Dao Duc K, Spradling AC, Greenblatt EJ. FMRP-dependent production of large dosage-sensitive proteins is highly conserved. Genetics 2022; 221:6613139. [PMID: 35731217 PMCID: PMC9339308 DOI: 10.1093/genetics/iyac094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022] Open
Abstract
Mutations in FMR1 are the most common heritable cause of autism spectrum disorder. FMR1 encodes an RNA-binding protein, FMRP, which binds to long, autism-relevant transcripts and is essential for normal neuronal and ovarian development. In contrast to the prevailing model that FMRP acts to block translation elongation, we previously found that FMRP activates the translation initiation of large proteins in Drosophila oocytes. We now provide evidence that FMRP-dependent translation is conserved and occurs in the mammalian brain. Our comparisons of the mammalian cortex and Drosophila oocyte ribosome profiling data show that translation of FMRP-bound mRNAs decreases to a similar magnitude in FMRP-deficient tissues from both species. The steady-state levels of several FMRP targets were reduced in the Fmr1 KO mouse cortex, including a ∼50% reduction of Auts2, a gene implicated in an autosomal dominant autism spectrum disorder. To distinguish between effects on elongation and initiation, we used a novel metric to detect the rate-limiting ribosome stalling. We found no evidence that FMRP target protein production is governed by translation elongation rates. FMRP translational activation of large proteins may be critical for normal human development, as more than 20 FMRP targets including Auts2 are dosage sensitive and are associated with neurodevelopmental disorders caused by haploinsufficiency.
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Affiliation(s)
- Keegan Flanagan
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Qi Yin
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Allan C Spradling
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Ethan J Greenblatt
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
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15
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Mai Le N, Li J. Ras-related C3 botulinum toxin substrate 1 role in Pathophysiology of Neurological diseases. BRAIN HEMORRHAGES 2022. [DOI: 10.1016/j.hest.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Nisar S, Bhat AA, Masoodi T, Hashem S, Akhtar S, Ali TA, Amjad S, Chawla S, Bagga P, Frenneaux MP, Reddy R, Fakhro K, Haris M. Genetics of glutamate and its receptors in autism spectrum disorder. Mol Psychiatry 2022; 27:2380-2392. [PMID: 35296811 PMCID: PMC9135628 DOI: 10.1038/s41380-022-01506-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 12/11/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental impairment characterized by deficits in social interaction skills, impaired communication, and repetitive and restricted behaviors that are thought to be due to altered neurotransmission processes. The amino acid glutamate is an essential excitatory neurotransmitter in the human brain that regulates cognitive functions such as learning and memory, which are usually impaired in ASD. Over the last several years, increasing evidence from genetics, neuroimaging, protein expression, and animal model studies supporting the notion of altered glutamate metabolism has heightened the interest in evaluating glutamatergic dysfunction in ASD. Numerous pharmacological, behavioral, and imaging studies have demonstrated the imbalance in excitatory and inhibitory neurotransmitters, thus revealing the involvement of the glutamatergic system in ASD pathology. Here, we review the effects of genetic alterations on glutamate and its receptors in ASD and the role of non-invasive imaging modalities in detecting these changes. We also highlight the potential therapeutic targets associated with impaired glutamatergic pathways.
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Affiliation(s)
- Sabah Nisar
- Laboratory of Molecular and Metabolic Imaging, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ajaz A Bhat
- Laboratory of Molecular and Metabolic Imaging, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Tariq Masoodi
- Laboratory of Molecular and Metabolic Imaging, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sheema Hashem
- Laboratory of Molecular and Metabolic Imaging, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sabah Akhtar
- Laboratory of Molecular and Metabolic Imaging, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Tayyiba Akbar Ali
- Laboratory of Molecular and Metabolic Imaging, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sara Amjad
- Shibli National College, Azamgarh, Uttar Pradesh, 276001, India
| | - Sanjeev Chawla
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Puneet Bagga
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael P Frenneaux
- Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Ravinder Reddy
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Khalid Fakhro
- Department of Human Genetics, Sidra Medicine, P.O. Box 26999, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Mohammad Haris
- Laboratory of Molecular and Metabolic Imaging, Sidra Medicine, P.O. Box 26999, Doha, Qatar.
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Laboratory of Animal Research, Qatar University, P.O. Box 2713, Doha, Qatar.
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17
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Dietary Restriction and Rapamycin Affect Brain Aging in Mice by Attenuating Age-Related DNA Methylation Changes. Genes (Basel) 2022; 13:genes13040699. [PMID: 35456505 PMCID: PMC9030181 DOI: 10.3390/genes13040699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/02/2022] [Accepted: 04/13/2022] [Indexed: 02/07/2023] Open
Abstract
The fact that dietary restriction (DR) and long-term rapamycin treatment (RALL) can ameliorate the aging process has been reported by many researchers. As the interface between external and genetic factors, epigenetic modification such as DNA methylation may have latent effects on the aging rate at the molecular level. To understand the mechanism behind the impacts of dietary restriction and rapamycin on aging, DNA methylation and gene expression changes were measured in the hippocampi of different-aged mice. Examining the single-base resolution of DNA methylation, we discovered that both dietary restriction and rapamycin treatment can maintain DNA methylation in a younger state compared to normal-aged mice. Through functional enrichment analysis of genes in which DNA methylation or gene expression can be affected by DR/RALL, we found that DR/RALL may retard aging through a relationship in which DNA methylation and gene expression work together not only in the same gene but also in the same biological process. This study is instructive for understanding the maintenance of DNA methylation by DR/RALL in the aging process, as well as the role of DR and RALL in the amelioration of aging.
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18
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Bölicke N, Albert M. Polycomb-mediated gene regulation in human brain development and neurodevelopmental disorders. Dev Neurobiol 2022; 82:345-363. [PMID: 35384339 DOI: 10.1002/dneu.22876] [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: 12/22/2021] [Revised: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 12/17/2022]
Abstract
The neocortex is considered the seat of higher cognitive function in humans. It develops from a sheet of neural progenitor cells, most of which eventually give rise to neurons. This process of cell fate determination is controlled by precise temporal and spatial gene expression patterns that in turn are affected by epigenetic mechanisms including Polycomb group (PcG) regulation. PcG proteins assemble in multiprotein complexes and catalyze repressive posttranslational histone modifications. Their association with neurodevelopmental disease and various types of cancer of the central nervous system, as well as observations in mouse models, has implicated these epigenetic modifiers in controlling various stages of cortex development. The precise mechanisms conveying PcG-associated transcriptional repression remain incompletely understood and are an active field of research. PcG activity appears to be highly context-specific, raising the question of species-specific differences in the regulation of neural stem and progenitor regulation. In this review, we will discuss our growing understanding of how PcG regulation affects human cortex development, based on studies in murine model systems, but focusing mostly on findings obtained from examining impaired PcG activity in the context of human neurodevelopmental disorders and cancer. Furthermore, we will highlight relevant experimental approaches for functional investigations of PcG regulation in human cortex development.
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Affiliation(s)
- Nora Bölicke
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Mareike Albert
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
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19
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Reinhardt F, Stadler PF. ExceS-A: an exon-centric split aligner. J Integr Bioinform 2022; 19:jib-2021-0040. [PMID: 35254744 PMCID: PMC9069663 DOI: 10.1515/jib-2021-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
Spliced alignments are a key step in the construction of high-quality homology-based annotations of protein sequences. The exon/intron structure, which is computed as part of spliced alignment procedures, often conveys important information for the distinguishing paralogous members of gene families. Here we present an exon-centric pipeline for spliced alignment that is intended in particular for applications that involve exon-by-exon comparisons of coding sequences. We show that the simple, blat-based approach has advantages over established tools in particular for genes with very large introns and applications to fragmented genome assemblies.
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Affiliation(s)
- Franziska Reinhardt
- Bioinformatics Group, Institute of Computer Science, Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Institute of Computer Science, Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
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20
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AUTS2 Gene: Keys to Understanding the Pathogenesis of Neurodevelopmental Disorders. Cells 2021; 11:cells11010011. [PMID: 35011572 PMCID: PMC8750789 DOI: 10.3390/cells11010011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/08/2021] [Accepted: 12/18/2021] [Indexed: 01/01/2023] Open
Abstract
Neurodevelopmental disorders (NDDs), including autism spectrum disorders (ASD) and intellectual disability (ID), are a large group of neuropsychiatric illnesses that occur during early brain development, resulting in a broad spectrum of syndromes affecting cognition, sociability, and sensory and motor functions. Despite progress in the discovery of various genetic risk factors thanks to the development of novel genomics technologies, the precise pathological mechanisms underlying the onset of NDDs remain elusive owing to the profound genetic and phenotypic heterogeneity of these conditions. Autism susceptibility candidate 2 (AUTS2) has emerged as a crucial gene associated with a wide range of neuropsychological disorders, such as ASD, ID, schizophrenia, and epilepsy. AUTS2 has been shown to be involved in multiple neurodevelopmental processes; in cell nuclei, it acts as a key transcriptional regulator in neurodevelopment, whereas in the cytoplasm, it participates in cerebral corticogenesis, including neuronal migration and neuritogenesis, through the control of cytoskeletal rearrangements. Postnatally, AUTS2 regulates the number of excitatory synapses to maintain the balance between excitation and inhibition in neural circuits. In this review, we summarize the knowledge regarding AUTS2, including its molecular and cellular functions in neurodevelopment, its genetics, and its role in behaviors.
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21
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Kanlayaprasit S, Thongkorn S, Panjabud P, Jindatip D, Hu VW, Kikkawa T, Osumi N, Sarachana T. Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. Int J Mol Sci 2021; 22:13201. [PMID: 34947998 PMCID: PMC8708761 DOI: 10.3390/ijms222413201] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/16/2022] Open
Abstract
Bisphenol A (BPA) is an environmental risk factor for autism spectrum disorder (ASD). BPA exposure dysregulates ASD-related genes in the hippocampus and neurological functions of offspring. However, whether prenatal BPA exposure has an impact on genes in the prefrontal cortex, another brain region highly implicated in ASD, and through what mechanisms have not been investigated. Here, we demonstrated that prenatal BPA exposure disrupts the transcriptome-interactome profiles of the prefrontal cortex of neonatal rats. Interestingly, the list of BPA-responsive genes was significantly enriched with known ASD candidate genes, as well as genes that were dysregulated in the postmortem brain tissues of ASD cases from multiple independent studies. Moreover, several differentially expressed genes in the offspring's prefrontal cortex were the targets of ASD-related transcription factors, including AR, ESR1, and RORA. The hypergeometric distribution analysis revealed that BPA may regulate the expression of such genes through these transcription factors in a sex-dependent manner. The molecular docking analysis of BPA and ASD-related transcription factors revealed novel potential targets of BPA, including RORA, SOX5, TCF4, and YY1. Our findings indicated that prenatal BPA exposure disrupts ASD-related genes in the offspring's prefrontal cortex and may increase the risk of ASD through sex-dependent molecular mechanisms, which should be investigated further.
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Grants
- FRB65_hea(80)_175_37_05 Fundamental Fund, Chulalongkorn University
- AHS-CU 61004 Faculty of Allied Health Sciences Research Fund, Chulalongkorn University
- GRU 6300437001-1 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- GRU_64_033_37_004 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship, Graduate School, Chulalongkorn University
- The Overseas Research Experience Scholarship for Graduate Students from Graduate School, Chulalongkorn University
- PHD/0029/2561 The Royal Golden Jubilee Ph.D. Programme Scholarship, Thailand Research Fund and National Research Council of Thailand
- National Research Council of Thailand (NRCT)
- GCUGR1125623067D-67 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125632108D-108 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- 2073011 Chulalongkorn University Laboratory Animal Center (CULAC) Grant
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Affiliation(s)
- Songphon Kanlayaprasit
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Surangrat Thongkorn
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Pawinee Panjabud
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Depicha Jindatip
- Systems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand;
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Valerie W. Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA;
| | - Takako Kikkawa
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai 980-8577, Miyagi, Japan; (T.K.); (N.O.)
| | - Noriko Osumi
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai 980-8577, Miyagi, Japan; (T.K.); (N.O.)
| | - Tewarit Sarachana
- Systems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand;
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22
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Pauli S, Berger H, Ufartes R, Borchers A. Comparing a Novel Malformation Syndrome Caused by Pathogenic Variants in FBRSL1 to AUTS2 Syndrome. Front Cell Dev Biol 2021; 9:779009. [PMID: 34805182 PMCID: PMC8602103 DOI: 10.3389/fcell.2021.779009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Truncating variants in specific exons of Fibrosin-like protein 1 (FBRSL1) were recently reported to cause a novel malformation and intellectual disability syndrome. The clinical spectrum includes microcephaly, facial dysmorphism, cleft palate, skin creases, skeletal anomalies and contractures, postnatal growth retardation, global developmental delay as well as respiratory problems, hearing impairment and heart defects. The function of FBRSL1 is largely unknown, but pathogenic variants in the FBRSL1 paralog Autism Susceptibility Candidate 2 (AUTS2) are causative for an intellectual disability syndrome with microcephaly (AUTS2 syndrome). Some patients with AUTS2 syndrome also show additional symptoms like heart defects and contractures overlapping with the phenotype presented by patients with FBRSL1 mutations. For AUTS2, a dual function, depending on different isoforms, was described and suggested for FBRSL1. Both, nuclear FBRSL1 and AUTS2 are components of the Polycomb subcomplexes PRC1.3 and PRC1.5. These complexes have essential roles in developmental processes, cellular differentiation and proliferation by regulating gene expression via histone modification. In addition, cytoplasmic AUTS2 controls neural development, neuronal migration and neurite extension by regulating the cytoskeleton. Here, we review recent data on FBRSL1 in respect to previously published data on AUTS2 to gain further insights into its molecular function, its role in development as well as its impact on human genetics.
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Affiliation(s)
- Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Hanna Berger
- Faculty of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| | - Roser Ufartes
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Annette Borchers
- Faculty of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
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23
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Liu S, Aldinger KA, Cheng CV, Kiyama T, Dave M, McNamara HK, Zhao W, Stafford JM, Descostes N, Lee P, Caraffi SG, Ivanovski I, Errichiello E, Zweier C, Zuffardi O, Schneider M, Papavasiliou AS, Perry MS, Humberson J, Cho MT, Weber A, Swale A, Badea TC, Mao CA, Garavelli L, Dobyns WB, Reinberg D. NRF1 association with AUTS2-Polycomb mediates specific gene activation in the brain. Mol Cell 2021; 81:4663-4676.e8. [PMID: 34637754 PMCID: PMC8604784 DOI: 10.1016/j.molcel.2021.09.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022]
Abstract
The heterogeneous family of complexes comprising Polycomb repressive complex 1 (PRC1) is instrumental for establishing facultative heterochromatin that is repressive to transcription. However, two PRC1 species, ncPRC1.3 and ncPRC1.5, are known to comprise novel components, AUTS2, P300, and CK2, that convert this repressive function to that of transcription activation. Here, we report that individuals harboring mutations in the HX repeat domain of AUTS2 exhibit defects in AUTS2 and P300 interaction as well as a developmental disorder reflective of Rubinstein-Taybi syndrome, which is mainly associated with a heterozygous pathogenic variant in CREBBP/EP300. Moreover, the absence of AUTS2 or mutation in its HX repeat domain gives rise to misregulation of a subset of developmental genes and curtails motor neuron differentiation of mouse embryonic stem cells. The transcription factor nuclear respiratory factor 1 (NRF1) has a novel and integral role in this neurodevelopmental process, being required for ncPRC1.3 recruitment to chromatin.
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Affiliation(s)
- Sanxiong Liu
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Chi Vicky Cheng
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Takae Kiyama
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Mitali Dave
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Wukui Zhao
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pedro Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Stefano G Caraffi
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Ivan Ivanovski
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy; Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Edoardo Errichiello
- Dipartimento di Medicina Molecolare, Università di Pavia, Pavia, Italy; IRCCS Mondino Foundation, Pavia, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054 Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Orsetta Zuffardi
- Dipartimento di Medicina Molecolare, Università di Pavia, Pavia, Italy
| | - Michael Schneider
- Carle Physicians Group, Section of Neurology, St. Christopher's Hospital for Children, Urbana, IL, USA
| | | | - M Scott Perry
- Comprehensive Epilepsy Program, Jane and John Justin Neuroscience Center, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Jennifer Humberson
- Division of Genetics, Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, USA
| | | | | | - Andrew Swale
- Liverpool Women's Hospital, Liverpool, UK; Manchester Centre for Genomic Medicine, Manchester, UK
| | - Tudor C Badea
- National Eye Institute, NIH, Bethesda, MD 20892, USA; Research and Development Institute, Transilvania University of Brasov, School of Medicine, Brasov, Romania
| | - Chai-An Mao
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Livia Garavelli
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics (Genetic Medicine), University of Washington, Seattle, WA, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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24
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High Behavioral Variability Mediated by Altered Neuronal Excitability in auts2 Mutant Zebrafish. eNeuro 2021; 8:ENEURO.0493-20.2021. [PMID: 34544758 PMCID: PMC8503961 DOI: 10.1523/eneuro.0493-20.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 01/28/2023] Open
Abstract
Autism spectrum disorders (ASDs) are characterized by abnormal behavioral traits arising from neural circuit dysfunction. While a number of genes have been implicated in ASDs, in most cases, a clear understanding of how mutations in these genes lead to circuit dysfunction and behavioral abnormality is absent. The autism susceptibility candidate 2 (AUTS2) gene is one such gene, associated with ASDs, intellectual disability and a range of other neurodevelopmental conditions. However, the role of AUTS2 in neural development and circuit function is not at all known. Here, we undertook functional analysis of Auts2a, the main homolog of AUTS2 in zebrafish, in the context of the escape behavior. Escape behavior in wild-type zebrafish is critical for survival and is therefore, reliable, rapid, and has well-defined kinematic properties. auts2a mutant zebrafish are viable, have normal gross morphology and can generate escape behavior with normal kinematics. However, the behavior is unreliable and delayed, with high trial-to-trial variability in the latency. Using calcium imaging we probed the activity of Mauthner neurons during otic vesicle (OV) stimulation and observed lower probability of activation and reduced calcium transients in the mutants. With direct activation of Mauthner by antidromic stimulation, the threshold for activation in mutants was higher than that in wild-type, even when inhibition was blocked. Taken together, these results point to reduced excitability of Mauthner neurons in auts2a mutant larvae leading to unreliable escape responses. Our results show a novel role for Auts2a in regulating neural excitability and reliability of behavior.
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25
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Tamburri S, Conway E, Pasini D. Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer. Trends Genet 2021; 38:333-352. [PMID: 34426021 DOI: 10.1016/j.tig.2021.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
Cell identity is tightly controlled by specific transcriptional programs which require post-translational modifications of histones. These histone modifications allow the establishment and maintenance of active and repressed chromatin domains. Histone H2A lysine 119 ubiquitination (H2AK119ub1) has an essential role in building repressive chromatin domains during development. It is regulated by the counteracting activities of the Polycomb repressive complex 1 (PRC1) and the Polycomb repressive-deubiquitinase (PR-DUB) complexes, two multi-subunit ensembles that write and erase this modification, respectively. We have catalogued the recurrent genetic alterations in subunits of the PRC1 and PR-DUB complexes in both neurodevelopmental disorders and cancer. These genetic lesions are often shared across disorders, and we highlight common mechanisms of H2AK119ub1 dysregulation and how they affect development in multiple disease contexts.
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Affiliation(s)
- Simone Tamburri
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
| | - Eric Conway
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
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26
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Bakoev S, Traspov A, Getmantseva L, Belous A, Karpushkina T, Kostyunina O, Usatov A, Tatarinova TV. Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach. PeerJ 2021; 9:e11580. [PMID: 34327051 PMCID: PMC8310618 DOI: 10.7717/peerj.11580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background A significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets. Methods The malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg. Results Forty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics. Data availability Genotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/.
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Affiliation(s)
- Siroj Bakoev
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia.,Centre for Strategic Planning and Management of Biomedical Health Risks, Moscow, Russia
| | - Aleksei Traspov
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia.,Centre for Strategic Planning and Management of Biomedical Health Risks, Moscow, Russia
| | - Lyubov Getmantseva
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Anna Belous
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Tatiana Karpushkina
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Olga Kostyunina
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | | | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, United States of America.,Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Vavilov Institute for General Genetics, Moscow, Russia.,School of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
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27
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Nesbit N, Wallace R, Harihar S, Zhou M, Jung JY, Silberstein M, Lee PH. Genomewide alteration of histone H3K4 methylation underlies genetic vulnerability to psychopathology. J Genet 2021. [DOI: 10.1007/s12041-021-01294-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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Castanza AS, Ramirez S, Tripathi PP, Daza RAM, Kalume FK, Ramirez JM, Hevner RF. AUTS2 Regulates RNA Metabolism and Dentate Gyrus Development in Mice. Cereb Cortex 2021; 31:4808-4824. [PMID: 34013328 DOI: 10.1093/cercor/bhab124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022] Open
Abstract
Human AUTS2 mutations are linked to a syndrome of intellectual disability, autistic features, epilepsy, and other neurological and somatic disorders. Although it is known that this unique gene is highly expressed in developing cerebral cortex, the molecular and developmental functions of AUTS2 protein remain unclear. Using proteomics methods to identify AUTS2 binding partners in neonatal mouse cerebral cortex, we found that AUTS2 associates with multiple proteins that regulate RNA transcription, splicing, localization, and stability. Furthermore, AUTS2-containing protein complexes isolated from cortical tissue bound specific RNA transcripts in RNA immunoprecipitation and sequencing assays. Deletion of all major functional isoforms of AUTS2 (full-length and C-terminal) by conditional excision of exon 15 caused breathing abnormalities and neonatal lethality when Auts2 was inactivated throughout the developing brain. Mice with limited inactivation of Auts2 in cerebral cortex survived but displayed abnormalities of cerebral cortex structure and function, including dentate gyrus hypoplasia with agenesis of hilar mossy neurons, and abnormal spiking activity on EEG. Also, RNA transcripts that normally associate with AUTS2 were dysregulated in mutant mice. Together, these findings indicate that AUTS2 regulates RNA metabolism and is essential for development of cerebral cortex, as well as subcortical breathing centers.
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Affiliation(s)
- Anthony S Castanza
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Sanja Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Prem P Tripathi
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Ray A M Daza
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Franck K Kalume
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Neurological Surgery, University of Washington, Seattle, WA 98014, USA
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Neurological Surgery, University of Washington, Seattle, WA 98014, USA
| | - Robert F Hevner
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Department of Neurological Surgery, University of Washington, Seattle, WA 98014, USA
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29
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Pang W, Yi X, Li L, Liu L, Xiang W, Xiao L. Untangle the Multi-Facet Functions of Auts2 as an Entry Point to Understand Neurodevelopmental Disorders. Front Psychiatry 2021; 12:580433. [PMID: 33967843 PMCID: PMC8102784 DOI: 10.3389/fpsyt.2021.580433] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/22/2021] [Indexed: 12/27/2022] Open
Abstract
Neurodevelopmental disorders are psychiatric diseases that are usually first diagnosed in infancy, childhood and adolescence. Autism spectrum disorder (ASD) is a neurodevelopmental disorder, characterized by core symptoms including impaired social communication, cognitive rigidity and repetitive behavior, accompanied by a wide range of comorbidities such as intellectual disability (ID) and dysmorphisms. While the cause remains largely unknown, genetic, epigenetic, and environmental factors are believed to contribute toward the onset of the disease. Autism Susceptibility Candidate 2 (Auts2) is a gene highly associated with ID and ASD. Therefore, understanding the function of Auts2 gene can provide a unique entry point to untangle the complex neuronal phenotypes of neurodevelpmental disorders. In this review, we discuss the recent discoveries regarding the molecular and cellular functions of Auts2. Auts2 was shown to be a key-regulator of transcriptional network and a mediator of epigenetic regulation in neurodevelopment, the latter potentially providing a link for the neuronal changes of ASD upon environmental risk-factor exposure. In addition, Auts2 could synchronize the balance between excitation and inhibition through regulating the number of excitatory synapses. Cytoplasmic Auts2 could join the fine-tuning of actin dynamics during neuronal migration and neuritogenesis. Furthermore, Auts2 was expressed in developing mouse and human brain regions such as the frontal cortex, dorsal thalamus, and hippocampus, which have been implicated in the impaired cognitive and social function of ASD. Taken together, a comprehensive understanding of Auts2 functions can give deep insights into the cause of the heterogenous manifestation of neurodevelopmental disorders such as ASD.
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Affiliation(s)
- Wenbin Pang
- Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
- National Health Commission (NHC) Key Laboratory of Control of Tropical Diseases, Hainan Medical University, Haikou, China
| | - Xinan Yi
- Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
| | - Ling Li
- Department of Pediatric Rehabilitation, Hainan Women and Children's Medical Center, Haikou, China
| | - Liyan Liu
- Department of Pediatric Rehabilitation, Hainan Women and Children's Medical Center, Haikou, China
| | - Wei Xiang
- National Health Commission (NHC) Key Laboratory of Control of Tropical Diseases, Hainan Medical University, Haikou, China
| | - Le Xiao
- Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
- Department of Pediatric Rehabilitation, Hainan Women and Children's Medical Center, Haikou, China
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30
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Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer. Sci Rep 2021; 11:6630. [PMID: 33758253 PMCID: PMC7988053 DOI: 10.1038/s41598-021-85812-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/02/2021] [Indexed: 01/31/2023] Open
Abstract
Androgens are a major driver of prostate cancer (PCa) and continue to be a critical treatment target for advanced disease, which includes castration therapy and antiandrogens. However, resistance to these therapies leading to metastatic castration-resistant prostate cancer (mCRPC), and the emergence of treatment-induced neuroendocrine disease (tNEPC) remains an ongoing challenge. Instability of the DNA methylome is well established as a major hallmark of PCa development and progression. Therefore, investigating the dynamics of the methylation changes going from the castration sensitive to the tNEPC state would provide insights into novel mechanisms of resistance. Using an established xenograft model of CRPC, genome-wide methylation analysis was performed on cell lines representing various stages of PCa progression. We confirmed extensive methylation changes with the development of CRPC and tNEPC using this model. This included key genes and pathways associated with cellular differentiation and neurodevelopment. Combined analysis of methylation and gene expression changes further highlighted genes that could potentially serve as therapeutic targets. Furthermore, tNEPC-related methylation signals from this model were detectable in circulating cell free DNA (cfDNA) from mCRPC patients undergoing androgen-targeting therapies and were associated with a faster time to clinical progression. These potential biomarkers could help with identifying patients with aggressive disease.
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Lim TB, Foo SYR, Chen CK. The Role of Epigenetics in Congenital Heart Disease. Genes (Basel) 2021; 12:genes12030390. [PMID: 33803261 PMCID: PMC7998561 DOI: 10.3390/genes12030390] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common birth defect among newborns worldwide and contributes to significant infant morbidity and mortality. Owing to major advances in medical and surgical management, as well as improved prenatal diagnosis, the outcomes for these children with CHD have improved tremendously so much so that there are now more adults living with CHD than children. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. For this reason, the complex process of cardiogenesis, which is governed by multiple interlinked and dose-dependent pathways, is a well investigated process. In addition to the sequence of the genome, the contribution of epigenetics to cardiogenesis is increasingly recognized. Significant progress has been made dissecting the epigenome of the heart and identified associations with cardiovascular diseases. The role of epigenetic regulation in cardiac development/cardiogenesis, using tissue and animal models, has been well reviewed. Here, we curate the current literature based on studies in humans, which have revealed associated and/or causative epigenetic factors implicated in CHD. We sought to summarize the current knowledge on the functional role of epigenetics in cardiogenesis as well as in distinct CHDs, with an aim to provide scientists and clinicians an overview of the abnormal cardiogenic pathways affected by epigenetic mechanisms, for a better understanding of their impact on the developing fetal heart, particularly for readers interested in CHD research.
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Affiliation(s)
- Tingsen Benson Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Sik Yin Roger Foo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
- Correspondence:
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32
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Jönsson ME, Garza R, Sharma Y, Petri R, Södersten E, Johansson JG, Johansson PA, Atacho DA, Pircs K, Madsen S, Yudovich D, Ramakrishnan R, Holmberg J, Larsson J, Jern P, Jakobsson J. Activation of endogenous retroviruses during brain development causes an inflammatory response. EMBO J 2021; 40:e106423. [PMID: 33644903 PMCID: PMC8090857 DOI: 10.15252/embj.2020106423] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for an inflammatory response, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9‐based gene disruption of the epigenetic co‐repressor protein Trim28, we found a dynamic H3K9me3‐dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERVs in excitatory neurons in the adult brain. Neuronal ERV expression was linked to activated microglia and the presence of ERV‐derived proteins in aggregate‐like structures. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in an inflammatory response.
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Affiliation(s)
- Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Rebecca Petri
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Erik Södersten
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Pia A Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann Am Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sofia Madsen
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
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33
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Gieldon L, Jauch A, Obeid K, Kaufmann L, Hinderhofer K, Haug U, Moog U. Germ cell mosaicism for AUTS2 exon 6 deletion. Am J Med Genet A 2021; 185:1261-1265. [PMID: 33577136 DOI: 10.1002/ajmg.a.62091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 11/11/2022]
Abstract
Haploinsufficiency of AUTS2 has been associated with neurodevelopmental disorders and dysmorphic features (MIM # 615834). More than 50 patients have been described, mostly carrying de novo deletions of one or more exons, including eight patients with exon 6 deletions. We report on two siblings, a girl and a boy aged 11 and 13 years, in whom the same pathogenic 85 kb deletion on 7q11.22 encompassing exon 6 of AUTS2 by SNP array analysis was identified. Both children had typical symptoms of AUTS2 syndrome such as intellectual impairment and behavioral problems, but with markedly different expression. SNP array analysis excluded the deletion in blood samples of both parents and a healthy brother. Conventional karyotyping of both parents and additional FISH analyses, marking the flanking regions of the deletion, did not show any structural rearrangements involving 7q11.22. A germ cell mosaicism was suggested as the most probable explanation for occurrence of the same deletion in these two siblings. To our knowledge this is the first report of germ cell mosaicism for AUTS2 syndrome. It additionally provides further evidence of intrafamilial phenotypic variability in AUTS2 syndrome and adds clinical information to the phenotypic spectrum of patients with AUTS2 exon 6 deletions.
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Affiliation(s)
- Laura Gieldon
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Katharina Obeid
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Ulrich Haug
- Center for Child Neurology and Social Pediatrics Maulbronn, Maulbronn, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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34
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AUTS2 isoforms control neuronal differentiation. Mol Psychiatry 2021; 26:666-681. [PMID: 30953002 DOI: 10.1038/s41380-019-0409-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 01/07/2023]
Abstract
Mutations in AUTS2 are associated with autism, intellectual disability, and microcephaly. AUTS2 is expressed in the brain and interacts with polycomb proteins, yet it is still unclear how mutations in AUTS2 lead to neurodevelopmental phenotypes. Here we report that when neuronal differentiation is initiated, there is a shift in expression from a long isoform to a short AUTS2 isoform. Yeast two-hybrid screen identified the splicing factor SF3B1 as an interactor of both isoforms, whereas the polycomb group proteins, PCGF3 and PCGF5, were found to interact exclusively with the long AUTS2 isoform. Reporter assays showed that the first exons of the long AUTS2 isoform function as a transcription repressor, but the part that consist of the short isoform acts as a transcriptional activator, both influenced by the cellular context. The expression levels of PCGF3 influenced the ability of the long AUTS2 isoform to activate or repress transcription. Mouse embryonic stem cells (mESCs) with heterozygote mutations in Auts2 had an increase in cell death during in vitro corticogenesis, which was significantly rescued by overexpressing the human AUTS2 transcripts. mESCs with a truncated AUTS2 protein (missing exons 12-20) showed premature neuronal differentiation, whereas cells overexpressing AUTS2, especially the long transcript, showed increase in expression of pluripotency markers and delayed differentiation. Taken together, our data suggest that the precise expression of AUTS2 isoforms is essential for regulating transcription and the timing of neuronal differentiation.
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35
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Nesbit N, Wallace R, Harihar S, Zhou M, Jung JY, Silberstein M, Lee PH. Genomewide alteration of histone H3K4 methylation underlies genetic vulnerability to psychopathology. J Genet 2021; 100:44. [PMID: 34282735 PMCID: PMC8459212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dysregulated histone methylation has emerged as a recurring theme in multiple neuropsychiatric disorders. However, it is yet unclear whether the altered histone methylation is associated with aetiologic mechanisms or an outcome of disease manifestation. In this study, we examined the genomewide association studies datasets of three major psychiatric disorders, schizophrenia (SCZ), bipolar disorder (BIP), and major depression disorder (MDD), which represents a total of 231,783 cases and 425,444 controls, to clarify the relationship. Our gene-set enrichment analysis results identified statistically significant association of genes involved in three histone methylation biological processes with the three adult-onset psychiatric disorders, which is mainly driven by the histone H3K4 methylation pathway (GO: 0051568). Further analysis of histone H3K4 methylation pathway genes revealed a widespread role of the genes in brain function and disease; 29 (52%) and 41 genes (73.2%) were associated with at least one brain-related trait or brain disorder, respectively. Spatiotemporal gene expression analysis suggests that these pathway genes play a critical role during the prenatal period and are consistent regulators in the cerebral cortex throughout an individual's life. AUTS2, DNMT1 and TET2 are genes of particular interest due to their pervasive role in various aspects of brain function. Our findings support a critical aetiologic role of H3K4 methylation genes shared across SCZ, BIP and MDD, providing new direction for the development of epigenetically-focussed drugs targeting common causal factors of these devastating disorders.
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Affiliation(s)
- Nicholas Nesbit
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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36
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Sellers RA, Robertson DL, Tassabehji M. Ancestry of the AUTS2 family-A novel group of polycomb-complex proteins involved in human neurological disease. PLoS One 2020; 15:e0232101. [PMID: 33306672 PMCID: PMC7732068 DOI: 10.1371/journal.pone.0232101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/07/2020] [Indexed: 01/10/2023] Open
Abstract
Autism susceptibility candidate 2 (AUTS2) is a neurodevelopmental regulator associated with an autosomal dominant intellectual disability syndrome, AUTS2 syndrome, and is implicated as an important gene in human-specific evolution. AUTS2 exists as part of a tripartite gene family, the AUTS2 family, which includes two relatively undefined proteins, Fibrosin (FBRS) and Fibrosin-like protein 1 (FBRSL1). Evolutionary ancestors of AUTS2 have not been formally identified outside of the Animalia clade. A Drosophila melanogaster protein, Tay bridge, with a role in neurodevelopment, has been shown to display limited similarity to the C-terminal of AUTS2, suggesting that evolutionary ancestors of the AUTS2 family may exist within other Protostome lineages. Here we present an evolutionary analysis of the AUTS2 family, which highlights ancestral homologs of AUTS2 in multiple Protostome species, implicates AUTS2 as the closest human relative to the progenitor of the AUTS2 family, and demonstrates that Tay bridge is a divergent ortholog of the ancestral AUTS2 progenitor gene. We also define regions of high relative sequence identity, with potential functional significance, shared by the extended AUTS2 protein family. Using structural predictions coupled with sequence conservation and human variant data from 15,708 individuals, a putative domain structure for AUTS2 was produced that can be used to aid interpretation of the consequences of nucleotide variation on protein structure and function in human disease. To assess the role of AUTS2 in human-specific evolution, we recalculated allele frequencies at previously identified human derived sites using large population genome data, and show a high prevalence of ancestral alleles, suggesting that AUTS2 may not be a rapidly evolving gene, as previously thought.
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Affiliation(s)
- Robert A. Sellers
- Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Glasgow, United Kingdom
| | - May Tassabehji
- Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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37
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Niu Y, Xie C, Du Z, Zeng J, Chen H, Jin L, Zhang Q, Yu H, Wang Y, Ping J, Yang C, Liu X, Li Y, Zhou G. Genome-wide association study identifies 7q11.22 and 7q36.3 associated with noise-induced hearing loss among Chinese population. J Cell Mol Med 2020; 25:411-420. [PMID: 33242228 PMCID: PMC7810922 DOI: 10.1111/jcmm.16094] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/02/2020] [Accepted: 10/28/2020] [Indexed: 12/25/2022] Open
Abstract
Noise-induced hearing loss (NIHL) seriously affects the life quality of humans and causes huge economic losses to society. To identify novel genetic loci involved in NIHL, we conducted a genome-wide association study (GWAS) for this symptom in Chinese populations. GWAS scan was performed in 89 NIHL subjects (cases) and 209 subjects with normal hearing who have been exposed to a similar noise environment (controls), followed by a replication study consisting of 53 cases and 360 controls. We identified that four candidate pathways were nominally significantly associated with NIHL, including the Erbb, Wnt, hedgehog and intraflagellar transport pathways. In addition, two novel index single-nucleotide polymorphisms, rs35075890 in the intron of AUTS2 gene at 7q11.22 (combined P = 1.3 × 10-6 ) and rs10081191 in the intron of PTPRN2 gene at 7q36.3 (combined P = 2.1 × 10-6 ), were significantly associated with NIHL. Furthermore, the expression quantitative trait loci analyses revealed that in brain tissues, the genotypes of rs35075890 are significantly associated with the expression levels of AUTS2, and the genotypes of rs10081191 are significantly associated with the expressions of PTPRN2 and WDR60. In conclusion, our findings highlight two novel loci at 7q11.22 and 7q36.3 conferring susceptibility to NIHL.
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Affiliation(s)
- Yuguang Niu
- Department of Otolaryngology, the First Medical Center of PLA General Hospital, Beijing, China
| | - Chengyong Xie
- Medical College of Guizhou University, Guiyang city, China
| | - Zhenhua Du
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jifeng Zeng
- Department of Otolaryngology, the No. 954 Hospital of PLA, Shannan City, China
| | - Hongxia Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Liang Jin
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qing Zhang
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China
| | - Huiying Yu
- Outpatient Department, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yahui Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jie Ping
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Chenning Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xinyi Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gangqiao Zhou
- Medical College of Guizhou University, Guiyang city, China.,State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, China.,Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China
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38
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Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
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39
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Yamashiro K, Hori K, Lai ESK, Aoki R, Shimaoka K, Arimura N, Egusa SF, Sakamoto A, Abe M, Sakimura K, Watanabe T, Uesaka N, Kano M, Hoshino M. AUTS2 Governs Cerebellar Development, Purkinje Cell Maturation, Motor Function and Social Communication. iScience 2020; 23:101820. [PMID: 33305180 PMCID: PMC7708818 DOI: 10.1016/j.isci.2020.101820] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/19/2020] [Accepted: 11/13/2020] [Indexed: 12/27/2022] Open
Abstract
Autism susceptibility candidate 2 (AUTS2), a risk gene for autism spectrum disorders (ASDs), is implicated in telencephalon development. Because AUTS2 is also expressed in the cerebellum where defects have been linked to ASDs, we investigated AUTS2 functions in the cerebellum. AUTS2 is specifically localized in Purkinje cells (PCs) and Golgi cells during postnatal development. Auts2 conditional knockout (cKO) mice exhibited smaller and deformed cerebella containing immature-shaped PCs with reduced expression of Cacna1a. Auts2 cKO and knock-down experiments implicated AUTS2 participation in elimination and translocation of climbing fiber synapses and restriction of parallel fiber synapse numbers. Auts2 cKO mice exhibited behavioral impairments in motor learning and vocal communications. Because Cacna1a is known to regulate synapse development in PCs, it suggests that AUTS2 is required for PC maturation to elicit normal development of PC synapses and thus the impairment of AUTS2 may cause cerebellar dysfunction related to psychiatric illnesses such as ASDs. Loss of Auts2 leads to the reduction of cerebellar size AUTS2 promotes the dendritic maturation of Purkinje cells AUTS2 participates in PF and CF synapse development of Purkinje cells Auts2 cKO mice exhibit the impaired motor learning and vocal communications
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Affiliation(s)
- Kunihiko Yamashiro
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan.,Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kei Hori
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Esther S K Lai
- Brain Mechanism for Behavior Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.,Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryo Aoki
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan.,Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kazumi Shimaoka
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Nariko Arimura
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Saki F Egusa
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Asami Sakamoto
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Takaki Watanabe
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Naofumi Uesaka
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.,Department of Cognitive Neurobiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan.,Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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40
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A genetic window to auditory-verbal problems in bipolar disorder. Psychiatr Genet 2020; 30:169-173. [PMID: 33165203 DOI: 10.1097/ypg.0000000000000265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bipolar disorder is a high prevalent psychiatric condition entailing recurrent episodes of elevated mood and depression, but also diverse cognitive problems. One deficit observed in patients concerns to auditory-verbal processing. Being a hereditary condition with a complex genetic architecture, it is not clear which genes contribute to this deficit. We show that candidates for bipolar disorder significantly overlap with candidates for clinical conditions resulting from a deficit in the phonological loop of working memory, particularly, developmental dyslexia and specific language impairment. The overlapping genes are involved in aspects of brain development and function (particularly, brain oscillations) potentially underlying phonological processing and accordingly, emerge as promising candidates for auditory-verbal deficits in bipolar disorder.
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41
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Li X, Liu T, Li Y, Li Q, Wang X, Hu X, Guo L, Zhang T, Liu T. Marmoset Brain ISH Data Revealed Molecular Difference Between Cortical Folding Patterns. Cereb Cortex 2020; 31:1660-1674. [PMID: 33152757 DOI: 10.1093/cercor/bhaa317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/23/2020] [Accepted: 09/29/2020] [Indexed: 01/14/2023] Open
Abstract
Literature studies have demonstrated the structural, connectional, and functional differences between cortical folding patterns in mammalian brains, such as convex and concave patterns. However, the molecular underpinning of such convex/concave differences remains largely unknown. Thanks to public access to a recently released set of marmoset whole-brain in situ hybridization data by RIKEN, Japan; this data's accessibility empowers us to improve our understanding of the organization, regulation, and function of genes and their relation to macroscale metrics of brains. In this work, magnetic resonance imaging and diffusion tensor imaging macroscale neuroimaging data in this dataset were used to delineate convex/concave patterns in marmoset and to examine their structural features. Machine learning and visualization tools were employed to investigate the possible transcriptome difference between cortical convex and concave patterns. Experimental results demonstrated that a collection of genes is differentially expressed in convex and concave patterns, and their expression profiles can robustly characterize and differentiate the two folding patterns. More importantly, neuroscientific interpretations of these differentially expressed genes, as well as axonal guidance pathway analysis and gene enrichment analysis, offer novel understanding of structural and functional differences between cortical folding patterns in different regions from a molecular perspective.
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Affiliation(s)
- Xiao Li
- Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tao Liu
- Center for Genomics and Computational Biology, College of Science, North China University of Science and Technology, 063210, China.,Center of Computational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Yujie Li
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA 30602, USA
| | - Qing Li
- The Information Processing Laboratory, School of Artificial Intelligence, Beijing Normal University, Beijing 100875, China
| | - Xianqiao Wang
- Computational Nano/Bio-Mechanics Lab, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Xintao Hu
- Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Lei Guo
- Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tuo Zhang
- Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA 30602, USA
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42
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AUTS2 Regulation of Synapses for Proper Synaptic Inputs and Social Communication. iScience 2020; 23:101183. [PMID: 32498016 PMCID: PMC7267731 DOI: 10.1016/j.isci.2020.101183] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/30/2020] [Accepted: 05/15/2020] [Indexed: 01/11/2023] Open
Abstract
Impairments in synapse development are thought to cause numerous psychiatric disorders. Autism susceptibility candidate 2 (AUTS2) gene has been associated with various psychiatric disorders, such as autism and intellectual disabilities. Although roles for AUTS2 in neuronal migration and neuritogenesis have been reported, its involvement in synapse regulation remains unclear. In this study, we found that excitatory synapses were specifically increased in the Auts2-deficient primary cultured neurons as well as Auts2 mutant forebrains. Electrophysiological recordings and immunostaining showed increases in excitatory synaptic inputs as well as c-fos expression in Auts2 mutant brains, suggesting that an altered balance of excitatory and inhibitory inputs enhances brain excitability. Auts2 mutant mice exhibited autistic-like behaviors including impairments in social interaction and altered vocal communication. Together, these findings suggest that AUTS2 regulates excitatory synapse number to coordinate E/I balance in the brain, whose impairment may underlie the pathology of psychiatric disorders in individuals with AUTS2 mutations. AUTS2 regulates excitatory synapse number in forebrain pyramidal neurons Loss of Auts2 leads to increased spine formation in development and adulthood Loss of Auts2 alters the balance of excitatory and inhibitory synaptic inputs Auts2 mutant mice exhibit cognitive and sociobehavioral deficits
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43
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Ufartes R, Berger H, Till K, Salinas G, Sturm M, Altmüller J, Nürnberg P, Thiele H, Funke R, Apeshiotis N, Langen H, Wollnik B, Borchers A, Pauli S. De novo mutations in FBRSL1 cause a novel recognizable malformation and intellectual disability syndrome. Hum Genet 2020; 139:1363-1379. [PMID: 32424618 PMCID: PMC7519918 DOI: 10.1007/s00439-020-02175-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/02/2020] [Indexed: 01/16/2023]
Abstract
We report truncating de novo variants in specific exons of FBRSL1 in three unrelated children with an overlapping syndromic phenotype with respiratory insufficiency, postnatal growth restriction, microcephaly, global developmental delay and other malformations. The function of FBRSL1 is largely unknown. Interestingly, mutations in the FBRSL1 paralogue AUTS2 lead to an intellectual disability syndrome (AUTS2 syndrome). We determined human FBRSL1 transcripts and describe protein-coding forms by Western blot analysis as well as the cellular localization by immunocytochemistry stainings. All detected mutations affect the two short N-terminal isoforms, which show a ubiquitous expression in fetal tissues. Next, we performed a Fbrsl1 knockdown in Xenopus laevis embryos to explore the role of Fbrsl1 during development and detected craniofacial abnormalities and a disturbance in neurite outgrowth. The aberrant phenotype in Xenopus laevis embryos could be rescued with a human N-terminal isoform, while the long isoform and the N-terminal isoform containing the mutation p.Gln163* isolated from a patient could not rescue the craniofacial defects caused by Fbrsl1 depletion. Based on these data, we propose that the disruption of the validated N-terminal isoforms of FBRSL1 at critical timepoints during embryogenesis leads to a hitherto undescribed complex neurodevelopmental syndrome.
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Affiliation(s)
- Roser Ufartes
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
| | - Hanna Berger
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| | - Katharina Till
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| | - Gabriela Salinas
- NGS Integrative Genomics Core Unit, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076, Tübingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch Str. 21, 50931, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Rudolf Funke
- Department of Neuropediatrics, Sozialpädiatrisches Zentrum, Mönchebergstr. 41-43, 34125, Kassel, Germany
| | | | - Hendrik Langen
- Department of Neuropediatrics, Sozialpädiatrisches Zentrum Hannover, Janusz-Korczak-Allee 8, 30173, Hannover, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines To Networks of Excitable Cells" (MBExC), University of Göttingen, 37073, Göttingen, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany. .,DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-University Marburg, Marburg, Germany.
| | - Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany.
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44
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Obeidat M, Faiz A, Li X, van den Berge M, Hansel NN, Joubert P, Hao K, Brandsma CA, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Man SFP, Paré PD, Sin DD. The pharmacogenomics of inhaled corticosteroids and lung function decline in COPD. Eur Respir J 2019; 54:13993003.00521-2019. [PMID: 31537701 DOI: 10.1183/13993003.00521-2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/22/2019] [Indexed: 11/05/2022]
Abstract
Inhaled corticosteroids (ICS) are widely prescribed for patients with chronic obstructive pulmonary disease (COPD), yet have variable outcomes and adverse reactions, which may be genetically determined. The primary aim of the study was to identify the genetic determinants for forced expiratory volume in 1 s (FEV1) changes related to ICS therapy.In the Lung Health Study (LHS)-2, 1116 COPD patients were randomised to the ICS triamcinolone acetonide (n=559) or placebo (n=557) with spirometry performed every 6 months for 3 years. We performed a pharmacogenomic genome-wide association study for the genotype-by-ICS treatment effect on 3 years of FEV1 changes (estimated as slope) in 802 genotyped LHS-2 participants. Replication was performed in 199 COPD patients randomised to the ICS, fluticasone or placebo.A total of five loci showed genotype-by-ICS interaction at p<5×10-6; of these, single nucleotide polymorphism (SNP) rs111720447 on chromosome 7 was replicated (discovery p=4.8×10-6, replication p=5.9×10-5) with the same direction of interaction effect. ENCODE (Encyclopedia of DNA Elements) data revealed that in glucocorticoid-treated (dexamethasone) A549 alveolar cell line, glucocorticoid receptor binding sites were located near SNP rs111720447. In stratified analyses of LHS-2, genotype at SNP rs111720447 was significantly associated with rate of FEV1 decline in patients taking ICS (C allele β 56.36 mL·year-1, 95% CI 29.96-82.76 mL·year-1) and in patients who were assigned to placebo, although the relationship was weaker and in the opposite direction to that in the ICS group (C allele β -27.57 mL·year-1, 95% CI -53.27- -1.87 mL·year-1).The study uncovered genetic factors associated with FEV1 changes related to ICS in COPD patients, which may provide new insight on the potential biology of steroid responsiveness in COPD.
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Affiliation(s)
- Ma'en Obeidat
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Dept of Pulmonology, GRIAC research institute, Groningen, The Netherlands
| | - Xuan Li
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Dept of Pulmonology, GRIAC research institute, Groningen, The Netherlands
| | - Nadia N Hansel
- Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - Ke Hao
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Dept of Pulmonology, GRIAC research institute, Groningen, The Netherlands
| | - Nicholas Rafaels
- Division of Biomedical Informatics and Personalized Medicine, Dept of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rasika Mathias
- Division of Genetic Epidemiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ingo Ruczinski
- Dept of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Terri H Beaty
- Dept of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Dept of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - S F Paul Man
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Peter D Paré
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Don D Sin
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
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45
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Levran O, Randesi M, Rotrosen J, Ott J, Adelson M, Kreek MJ. A 3' UTR SNP rs885863, a cis-eQTL for the circadian gene VIPR2 and lincRNA 689, is associated with opioid addiction. PLoS One 2019; 14:e0224399. [PMID: 31689297 PMCID: PMC6830932 DOI: 10.1371/journal.pone.0224399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/12/2019] [Indexed: 12/16/2022] Open
Abstract
There is a reciprocal relationship between the circadian and the reward systems. Polymorphisms in several circadian rhythm-related (clock) genes were associated with drug addiction. This study aims to search for associations between 895 variants in 39 circadian rhythm-related genes and opioid addiction (OUD). Genotyping was performed with the Smokescreen® array. Ancestry was verified by principal/MDS component analysis and the sample was limited to European Americans (EA) (OUD; n = 435, controls; n = 138). Nominally significant associations (p < 0.01) were detected for several variants in genes encoding vasoactive intestinal peptide receptor 2 (VIPR2), period circadian regulator 2 (PER2), casein kinase 1 epsilon (CSNK1E), and activator of transcription and developmental regulator (AUTS2), but no signal survived correction for multiple testing. There was intriguing association signal for the untranslated region (3’ UTR) variant rs885863 in VIPR2, (p = .0065; OR = 0.51; 95% CI 0.31–0.51). The result was corroborated in an independent EA OUD sample (n = 398, p = 0.0036; for the combined samples). Notably, this SNP is an expression quantitative trait locus (cis-eQTL) for VIPR2 and a long intergenic non-coding RNA, lincRNA 689, in a tissue-specific manner, based on the Genotype-Tissue Expression (GTEx) project. Vasoactive intestinal peptide (VIP) is an important peptide of light-activated suprachiasmatic nucleus cells. It regulates diverse physiological processes including circadian rhythms, learning and memory, and stress response. This is the first report of an association of a VIPR2 variant and OUD. Additionally, analysis of combinations of single nucleotide polymorphisms (SNPs) genotypes revealed an association of PER2 SNP rs80136044, and SNP rs4128839, located 41.6 kb downstream of neuropeptide Y receptor type 1 gene, NPY1R (p = 3.4 × 10−6, OR = 11.4, 95% CI 2.7–48.2). The study provides preliminary insight into the relationship between genetic variants in circadian rhythm genes and long non-coding RNA (lncRNAs) in their vicinity, and opioid addiction.
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Affiliation(s)
- Orna Levran
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| | - Matthew Randesi
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York, United States of America
| | - John Rotrosen
- NYU School of Medicine, New York, New York, United States of America
| | - Jurg Ott
- The Laboratory of Statistical Genetics, The Rockefeller University, New York, New York, United States of America
| | - Miriam Adelson
- Dr. Miriam and Sheldon G. Adelson Clinic for Drug Abuse Treatment and Research, Las Vegas, Nevada, United States of America
| | - Mary Jeanne Kreek
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York, United States of America
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46
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Weisner PA, Chen CY, Sun Y, Yoo J, Kao WC, Zhang H, Baltz ET, Troy JM, Stubbs L. A Mouse Mutation That Dysregulates Neighboring Galnt17 and Auts2 Genes Is Associated with Phenotypes Related to the Human AUTS2 Syndrome. G3 (BETHESDA, MD.) 2019; 9:3891-3906. [PMID: 31554716 PMCID: PMC6829118 DOI: 10.1534/g3.119.400723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/19/2019] [Indexed: 01/23/2023]
Abstract
AUTS2 was originally discovered as the gene disrupted by a translocation in human twins with Autism spectrum disorder, intellectual disability, and epilepsy. Since that initial finding, AUTS2-linked mutations and variants have been associated with a very broad array of neuropsychiatric disorders, sugg esting that AUTS2 is required for fundamental steps of neurodevelopment. However, genotype-phenotype correlations in this region are complicated, because most mutations could also involve neighboring genes. Of particular interest is the nearest downstream neighbor of AUTS2, GALNT17, which encodes a brain-expressed N-acetylgalactosaminyltransferase of unknown brain function. Here we describe a mouse (Mus musculus) mutation, T(5G2;8A1)GSO (abbreviated 16Gso), a reciprocal translocation that breaks between Auts2 and Galnt17 and dysregulates both genes. Despite this complex regulatory effect, 16Gso homozygotes model certain human AUTS2-linked phenotypes very well. In addition to abnormalities in growth, craniofacial structure, learning and memory, and behavior, 16Gso homozygotes display distinct pathologies of the cerebellum and hippocampus that are similar to those associated with autism and other types of AUTS2-linked neurological disease. Analyzing mutant cerebellar and hippocampal transcriptomes to explain this pathology, we identified disturbances in pathways related to neuron and synapse maturation, neurotransmitter signaling, and cellular stress, suggesting possible cellular mechanisms. These pathways, coupled with the translocation's selective effects on Auts2 isoforms and coordinated dysregulation of Galnt17, suggest novel hypotheses regarding the etiology of the human "AUTS2 syndrome" and the wide array of neurodevelopmental disorders linked to variance in this genomic region.
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Affiliation(s)
- P Anne Weisner
- Carl R. Woese Institute for Genomic Biology
- Neuroscience Program
| | - Chih-Ying Chen
- Carl R. Woese Institute for Genomic Biology
- Department of Cell and Developmental Biology, and
| | - Younguk Sun
- Carl R. Woese Institute for Genomic Biology
- Department of Cell and Developmental Biology, and
| | | | | | | | | | - Joseph M Troy
- Carl R. Woese Institute for Genomic Biology
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana IL 61802
| | - Lisa Stubbs
- Carl R. Woese Institute for Genomic Biology,
- Neuroscience Program
- Department of Cell and Developmental Biology, and
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana IL 61802
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47
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Saeki S, Enokizono T, Imagawa K, Fukushima H, Kajikawa D, Sakai A, Tanaka M, Ohto T, Suzuki H, Uehara T, Takenouchi T, Kenjiro K, Takada H. A case of autism spectrum disorder with cleft lip and palate carrying a mutation in exon 8 of AUTS2. Clin Case Rep 2019; 7:2059-2063. [PMID: 31788251 PMCID: PMC6878208 DOI: 10.1002/ccr3.2377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/16/2019] [Accepted: 07/13/2019] [Indexed: 11/11/2022] Open
Abstract
We report a patient with autism and cleft lip and palate carrying a de novo heterozygous AUTS2 mutation, c.1464_1467del ACTC (p.Tyr488*). Although the causal relationship between cleft lip and palate and this mutation is unclear, this case report may expand the clinical phenotype of AUTS2 syndrome.
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Affiliation(s)
- Saki Saeki
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Takashi Enokizono
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Kazuo Imagawa
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Hiroko Fukushima
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Daigo Kajikawa
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Aiko Sakai
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Mai Tanaka
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Tatsuyuki Ohto
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Hisato Suzuki
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | - Tomoko Uehara
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | | | - Kosaki Kenjiro
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | - Hidetoshi Takada
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
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48
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Corponi F, Fabbri C, Serretti A. Pharmacogenetics and Depression: A Critical Perspective. Psychiatry Investig 2019; 16:645-653. [PMID: 31455064 PMCID: PMC6761796 DOI: 10.30773/pi.2019.06.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/16/2019] [Indexed: 12/17/2022] Open
Abstract
Depression leads the higher personal and socio-economical burden within psychiatric disorders. Despite the fact that over 40 antidepressants (ADs) are available, suboptimal response still poses a major challenge and is thought to be partially a result of genetic variation. Pharmacogenetics studies the effects of genetic variants on treatment outcomes with the aim of providing tailored treatments, thereby maximizing efficacy and tolerability. After two decades of pharmacogenetic research, variants in genes coding for the cytochromes involved in ADs metabolism (CYP2D6 and CYP2C19) are now considered biomarkers with sufficient scientific support for clinical application, despite the lack of conclusive cost/effectiveness evidence. The effect of variants in genes modulating ADs mechanisms of action (pharmacodynamics) is still controversial, because of the much higher complexity of ADs pharmacodynamics compared to ADs metabolism. Considerable progress has been made since the era of candidate gene studies: the genomic revolution has made possible to assess genetic variance on an unprecedented scale, throughout the whole genome, and to analyze the cumulative effect of different variants. The results have revealed key information on the biological mechanisms mediating ADs effect and identified hypothetical new pharmacological targets. They also paved the way for future availability of polygenic pharmacogenetic panels to predict treatment outcome, which are expected to explain much higher variance in ADs response compared to CYP2D6 and CYP2C19 only. As the demand and availability of AD pharmacogenetic testing is projected to increase, it is important for clinicians to keep abreast of this evolving area to facilitate informed discussions with their patients.
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Affiliation(s)
- Filippo Corponi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Chiara Fabbri
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, United Kingdom
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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49
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Hamada N, Ogaya S, Nakashima M, Nishijo T, Sugawara Y, Iwamoto I, Ito H, Maki Y, Shirai K, Baba S, Maruyama K, Saitsu H, Kato M, Matsumoto N, Momiyama T, Nagata KI. De novo PHACTR1 mutations in West syndrome and their pathophysiological effects. Brain 2019; 141:3098-3114. [PMID: 30256902 DOI: 10.1093/brain/awy246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022] Open
Abstract
Trio-based whole exome sequencing identified two de novo heterozygous missense mutations [c.1449T > C/p.(Leu500Pro) and c.1436A > T/p.(Asn479Ile)] in PHACTR1, encoding a molecule critical for the regulation of protein phosphatase 1 (PP1) and the actin cytoskeleton, in unrelated Japanese individuals with West syndrome (infantile spasms with intellectual disability). We then examined the role of Phactr1 in the development of mouse cerebral cortex and the pathophysiological significance of these two mutations and others [c.1561C > T/p.(Arg521Cys) and c.1553T > A/p.(Ile518Asn)], which had been reported in undiagnosed patients with intellectual disability. Immunoprecipitation analyses revealed that actin-binding activity of PHACTR1 was impaired by the p.Leu500Pro, p.Asn479Ile and p.Ile518Asn mutations while the p.Arg521Cys mutation exhibited impaired binding to PP1. Acute knockdown of mouse Phactr1 using in utero electroporation caused defects in cortical neuron migration during corticogenesis, which were rescued by an RNAi-resistant PHACTR1 but not by the four mutants. Experiments using knockdown combined with expression mutants, aimed to mimic the effects of the heterozygous mutations under conditions of haploinsufficiency, suggested a dominant negative effect of the mutant allele. As for dendritic development in vivo, only the p.Arg521Cys mutant was determined to have dominant negative effects, because the three other mutants appeared to be degraded with these experimental conditions. Electrophysiological analyses revealed abnormal synaptic properties in Phactr1-deficient excitatory cortical neurons. Our data show that the PHACTR1 mutations may cause morphological and functional defects in cortical neurons during brain development, which is likely to be related to the pathophysiology of West syndrome and other neurodevelopmental disorders.
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Affiliation(s)
- Nanako Hamada
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya, Kasugai, Aichi, Japan.,Research Fellow of Japan Society for the Promotion of Science, Japan
| | - Shunsuke Ogaya
- Department of Pediatric Neurology, Central Hospital, Aichi Human Service Center, 713-8 Kamiya, Kasugai, Aichi, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Japan
| | - Takuma Nishijo
- Department of Pharmacology, Jikei University School of Medicine, 3-19-18 Nishishimbashi, Minato-ku, Tokyo, Japan
| | - Yuji Sugawara
- Department of Pediatrics, Soka Municipal Hospital, 2-21-1 Soka, Soka, Saitama, Japan
| | - Ikuko Iwamoto
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya, Kasugai, Aichi, Japan
| | - Hidenori Ito
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya, Kasugai, Aichi, Japan
| | - Yuki Maki
- Department of Pediatric Neurology, Central Hospital, Aichi Human Service Center, 713-8 Kamiya, Kasugai, Aichi, Japan
| | - Kentaro Shirai
- Department of Pediatrics, Tsuchiura Kyodo Hospital, 4-1-1 Ootsuno, Tsuchiura, Ibaraki, Japan
| | - Shimpei Baba
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei-Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, Shizuoka, Japan
| | - Koichi Maruyama
- Department of Pediatric Neurology, Central Hospital, Aichi Human Service Center, 713-8 Kamiya, Kasugai, Aichi, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Japan
| | - Toshihiko Momiyama
- Department of Pharmacology, Jikei University School of Medicine, 3-19-18 Nishishimbashi, Minato-ku, Tokyo, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya, Kasugai, Aichi, Japan.,Department of Neurochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, Japan
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50
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Doan RN, Shin T, Walsh CA. Evolutionary Changes in Transcriptional Regulation: Insights into Human Behavior and Neurological Conditions. Annu Rev Neurosci 2019; 41:185-206. [PMID: 29986162 DOI: 10.1146/annurev-neuro-080317-062104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the biological basis for human-specific cognitive traits presents both immense challenges and unique opportunities. Although the question of what makes us human has been investigated with several different methods, the rise of comparative genomics, epigenomics, and medical genetics has provided tools to help narrow down and functionally assess the regions of the genome that seem evolutionarily relevant along the human lineage. In this review, we focus on how medical genetic cases have provided compelling functional evidence for genes and loci that appear to have interesting evolutionary signatures in humans. Furthermore, we examine a special class of noncoding regions, human accelerated regions (HARs), that have been suggested to show human-lineage-specific divergence, and how the use of clinical and population data has started to provide functional information to examine these regions. Finally, we outline methods that provide new insights into functional noncoding sequences in evolution.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts 02138, USA
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