1
|
Guo X, Lei M, Zhao J, Wu M, Ren Z, Yang X, Ouyang C, Liu X, Liu C, Chen Q. Tirzepatide ameliorates spatial learning and memory impairment through modulation of aberrant insulin resistance and inflammation response in diabetic rats. Front Pharmacol 2023; 14:1146960. [PMID: 37701028 PMCID: PMC10493299 DOI: 10.3389/fphar.2023.1146960] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Background: One of the typical symptoms of diabetes mellitus patients was memory impairment, which was followed by gradual cognitive deterioration and for which there is no efficient treatment. The anti-diabetic incretin hormones glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) were demonstrated to have highly neuroprotective benefits in animal models of AD. We wanted to find out how the GLP-1/GIP dual agonist tirzepatide affected diabetes's impairment of spatial learning memory. Methods: High fat diet and streptozotocin injection-induced diabetic rats were injected intraperitoneally with Tirzepatide (1.35 mg/kg) once a week. The protective effects were assessed using the Morris water maze test, immunofluorescence, and Western blot analysis. Golgi staining was adopted for quantified dendritic spines. Results: Tirzepatide significantly improved impaired glucose tolerance, fasting blood glucose level, and insulin level in diabetic rats. Then, tirzepatide dramatically alleviated spatial learning and memory impairment, inhibited Aβ accumulation, prevented structural damage, boosted the synthesis of synaptic proteins and increased dendritic spines formation in diabetic hippocampus. Furthermore, some aberrant changes in signal molecules concerning inflammation signaling pathways were normalized after tirzepatide treatment in diabetic rats. Finally, PI3K/Akt/GSK3β signaling pathway was restored by tirzepatide. Conclusion: Tirzepatide obviously exerts a protective effect against spatial learning and memory impairment, potentially through regulating abnormal insulin resistance and inflammatory responses.
Collapse
Affiliation(s)
- Xiying Guo
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Min Lei
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Jiangyan Zhao
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Min Wu
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Zhanhong Ren
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Xiaosong Yang
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Changhan Ouyang
- Pharmacy College, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Xiufen Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| | - Qingjie Chen
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Medical Research Institute, Hubei University of Science and Technology, Xianning, China
| |
Collapse
|
2
|
Construction and Validation of a Newly Prognostic Signature for CRISPR-Cas9-Based Cancer Dependency Map Genes in Breast Cancer. JOURNAL OF ONCOLOGY 2022; 2022:4566577. [PMID: 35096059 PMCID: PMC8791742 DOI: 10.1155/2022/4566577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022]
Abstract
Cancer Dependency Map (CDM) genes comprise an extensive series of genome-scale RNAi-based loss-of-function tests; hence, it served as a method based on the CRISPR-Cas9 technique that could assist scientists in investigating potential gene functions. These CDM genes have a role in tumor cell survival and proliferation, suggesting that they may be used as new therapeutic targets for some malignant tumors. So far, there have been less research on the involvement of CDM genes in breast cancer, and only a tiny percentage of CDM genes have been studied. In this study, information of patients with breast cancer was extracted from The Cancer Genome Atlas (TCGA), from which differentially expressed CDM genes in breast cancer were determined. A variety of bioinformatics techniques were used to assess the functions and prognostic relevance of these confirmed CDM genes. In all, 290 CDM genes were found differentially expressed. Six CDM genes (SRF, RAD51, PMF1, EXOSC3, EXOC1, and TSEN54) were found to be associated with the prognosis of breast cancer samples. Based on the expression of the identified CDM genes and their coefficients, a prognosis model was constructed for prediction, according to which patients with breast cancer were separated into two risk groups. Those with high risk had substantially poorer overall survival (OS) than patients in the other risk group in the TCGA training set, TCGA testing set, and an external cohort from Gene Expression Omnibus (GEO) database. The area under the receiver operating characteristic (ROC) curve for this prognostic signature was, respectively, 0.717 and 0.635 for TCGA training and testing sets, demonstrating its reliability in predicting the prognosis of patients with breast cancer. We next created a nomogram using the six CDM genes discovered to create a therapeutically useful model. The Human Protein Atlas database was used to acquire all immunohistochemistry staining images of the discovered CDM genes. The proportions of tumor-infiltrating immune cells, as well as the expression levels of checkpoint genes, varied substantially between the two risk groups, according to the analyses of immune response. In conclusion, the findings of this research may aid in the understanding of the prognostic value and biological roles of CDM genes in breast cancer.
Collapse
|
3
|
Wang W, Wang GZ. Understanding Molecular Mechanisms of the Brain Through Transcriptomics. Front Physiol 2019; 10:214. [PMID: 30930788 PMCID: PMC6428721 DOI: 10.3389/fphys.2019.00214] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/20/2019] [Indexed: 11/30/2022] Open
Abstract
The brain is the most complicated organ in the human body with more than ten thousand genes expressed in each region. The molecular activity of the brain is divergent in various brain regions, both spatially and temporally. The function of each brain region lies in the fact that each region has different gene expression profiles, the possibility of differential RNA splicing, as well as various post-transcriptional and translational modification processes. Understanding the overall activity of the brain at the molecular level is essential for a comprehensive understanding of how the brain works. Fortunately, the development of next generation sequencing technology has made it possible to measure the molecular activity of a specific tissue as a daily routine approach of research. Therefore, at the molecular level, the application of sequencing technology to investigate the molecular organization of the brain has become a novel field, and significant progress has been made recently in this field. In this paper, we reviewed the major computational methods used in the analysis of brain transcriptome, including the application of these methods to the research of human and non-human mammal brains. Finally, we discussed the utilization of transcriptome methods in neurological diseases.
Collapse
Affiliation(s)
| | - Guang-Zhong Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
4
|
Bettencourt C, Forabosco P, Wiethoff S, Heidari M, Johnstone DM, Botía JA, Collingwood JF, Hardy J, Milward EA, Ryten M, Houlden H. Gene co-expression networks shed light into diseases of brain iron accumulation. Neurobiol Dis 2016; 87:59-68. [PMID: 26707700 PMCID: PMC4731015 DOI: 10.1016/j.nbd.2015.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 11/18/2015] [Accepted: 12/14/2015] [Indexed: 12/21/2022] Open
Abstract
Aberrant brain iron deposition is observed in both common and rare neurodegenerative disorders, including those categorized as Neurodegeneration with Brain Iron Accumulation (NBIA), which are characterized by focal iron accumulation in the basal ganglia. Two NBIA genes are directly involved in iron metabolism, but whether other NBIA-related genes also regulate iron homeostasis in the human brain, and whether aberrant iron deposition contributes to neurodegenerative processes remains largely unknown. This study aims to expand our understanding of these iron overload diseases and identify relationships between known NBIA genes and their main interacting partners by using a systems biology approach. We used whole-transcriptome gene expression data from human brain samples originating from 101 neuropathologically normal individuals (10 brain regions) to generate weighted gene co-expression networks and cluster the 10 known NBIA genes in an unsupervised manner. We investigated NBIA-enriched networks for relevant cell types and pathways, and whether they are disrupted by iron loading in NBIA diseased tissue and in an in vivo mouse model. We identified two basal ganglia gene co-expression modules significantly enriched for NBIA genes, which resemble neuronal and oligodendrocytic signatures. These NBIA gene networks are enriched for iron-related genes, and implicate synapse and lipid metabolism related pathways. Our data also indicates that these networks are disrupted by excessive brain iron loading. We identified multiple cell types in the origin of NBIA disorders. We also found unforeseen links between NBIA networks and iron-related processes, and demonstrate convergent pathways connecting NBIAs and phenotypically overlapping diseases. Our results are of further relevance for these diseases by providing candidates for new causative genes and possible points for therapeutic intervention.
Collapse
Affiliation(s)
- Conceição Bettencourt
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK.
| | - Paola Forabosco
- Istituto di Ricerca Genetica e Biomedica CNR, Cagliari, Italy
| | - Sarah Wiethoff
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, Tübingen, Germany
| | - Moones Heidari
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia; Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, NSW, Australia
| | - Daniel M Johnstone
- Bosch Institute and Discipline of Physiology, University of Sydney, NSW, Australia
| | - Juan A Botía
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | | | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Elizabeth A Milward
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia; Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, NSW, Australia
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| |
Collapse
|
5
|
Garaffo G, Conte D, Provero P, Tomaiuolo D, Luo Z, Pinciroli P, Peano C, D'Atri I, Gitton Y, Etzion T, Gothilf Y, Gays D, Santoro MM, Merlo GR. The Dlx5 and Foxg1 transcription factors, linked via miRNA-9 and -200, are required for the development of the olfactory and GnRH system. Mol Cell Neurosci 2015; 68:103-19. [PMID: 25937343 PMCID: PMC4604252 DOI: 10.1016/j.mcn.2015.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 04/20/2015] [Accepted: 04/29/2015] [Indexed: 01/26/2023] Open
Abstract
During neuronal development and maturation, microRNAs (miRs) play diverse functions ranging from early patterning, proliferation and commitment to differentiation, survival, homeostasis, activity and plasticity of more mature and adult neurons. The role of miRs in the differentiation of olfactory receptor neurons (ORNs) is emerging from the conditional inactivation of Dicer in immature ORN, and the depletion of all mature miRs in this system. Here, we identify specific miRs involved in olfactory development, by focusing on mice null for Dlx5, a homeogene essential for both ORN differentiation and axon guidance and connectivity. Analysis of miR expression in Dlx5−/− olfactory epithelium pointed to reduced levels of miR-9, miR-376a and four miRs of the -200 class in the absence of Dlx5. To functionally examine the role of these miRs, we depleted miR-9 and miR-200 class in reporter zebrafish embryos and observed delayed ORN differentiation, altered axonal trajectory/targeting, and altered genesis and position of olfactory-associated GnRH neurons, i.e. a phenotype known as Kallmann syndrome in humans. miR-9 and miR-200-class negatively control Foxg1 mRNA, a fork-head transcription factor essential for development of the olfactory epithelium and of the forebrain, known to maintain progenitors in a stem state. Increased levels of z-foxg1 mRNA resulted in delayed ORN differentiation and altered axon trajectory, in zebrafish embryos. This work describes for the first time the role of specific miR (-9 and -200) in olfactory/GnRH development, and uncovers a Dlx5–Foxg1 regulation whose alteration affects receptor neuron differentiation, axonal targeting, GnRH neuron development, the hallmarks of the Kallmann syndrome. Dlx5 controls the expressions of miR9 and miR-200, which target the Foxg1 mRNA miR-9 and -200 are needed for olfactory neurons differentiation and axon extension miR-9 and -200 are required for the genesis and position of GnRH neurons. Altered expression of miR-9 and -200 might contribute to the Kallmann disease.
Collapse
Affiliation(s)
- Giulia Garaffo
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy
| | - Daniele Conte
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy
| | - Paolo Provero
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy
| | - Daniela Tomaiuolo
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy
| | - Zheng Luo
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy
| | - Patrizia Pinciroli
- Doctorate School in Molecular Medicine, Dept. Medical Biotechnology Translational Medicine (BIOMETRA), University of Milano, Italy
| | - Clelia Peano
- Inst. of Biomedical Technology, National Research Council, ITB-CNR Segrate (MI) Italy
| | - Ilaria D'Atri
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy
| | - Yorick Gitton
- UMR7221 CNRS/MNHN - Evolution des régulations endocriniennes - Paris, France
| | - Talya Etzion
- Dept. Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; VIB, Vesalius Research Center, KU Leuven, Belgium
| | - Yoav Gothilf
- Dept. Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; VIB, Vesalius Research Center, KU Leuven, Belgium
| | - Dafne Gays
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy
| | - Massimo M Santoro
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy; Dept. Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; VIB, Vesalius Research Center, KU Leuven, Belgium
| | - Giorgio R Merlo
- Dept. Molecular Biotechnology and Health Sciences, University of Torino, Italy.
| |
Collapse
|
6
|
Corradini BR, Iamashita P, Tampellini E, Farfel JM, Grinberg LT, Moreira-Filho CA. Complex network-driven view of genomic mechanisms underlying Parkinson's disease: analyses in dorsal motor vagal nucleus, locus coeruleus, and substantia nigra. BIOMED RESEARCH INTERNATIONAL 2014; 2014:543673. [PMID: 25525598 PMCID: PMC4261556 DOI: 10.1155/2014/543673] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/15/2014] [Indexed: 12/16/2022]
Abstract
Parkinson's disease (PD)—classically characterized by severe loss of dopaminergic neurons in the substantia nigra pars compacta—has a caudal-rostral progression, beginning in the dorsal motor vagal nucleus and, in a less extent, in the olfactory system, progressing to the midbrain and eventually to the basal forebrain and the neocortex. About 90% of the cases are idiopathic. To study the molecular mechanisms involved in idiopathic PD we conducted a comparative study of transcriptional interaction networks in the dorsal motor vagal nucleus (VA), locus coeruleus (LC), and substantia nigra (SN) of idiopathic PD in Braak stages 4-5 (PD) and disease-free controls (CT) using postmortem samples. Gene coexpression networks (GCNs) for each brain region (patients and controls) were obtained to identify highly connected relevant genes (hubs) and densely interconnected gene sets (modules). GCN analyses showed differences in topology and module composition between CT and PD networks for each anatomic region. In CT networks, VA, LC, and SN hub modules are predominantly associated with neuroprotection and homeostasis in the ageing brain, whereas in the patient's group, for the three brain regions, hub modules are mostly related to stress response and neuron survival/degeneration mechanisms.
Collapse
Affiliation(s)
- Beatriz Raposo Corradini
- Department of Pediatrics, Faculdade de Medicina da USP (FMUSP), Avenida Dr. Enéas Carvalho Aguiar 647, 5 Andar, 05403-900 São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da USP (FMUSP), Avenida Dr. Enéas Carvalho Aguiar 647, 5 Andar, 05403-900 São Paulo, SP, Brazil
| | - Edilaine Tampellini
- Brazilian Aging Brain Study Group (BEHEEC), LIM 22, FMUSP, 01246-903 São Paulo, SP, Brazil
- Hospital Israelita Albert Einstein, 05652-900 São Paulo, SP, Brazil
| | - José Marcelo Farfel
- Hospital Israelita Albert Einstein, 05652-900 São Paulo, SP, Brazil
- Division of Geriatrics, FMUSP, 01246-903 São Paulo, SP, Brazil
| | - Lea Tenenholz Grinberg
- Brazilian Aging Brain Study Group (BEHEEC), LIM 22, FMUSP, 01246-903 São Paulo, SP, Brazil
- Department of Pathology, FMUSP, 01246-903 São Paulo, SP, Brazil
- Department of Neurology and Pathology, University of California, San Francisco, CA 94143, USA
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da USP (FMUSP), Avenida Dr. Enéas Carvalho Aguiar 647, 5 Andar, 05403-900 São Paulo, SP, Brazil
| |
Collapse
|
7
|
Thomas AC, Williams H, Setó-Salvia N, Bacchelli C, Jenkins D, O'Sullivan M, Mengrelis K, Ishida M, Ocaka L, Chanudet E, James C, Lescai F, Anderson G, Morrogh D, Ryten M, Duncan AJ, Pai YJ, Saraiva JM, Ramos F, Farren B, Saunders D, Vernay B, Gissen P, Straatmaan-Iwanowska A, Baas F, Wood NW, Hersheson J, Houlden H, Hurst J, Scott R, Bitner-Glindzicz M, Moore GE, Sousa SB, Stanier P. Mutations in SNX14 cause a distinctive autosomal-recessive cerebellar ataxia and intellectual disability syndrome. Am J Hum Genet 2014; 95:611-21. [PMID: 25439728 DOI: 10.1016/j.ajhg.2014.10.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/13/2014] [Indexed: 12/30/2022] Open
Abstract
Intellectual disability and cerebellar atrophy occur together in a large number of genetic conditions and are frequently associated with microcephaly and/or epilepsy. Here we report the identification of causal mutations in Sorting Nexin 14 (SNX14) found in seven affected individuals from three unrelated consanguineous families who presented with recessively inherited moderate-severe intellectual disability, cerebellar ataxia, early-onset cerebellar atrophy, sensorineural hearing loss, and the distinctive association of progressively coarsening facial features, relative macrocephaly, and the absence of seizures. We used homozygosity mapping and whole-exome sequencing to identify a homozygous nonsense mutation and an in-frame multiexon deletion in two families. A homozygous splice site mutation was identified by Sanger sequencing of SNX14 in a third family, selected purely by phenotypic similarity. This discovery confirms that these characteristic features represent a distinct and recognizable syndrome. SNX14 encodes a cellular protein containing Phox (PX) and regulator of G protein signaling (RGS) domains. Weighted gene coexpression network analysis predicts that SNX14 is highly coexpressed with genes involved in cellular protein metabolism and vesicle-mediated transport. All three mutations either directly affected the PX domain or diminished SNX14 levels, implicating a loss of normal cellular function. This manifested as increased cytoplasmic vacuolation as observed in cultured fibroblasts. Our findings indicate an essential role for SNX14 in neural development and function, particularly in development and maturation of the cerebellum.
Collapse
Affiliation(s)
- Anna C Thomas
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Hywel Williams
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Núria Setó-Salvia
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Chiara Bacchelli
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Dagan Jenkins
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Mary O'Sullivan
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Miho Ishida
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Louise Ocaka
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Estelle Chanudet
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Chela James
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Francesco Lescai
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Deborah Morrogh
- NE Thames Regional Genetics Laboratory Service, London WC1N 3BH, UK
| | - Mina Ryten
- UCL Institute of Neurology, London WC1N 3BG, UK; Department of Clinical Genetics, Guy's Hospital, London SE1 9RT, UK
| | - Andrew J Duncan
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Yun Jin Pai
- Developmental Biology and Cancer, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Jorge M Saraiva
- Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
| | - Fabiana Ramos
- Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Bernadette Farren
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Dawn Saunders
- Radiology, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Bertrand Vernay
- Developmental Biology and Cancer, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Paul Gissen
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Frank Baas
- Department of Genome Analysis, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, the Netherlands
| | | | | | | | - Jane Hurst
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Richard Scott
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Gudrun E Moore
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Sérgio B Sousa
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal.
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK.
| |
Collapse
|
8
|
Bettencourt C, Ryten M, Forabosco P, Schorge S, Hersheson J, Hardy J, Houlden H. Insights from cerebellar transcriptomic analysis into the pathogenesis of ataxia. JAMA Neurol 2014; 71:831-9. [PMID: 24862029 PMCID: PMC4469030 DOI: 10.1001/jamaneurol.2014.756] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
IMPORTANCE The core clinical and neuropathological feature of the autosomal dominant spinocerebellar ataxias (SCAs) is cerebellar degeneration. Mutations in the known genes explain only 50% to 60% of SCA cases. To date, no effective treatments exist, and the knowledge of drug-treatable molecular pathways is limited. The examination of overlapping mechanisms and the interpretation of how ataxia genes interact will be important in the discovery of potential disease-modifying agents. OBJECTIVES To address the possible relationships among known SCA genes, predict their functions, identify overlapping pathways, and provide a framework for candidate gene discovery using whole-transcriptome expression data. DESIGN, SETTING, AND PARTICIPANTS We have used a systems biology approach based on whole-transcriptome gene expression analysis. As part of the United Kingdom Brain Expression Consortium, we analyzed the expression profile of 788 brain samples obtained from 101 neuropathologically healthy individuals (10 distinct brain regions each). Weighted gene coexpression network analysis was used to cluster 24 SCA genes into gene coexpression modules in an unsupervised manner. The overrepresentation of SCA transcripts in modules identified in the cerebellum was assessed. Enrichment analysis was performed to infer the functions and molecular pathways of genes in biologically relevant modules. MAIN OUTCOMES AND MEASURES Molecular functions and mechanisms implicating SCA genes, as well as lists of relevant coexpressed genes as potential candidates for novel SCA causative or modifier genes. RESULTS Two cerebellar gene coexpression modules were statistically enriched in SCA transcripts (P = .021 for the tan module and P = 2.87 × 10-5 for the light yellow module) and contained established granule and Purkinje cell markers, respectively. One module includes genes involved in the ubiquitin-proteasome system and contains SCA genes usually associated with a complex phenotype, while the other module encloses many genes important for calcium homeostasis and signaling and contains SCA genes associated mostly with pure ataxia. CONCLUSIONS AND RELEVANCE Using normal gene expression in the human brain, we identified significant cell types and pathways in SCA pathogenesis. The overrepresentation of genes involved in calcium homeostasis and signaling may indicate an important target for therapy in the future. Furthermore, the gene networks provide new candidate genes for ataxias or novel genes that may be critical for cerebellar function.
Collapse
Affiliation(s)
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, England2Department of Medical and Molecular Genetics, King's College London, London, England
| | - Paola Forabosco
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Stephanie Schorge
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, England
| | - Joshua Hersheson
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, England
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, England
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, England
| |
Collapse
|
9
|
Konopka G, Wexler E, Rosen E, Mukamel Z, Osborn GE, Chen L, Lu D, Gao F, Gao K, Lowe JK, Geschwind DH. Modeling the functional genomics of autism using human neurons. Mol Psychiatry 2012; 17:202-14. [PMID: 21647150 PMCID: PMC3170664 DOI: 10.1038/mp.2011.60] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human neural progenitors from a variety of sources present new opportunities to model aspects of human neuropsychiatric disease in vitro. Such in vitro models provide the advantages of a human genetic background combined with rapid and easy manipulation, making them highly useful adjuncts to animal models. Here, we examined whether a human neuronal culture system could be utilized to assess the transcriptional program involved in human neural differentiation and to model some of the molecular features of a neurodevelopmental disorder, such as autism. Primary normal human neuronal progenitors (NHNPs) were differentiated into a post-mitotic neuronal state through addition of specific growth factors and whole-genome gene expression was examined throughout a time course of neuronal differentiation. After 4 weeks of differentiation, a significant number of genes associated with autism spectrum disorders (ASDs) are either induced or repressed. This includes the ASD susceptibility gene neurexin 1, which showed a distinct pattern from neurexin 3 in vitro, and which we validated in vivo in fetal human brain. Using weighted gene co-expression network analysis, we visualized the network structure of transcriptional regulation, demonstrating via this unbiased analysis that a significant number of ASD candidate genes are coordinately regulated during the differentiation process. As NHNPs are genetically tractable and manipulable, they can be used to study both the effects of mutations in multiple ASD candidate genes on neuronal differentiation and gene expression in combination with the effects of potential therapeutic molecules. These data also provide a step towards better understanding of the signaling pathways disrupted in ASD.
Collapse
|