1
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Massey S, Ang CS, Davidson NM, Quigley A, Rollo B, Harris AR, Kapsa RMI, Christodoulou J, Van Bergen NJ. Novel CDKL5 targets identified in human iPSC-derived neurons. Cell Mol Life Sci 2024; 81:347. [PMID: 39136782 PMCID: PMC11335273 DOI: 10.1007/s00018-024-05389-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/01/2024] [Accepted: 07/31/2024] [Indexed: 08/22/2024]
Abstract
CDKL5 Deficiency Disorder (CDD) is a debilitating epileptic encephalopathy disorder affecting young children with no effective treatments. CDD is caused by pathogenic variants in Cyclin-Dependent Kinase-Like 5 (CDKL5), a protein kinase that regulates key phosphorylation events in neurons. For therapeutic intervention, it is essential to understand molecular pathways and phosphorylation targets of CDKL5. Using an unbiased phosphoproteomic approach we identified novel targets of CDKL5, including GTF2I, PPP1R35, GATAD2A and ZNF219 in human iPSC-derived neuronal cells. The phosphoserine residue in the target proteins lies in the CDKL5 consensus motif. We validated direct phosphorylation of GTF2I and PPP1R35 by CDKL5 using complementary approaches. GTF2I controls axon guidance, cell cycle and neurodevelopment by regulating expression of neuronal genes. PPP1R35 is critical for centriole elongation and cilia morphology, processes that are impaired in CDD. PPP1R35 interacts with CEP131, a known CDKL5 phospho-target. GATAD2A and ZNF219 belong to the Nucleosome Remodelling Deacetylase (NuRD) complex, which regulates neuronal activity-dependent genes and synaptic connectivity. In-depth knowledge of molecular pathways regulated by CDKL5 will allow a better understanding of druggable disease pathways to fast-track therapeutic development.
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Affiliation(s)
- Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Ching-Seng Ang
- The Bio21 Institute of Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Nadia M Davidson
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, 3052, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Anita Quigley
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC, Australia
- Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Centre for Clinical Neurosciences and Neurological Research, St. Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Department of Medicine, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
| | - Ben Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexander R Harris
- Department of Biomedical Engineering, University of Melbourne, Melbourne, 3010, Australia
| | - Robert M I Kapsa
- Electrical and Biomedical Engineering, School of Engineering, RMIT University, Melbourne, VIC, Australia
- Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Centre for Clinical Neurosciences and Neurological Research, St. Vincent's Hospital Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
- Department of Medicine, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Melbourne, VIC, 3065, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, 3052, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, 3052, Australia.
- Department of Paediatrics, University of Melbourne, c/o MCRI, 50 Flemington Road, Parkville, VIC, 3052, Australia.
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2
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Liu F, Yang Y, Xu XS, Yuan M. MESBC: A novel mutually exclusive spectral biclustering method for cancer subtyping. Comput Biol Chem 2024; 109:108009. [PMID: 38219419 DOI: 10.1016/j.compbiolchem.2023.108009] [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: 07/11/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/16/2024]
Abstract
Many soft biclustering algorithms have been developed and applied to various biological and biomedical data analyses. However, few mutually exclusive (hard) biclustering algorithms have been proposed, which could better identify disease or molecular subtypes with survival significance based on genomic or transcriptomic data. In this study, we developed a novel mutually exclusive spectral biclustering (MESBC) algorithm based on spectral method to detect mutually exclusive biclusters. MESBC simultaneously detects relevant features (genes) and corresponding conditions (patients) subgroups and, therefore, automatically uses the signature features for each subtype to perform the clustering. Extensive simulations revealed that MESBC provided superior accuracy in detecting pre-specified biclusters compared with the non-negative matrix factorization (NMF) and Dhillon's algorithm, particularly in very noisy data. Further analysis of the algorithm on real datasets obtained from the TCGA database showed that MESBC provided more accurate (i.e., smaller p-value) overall survival prediction in patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) cancers when compared to the existing, gold-standard subtypes for lung cancers (integrative clustering). Furthermore, MESBC detected several genes with significant prognostic value in both LUAD and LUSC patients. External validation on an independent, unseen GEO dataset of LUAD showed that MESBC-derived clusters based on TCGA data still exhibited clear biclustering patterns and consistent, outstanding prognostic predictability, demonstrating robust generalizability of MESBC. Therefore, MESBC could potentially be used as a risk stratification tool to optimize the treatment for the patient, improve the selection of patients for clinical trials, and contribute to the development of novel therapeutic agents.
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Affiliation(s)
- Fengrong Liu
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | - Yaning Yang
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | | | - Min Yuan
- School of Public Health Administration, Anhui Medical University, Hefei 230032, China.
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3
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Bläsius K, Ludwig L, Knapp S, Flaßhove C, Sonnabend F, Keller D, Tacken N, Gao X, Kahveci-Türköz S, Grannemann C, Babendreyer A, Adrain C, Huth S, Baron JM, Ludwig A, Düsterhöft S. Pathological mutations reveal the key role of the cytosolic iRhom2 N-terminus for phosphorylation-independent 14-3-3 interaction and ADAM17 binding, stability, and activity. Cell Mol Life Sci 2024; 81:102. [PMID: 38409522 PMCID: PMC10896983 DOI: 10.1007/s00018-024-05132-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Abstract
The protease ADAM17 plays an important role in inflammation and cancer and is regulated by iRhom2. Mutations in the cytosolic N-terminus of human iRhom2 cause tylosis with oesophageal cancer (TOC). In mice, partial deletion of the N-terminus results in a curly hair phenotype (cub). These pathological consequences are consistent with our findings that iRhom2 is highly expressed in keratinocytes and in oesophageal cancer. Cub and TOC are associated with hyperactivation of ADAM17-dependent EGFR signalling. However, the underlying molecular mechanisms are not understood. We have identified a non-canonical, phosphorylation-independent 14-3-3 interaction site that encompasses all known TOC mutations. Disruption of this site dysregulates ADAM17 activity. The larger cub deletion also includes the TOC site and thus also dysregulated ADAM17 activity. The cub deletion, but not the TOC mutation, also causes severe reductions in stimulated shedding, binding, and stability of ADAM17, demonstrating the presence of additional regulatory sites in the N-terminus of iRhom2. Overall, this study contrasts the TOC and cub mutations, illustrates their different molecular consequences, and reveals important key functions of the iRhom2 N-terminus in regulating ADAM17.
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Affiliation(s)
- Katharina Bläsius
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Lena Ludwig
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Sarah Knapp
- Institute of Biochemistry and Molecular Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Charlotte Flaßhove
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Friederike Sonnabend
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Diandra Keller
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Nikola Tacken
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Xintong Gao
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Selcan Kahveci-Türköz
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Caroline Grannemann
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Aaron Babendreyer
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Colin Adrain
- Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, Northern Ireland
| | - Sebastian Huth
- Department of Dermatology and Allergology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Jens Malte Baron
- Department of Dermatology and Allergology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Andreas Ludwig
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Stefan Düsterhöft
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
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4
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Vaidya K, Rodrigues G, Gupta S, Devarajan A, Yeolekar M, Madhusudhan MS, Kamat SS. Identification of sequence determinants for the ABHD14 enzymes. Proteins 2023. [PMID: 37974539 DOI: 10.1002/prot.26632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/14/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Over the course of evolution, enzymes have developed remarkable functional diversity in catalyzing important chemical reactions across various organisms, and understanding how new enzyme functions might have evolved remains an important question in modern enzymology. To systematically annotate functions, based on their protein sequences and available biochemical studies, enzymes with similar catalytic mechanisms have been clustered together into an enzyme superfamily. Typically, enzymes within a superfamily have similar overall three-dimensional structures, conserved catalytic residues, but large variations in substrate recognition sites and residues to accommodate the diverse biochemical reactions that are catalyzed within the superfamily. The serine hydrolases are an excellent example of such an enzyme superfamily. Based on known enzymatic activities and protein sequences, they are split almost equally into the serine proteases and metabolic serine hydrolases. Within the metabolic serine hydrolases, there are two outlying members, ABHD14A and ABHD14B, that have high sequence similarity, but their biological functions remained cryptic till recently. While ABHD14A still lacks any functional annotation to date, we recently showed that ABHD14B functions as a lysine deacetylase in mammals. Given their high sequence similarity, automated databases often wrongly assign ABHD14A and ABHD14B as the same enzyme, and therefore, annotating functions to them in various organisms has been problematic. In this article, we present a bioinformatics study coupled with biochemical experiments, which identifies key sequence determinants for both ABHD14A and ABHD14B, and enable better classification for them. In addition, we map these enzymes on an evolutionary timescale and provide a much-wanted resource for studying these interesting enzymes in different organisms.
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Affiliation(s)
- Kaveri Vaidya
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Golding Rodrigues
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Sonali Gupta
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Archit Devarajan
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Mihika Yeolekar
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - M S Madhusudhan
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
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5
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Bales KL, Hang S, Paulus JP, Jahanfard E, Manca C, Jost G, Boyer C, Bern R, Yerumyan D, Rogers S, Mederos SL. Individual differences in social homeostasis. Front Behav Neurosci 2023; 17:1068609. [PMID: 36969803 PMCID: PMC10036751 DOI: 10.3389/fnbeh.2023.1068609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/15/2023] [Indexed: 03/12/2023] Open
Abstract
The concept of “social homeostasis”, introduced by Matthews and Tye in 2019, has provided a framework with which to consider our changing individual needs for social interaction, and the neurobiology underlying this system. This model was conceived as including detector systems, a control center with a setpoint, and effectors which allow us to seek out or avoid additional social contact. In this article, we review and theorize about the many different factors that might contribute to the setpoint of a person or animal, including individual, social, cultural, and other environmental factors. We conclude with a consideration of the empirical challenges of this exciting new model.
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Affiliation(s)
- Karen L. Bales
- Department of Psychology, University of California, Davis, >Davis, CA, United States
- *Correspondence: Karen L. Bales
| | - Sally Hang
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - John P. Paulus
- Graduate Group in Neuroscience, University of California, Davis, Davis, CA, United States
| | - Elaina Jahanfard
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Claudia Manca
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Geneva Jost
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Chase Boyer
- Graduate Group in Human Development, University of California, Davis, Davis, CA, United States
| | - Rose Bern
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Daniella Yerumyan
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Sophia Rogers
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Sabrina L. Mederos
- Graduate Group in Animal Behavior, University of California, Davis, Davis, CA, United States
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6
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Human Brain Models of Intellectual Disability: Experimental Advances and Novelties. Int J Mol Sci 2022; 23:ijms23126476. [PMID: 35742919 PMCID: PMC9224308 DOI: 10.3390/ijms23126476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Intellectual disability (ID) is characterized by deficits in conceptual, social and practical domains. ID can be caused by both genetic defects and environmental factors and is extremely heterogeneous, which complicates the diagnosis as well as the deciphering of the underlying pathways. Multiple scientific breakthroughs during the past decades have enabled the development of novel ID models. The advent of induced pluripotent stem cells (iPSCs) enables the study of patient-derived human neurons in 2D or in 3D organoids during development. Gene-editing tools, such as CRISPR/Cas9, provide isogenic controls and opportunities to design personalized gene therapies. In practice this has contributed significantly to the understanding of ID and opened doors to identify novel therapeutic targets. Despite these advances, a number of areas of improvement remain for which novel technologies might entail a solution in the near future. The purpose of this review is to provide an overview of the existing literature on scientific breakthroughs that have been advancing the way ID can be studied in the human brain. The here described human brain models for ID have the potential to accelerate the identification of underlying pathophysiological mechanisms and the development of therapies.
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7
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Çalışkan E, Şahin MN, Güldağ MA. Oxytocin and Oxytocin Receptor Gene Regulation in Williams Syndrome: A Systematic Review. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2021; 94:623-635. [PMID: 34970101 PMCID: PMC8686774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Williams Syndrome (WS) is a rare genetic multisystem disorder that occurs because of a deletion of approximately 25 genes in the 7q11.23 chromosome region. This causes dysmorphic facial appearances, multiple congenital cardiovascular defects, delayed motor skills, and abnormalities in connective tissues and the endocrine system. The patients are mostly diagnosed with mild to moderate mental retardation, however, they have a hyper sociable, socially dis-inhibited, and outgoing personality, empathetic behavior, and are highly talkative. Oxytocin (OT), a neuropeptide synthesized at the hypothalamus, plays an important role in cognition and behavior, and is thought to be affecting WS patients' attitudes at its different amounts. Oxytocin receptor gene (OXTR), on chromosome 3p25.3, is considered regulating oxytocin receptors, via which OT exerts its effect. WS is a crucial disorder to understand gene, hormone, brain, and behavior associations in terms of sociality and neuropsychiatric conditions. Alterations to the WS gene region offer an opportunity to deepen our understandings of autism spectrum disorder, schizophrenia, anxiety, or depression. We aim to systematically present the data available of OT/OXTR regulation and expression, and the evidence for whether these mechanisms are dysregulated in WS. These results are important, as they predict strong epigenetic control over social behavior by methylation, single nucleotide polymorphisms, and other alterations. The comparison and collaboration of these studies may help to establish a better treatment or management approach for patients with WS if backed up with future research.
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Affiliation(s)
- Elif Çalışkan
- Trakya University School of Medicine, Edirne,
Turkey,To whom all correspondence should be addressed:
Elif Çalışkan, Trakya University School of Medicine, Edirne, Turkey;
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8
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Ortiz-Romero P, González-Simón A, Egea G, Pérez-Jurado LA, Campuzano V. Co-Treatment With Verapamil and Curcumin Attenuates the Behavioral Alterations Observed in Williams-Beuren Syndrome Mice by Regulation of MAPK Pathway and Microglia Overexpression. Front Pharmacol 2021; 12:670785. [PMID: 34413771 PMCID: PMC8369570 DOI: 10.3389/fphar.2021.670785] [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: 02/22/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Williams-Beuren syndrome (WBS) is a rare neurodevelopmental disorder characterized by a distinctive cognitive phenotype for which there are currently no effective treatments. We investigated the progression of behavioral deficits present in WBS complete deletion (CD) mice, after chronic treatment with curcumin, verapamil, and a combination of both. These compounds have been proven to have beneficial effects over different cognitive aspects of various murine models and, thus, may have neuroprotective effects in WBS. Treatment was administered orally dissolved in drinking water. A set of behavioral tests demonstrated the efficiency of combinatorial treatment. Some histological and molecular analyses were performed to analyze the effects of treatment and its underlying mechanism. CD mice showed an increased density of activated microglia in the motor cortex and CA1 hippocampal region, which was prevented by co-treatment. Behavioral improvement correlated with the molecular recovery of several affected pathways regarding MAPK signaling, in tight relation to the control of synaptic transmission, and inflammation. Therefore, the results show that co-treatment prevented behavioral deficits by recovering altered gene expression in the cortex of CD mice and reducing activated microglia. These findings unravel the mechanisms underlying the beneficial effects of this novel treatment on behavioral deficits observed in CD mice and suggest that the combination of curcumin and verapamil could be a potential candidate to treat the cognitive impairments in WBS patients.
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Affiliation(s)
- Paula Ortiz-Romero
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Alejandro González-Simón
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Gustavo Egea
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi I Sunyer, IDIBAPS-UB, Barcelona, Spain
| | - Luis A Pérez-Jurado
- Unitat de Genètica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain.,Servei de Genètica, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Victoria Campuzano
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
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9
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Dai L, Weiss RB, Dunn DM, Ramirez A, Paul S, Korenberg JR. Core transcriptional networks in Williams syndrome: IGF1-PI3K-AKT-mTOR, MAPK and actin signaling at the synapse echo autism. Hum Mol Genet 2021; 30:411-429. [PMID: 33564861 DOI: 10.1093/hmg/ddab041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Gene networks for disorders of social behavior provide the mechanisms critical for identifying therapeutic targets and biomarkers. Large behavioral phenotypic effects of small human deletions make the positive sociality of Williams syndrome (WS) ideal for determining transcriptional networks for social dysfunction currently based on DNA variations for disorders such as autistic spectrum disorder (ASD) and schizophrenia (SCHZ). Consensus on WS networks has been elusive due to the need for larger cohort size, sensitive genome-wide detection and analytic tools. We report a core set of WS network perturbations in a cohort of 58 individuals (34 with typical, 6 atypical deletions and 18 controls). Genome-wide exon-level expression arrays robustly detected changes in differentially expressed gene (DEG) transcripts from WS deleted genes that ranked in the top 11 of 12 122 transcripts, validated by quantitative reverse transcription PCR, RNASeq and western blots. WS DEG's were strictly dosed in the full but not the atypical deletions that revealed a breakpoint position effect on non-deleted CLIP2, a caveat for current phenotypic mapping based on copy number variants. Network analyses tested the top WS DEG's role in the dendritic spine, employing GeneMANIA to harmonize WS DEGs with comparable query gene-sets. The results indicate perturbed actin cytoskeletal signaling analogous to the excitatory dendritic spines. Independent protein-protein interaction analyses of top WS DEGs generated a 100-node graph annotated topologically revealing three interacting pathways, MAPK, IGF1-PI3K-AKT-mTOR/insulin and actin signaling at the synapse. The results indicate striking similarity of WS transcriptional networks to genome-wide association study-based ASD and SCHZ risk suggesting common network dysfunction for these disorders of divergent sociality.
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Affiliation(s)
- Li Dai
- Center for Integrated Neuroscience and Human Behavior, Brain Institute, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Anna Ramirez
- Center for Integrated Neuroscience and Human Behavior, Brain Institute, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Julie R Korenberg
- Center for Integrated Neuroscience and Human Behavior, Brain Institute, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA.,Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
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10
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Niego A, Benítez-Burraco A. Autism and Williams syndrome: Dissimilar socio-cognitive profiles with similar patterns of abnormal gene expression in the blood. AUTISM : THE INTERNATIONAL JOURNAL OF RESEARCH AND PRACTICE 2020; 25:464-489. [PMID: 33143449 DOI: 10.1177/1362361320965074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
LAY ABSTRACT Autism spectrum disorders and Williams syndrome are complex cognitive conditions exhibiting quite opposite features in the social domain: whereas people with autism spectrum disorders are mostly hyposocial, subjects with Williams syndrome are usually reported as hypersocial. At the same time, autism spectrum disorders and Williams syndrome share some common underlying behavioral and cognitive deficits. It is not clear, however, which genes account for the attested differences (and similarities) in the socio-cognitive domain. In this article, we adopted a comparative molecular approach and looked for genes that might be differentially (or similarly) regulated in the blood of people with these conditions. We found a significant overlap between genes dysregulated in the blood of patients compared to neurotypical controls, with most of them being upregulated or, in some cases, downregulated. Still, genes with similar expression trends can exhibit quantitative differences between conditions, with most of them being more dysregulated in Williams syndrome than in autism spectrum disorders. Differentially expressed genes are involved in aspects of brain development and function (particularly dendritogenesis) and are expressed in brain areas (particularly the cerebellum, the thalamus, and the striatum) of relevance for the autism spectrum disorder and the Williams syndrome etiopathogenesis. Overall, these genes emerge as promising candidates for the similarities and differences between the autism spectrum disorder and the Williams syndrome socio-cognitive profiles.
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11
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Kimura R, Tomiwa K, Inoue R, Suzuki S, Nakata M, Awaya T, Kato T, Okazaki S, Heike T, Hagiwara M. Dysregulation of the oxytocin receptor gene in Williams syndrome. Psychoneuroendocrinology 2020; 115:104631. [PMID: 32114409 DOI: 10.1016/j.psyneuen.2020.104631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/06/2020] [Accepted: 02/19/2020] [Indexed: 10/25/2022]
Abstract
Williams syndrome (WS) is caused by a microdeletion of chromosome 7q11.23, and is characterized by various physical and cognitive symptoms. In particular, WS is characterized by hypersocial (overfriendly) behavior; WS has gained attention as aspects of the WS phenotype contrast with those of autism spectrum disorder (ASD). The oxytocin receptor gene (OXTR) contributes to social phenotypes in relation to regulation of oxytocin (OXT) secretion. Additionally, mounting evidence has recently shown that DNA methylation of OXTR is associated with human social behavior. However, the role of OXTR in WS remains unclear. This study investigated the regulation of OXTR in WS. We examined the gene expression levels in blood from WS patients and controls, and then analyzed the methylation levels in two independent cohorts. We showed that OXTR was down-regulated and hypermethylated in WS patients compared to controls. Our findings may provide an insight into OXTR in mediating complex social phenotypes in WS.
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Affiliation(s)
- Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
| | - Kiyotaka Tomiwa
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Department of Child Neurology, Osaka City General Hospital, Osaka 534-0021 Japan; Todaiji Ryoiku Hospital for Children, Nara 630-8211, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Agriculture and Life Science, Kyoto Prefectural University, Kyoto, 606-8522, Japan
| | - Shiho Suzuki
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Masatoshi Nakata
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takeo Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki 660-8550, Japan
| | - Shin Okazaki
- Department of Child Neurology, Osaka City General Hospital, Osaka 534-0021 Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki 660-8550, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
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12
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Xie J, Ma A, Fennell A, Ma Q, Zhao J. It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. Brief Bioinform 2020; 20:1449-1464. [PMID: 29490019 DOI: 10.1093/bib/bby014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. These algorithms and tools have been applied to a wide variety of data types, including but not limited to, genomes, transcriptomes, exomes, epigenomes, phenomes and pharmacogenomes. However, there is still a considerable gap between biclustering methodology development and comprehensive data interpretation, mainly because of the lack of knowledge for the selection of appropriate biclustering tools and further supporting computational techniques in specific studies. Here, we first deliver a brief introduction to the existing biclustering algorithms and tools in public domain, and then systematically summarize the basic applications of biclustering for biological data and more advanced applications of biclustering for biomedical data. This review will assist researchers to effectively analyze their big data and generate valuable biological knowledge and novel insights with higher efficiency.
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13
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Codina-Sola M, Costa-Roger M, Pérez-García D, Flores R, Palacios-Verdú MG, Cusco I, Pérez-Jurado LA. Genetic factors contributing to autism spectrum disorder in Williams-Beuren syndrome. J Med Genet 2019; 56:801-808. [PMID: 31413120 PMCID: PMC6929708 DOI: 10.1136/jmedgenet-2019-106080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND The hallmark of the neurobehavioural phenotype of Williams-Beuren syndrome (WBS) is increased sociability and relatively preserved language skills, often described as opposite to autism spectrum disorders (ASD). However, the prevalence of ASD in WBS is 6-10 times higher than in the general population. We have investigated the genetic factors that could contribute to the ASD phenotype in individuals with WBS. METHODS We studied four males and four females with WBS and a confirmed diagnosis of ASD by the Autism Diagnostic Interview-Revised. We performed a detailed molecular characterisation of the deletion and searched for genomic variants using exome sequencing. RESULTS A de novo deletion of 1.55 Mb (6 cases) or 1.83 Mb (2 cases) at 7q11.23 was detected, being in 7/8 patients of paternal origin. No common breakpoint, deletion mechanism or size was found. Two cases were hemizygous for the rare T allele at rs12539160 in MLXIPL, previously associated with ASD. Inherited rare variants in ASD-related or functionally constrained genes and a de novo nonsense mutation in the UBR5 gene were identified in six cases, with higher burden in females compared with males (p=0.016). CONCLUSIONS The increased susceptibility to ASD in patients with WBS might be due to additive effects of the common WBS deletion, inherited and de novo rare sequence variants in ASD-related genes elsewhere in the genome, with higher burden of deleterious mutations required for females, and possible hypomorphic variants in the hemizygous allele or cis-acting mechanisms on imprinting.
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Affiliation(s)
- Marta Codina-Sola
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- Clinical and Molecular Genetics Area, Vall Hebrón Hospital Research Institute (VHIR), Hospital Vall d'Hebron, Barcelona, Spain
| | - Mar Costa-Roger
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
| | - Debora Pérez-García
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
| | - Raquel Flores
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
| | - Maria Gabriela Palacios-Verdú
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- Fundacio Dexeus Salut de la Dona, Barcelona, Spain
| | - Ivon Cusco
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- Clinical and Molecular Genetics Area, Vall Hebrón Hospital Research Institute (VHIR), Hospital Vall d'Hebron, Barcelona, Spain
| | - Luis Alberto Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- SA Clinical Genetics, Women's and Children's Hospital, South Australian Health and Medical Research Institute (SAHMRI) and University of Adelaide, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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A transcriptomic study of Williams-Beuren syndrome associated genes in mouse embryonic stem cells. Sci Data 2019; 6:262. [PMID: 31695049 PMCID: PMC6834640 DOI: 10.1038/s41597-019-0281-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Williams-Beuren syndrome (WBS) is a relatively rare disease caused by the deletion of 1.5 to 1.8 Mb on chromosome 7 which contains approximately 28 genes. This multisystem disorder is mainly characterized by supravalvular aortic stenosis, mental retardation, and distinctive facial features. We generated mouse embryonic stem (ES) cells clones expressing each of the 4 human WBS genes (WBSCR1, GTF2I, GTF2IRD1 and GTF2IRD2) found in the specific delated region 7q11.23 causative of the WBS. We generated at least three stable clones for each gene with stable integration in the ROSA26 locus of a tetracycline-inducible upstream of the coding sequence of the genet tagged with a 3xFLAG epitope. Three clones for each gene were transcriptionally profiled in inducing versus non-inducing conditions for a total of 24 profiles. This small collection of human WBS-ES cell clones represents a resource to facilitate the study of the function of these genes during differentiation. Measurement(s) | transcription profiling assay • regulation of transcription, DNA-templated | Technology Type(s) | microarray assay • gene overexpression | Factor Type(s) | WBSCR1, GTF2I, GTF2IRD1 and GTF2IRD2 | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.10003127
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15
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Kimura R, Swarup V, Tomiwa K, Gandal MJ, Parikshak NN, Funabiki Y, Nakata M, Awaya T, Kato T, Iida K, Okazaki S, Matsushima K, Kato T, Murai T, Heike T, Geschwind DH, Hagiwara M. Integrative network analysis reveals biological pathways associated with Williams syndrome. J Child Psychol Psychiatry 2019; 60:585-598. [PMID: 30362171 PMCID: PMC7379192 DOI: 10.1111/jcpp.12999] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Williams syndrome (WS) is a neurodevelopmental disorder that has been attributed to heterozygous deletions in chromosome 7q11.23 and exhibits a variety of physical, cognitive, and behavioral features. However, the genetic basis of this phenotypic variability is unclear. In this study, we identified genetic clues underlying these complex phenotypes. METHODS Neurobehavioral function was assessed in WS patients and healthy controls. Total RNA was extracted from peripheral blood and subjected to microarray analysis, RNA-sequencing, and qRT-PCR. Weighted gene co-expression network analysis was performed to identify specific alterations related to intermediate disease phenotypes. To functionally interpret each WS-related module, gene ontology and disease-related gene enrichment were examined. We also investigated the micro (mi)RNA expression profiles and miRNA co-expression networks to better explain the regulation of the transcriptome in WS. RESULTS Our analysis identified four significant co-expression modules related to intermediate WS phenotypes. Notably, the three upregulated WS-related modules were composed exclusively of genes located outside the 7q11.23 region. They were significantly enriched in genes related to B-cell activation, RNA processing, and RNA transport. BCL11A, which is known for its association with speech disorders and intellectual disabilities, was identified as one of the hub genes in the top WS-related module. Finally, these key upregulated mRNA co-expression modules appear to be inversely correlated with a specific downregulated WS-related miRNA co-expression module. CONCLUSIONS Dysregulation of the mRNA/miRNA network involving genes outside of the 7q11.23 region is likely related to the complex phenotypes observed in WS patients.
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Affiliation(s)
- Ryo Kimura
- Department of Anatomy and Developmental BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Vivek Swarup
- Program in NeurogeneticsDepartment of NeurologyDavid Geffen School of MedicineUniversity of California Los AngelesLos AngelesCAUSA
| | - Kiyotaka Tomiwa
- Department of PediatricsGraduate School of MedicineKyoto UniversityKyotoJapan,Department of Child NeurologyOsaka City General HospitalOsakaJapan,Todaiji Ryoiku Hospital for ChildrenNaraJapan
| | - Michael J. Gandal
- Program in NeurogeneticsDepartment of NeurologyDavid Geffen School of MedicineUniversity of California Los AngelesLos AngelesCAUSA
| | - Neelroop N. Parikshak
- Program in NeurogeneticsDepartment of NeurologyDavid Geffen School of MedicineUniversity of California Los AngelesLos AngelesCAUSA
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral ScienceGraduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan,Department of PsychiatryGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Masatoshi Nakata
- Department of Anatomy and Developmental BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Tomonari Awaya
- Department of Anatomy and Developmental BiologyGraduate School of MedicineKyoto UniversityKyotoJapan,Department of PediatricsGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Takeo Kato
- Department of PediatricsGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Kei Iida
- Medical Research Support CenterGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Shin Okazaki
- Department of Child NeurologyOsaka City General HospitalOsakaJapan
| | - Kanae Matsushima
- Department of Human Health ScienceGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Toshihiro Kato
- Department of Human Health ScienceGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Toshiya Murai
- Department of PsychiatryGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Toshio Heike
- Department of PediatricsGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Daniel H. Geschwind
- Program in NeurogeneticsDepartment of NeurologyDavid Geffen School of MedicineUniversity of California Los AngelesLos AngelesCAUSA
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
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16
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Prunotto A, Stevenson BJ, Berthonneche C, Schüpfer F, Beckmann JS, Maurer F, Bergmann S. RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response. BMC Genomics 2016; 17:717. [PMID: 27604219 PMCID: PMC5015234 DOI: 10.1186/s12864-016-3059-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 09/01/2016] [Indexed: 01/17/2023] Open
Abstract
Background The transcriptional response to many widely used drugs and its modulation by genetic variability is poorly understood. Here we present an analysis of RNAseq profiles from heart tissue of 18 inbred mouse strains treated with the β-blocker atenolol (ATE) and the β-agonist isoproterenol (ISO). Results Differential expression analyses revealed a large set of genes responding to ISO (n = 1770 at FDR = 0.0001) and a comparatively small one responding to ATE (n = 23 at FDR = 0.0001). At a less stringent definition of differential expression, the transcriptional responses to these two antagonistic drugs are reciprocal for many genes, with an overall anti-correlation of r = −0.3. This trend is also observed at the level of most individual strains even though the power to detect differential expression is significantly reduced. The inversely expressed gene sets are enriched with genes annotated for heart-related functions. Modular analysis revealed gene sets that exhibit coherent transcription profiles across some strains and/or treatments. Correlations between these modules and a broad spectrum of cardiovascular traits are stronger than expected by chance. This provides evidence for the overall importance of transcriptional regulation for these organismal responses and explicits links between co-expressed genes and the traits they are associated with. Gene set enrichment analysis of differentially expressed groups of genes pointed to pathways related to heart development and functionality. Conclusions Our study provides new insights into the transcriptional response of the heart to perturbations of the β-adrenergic system, implicating several new genes that had not been associated to this system previously. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3059-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Prunotto
- Department of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Corinne Berthonneche
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland
| | - Fanny Schüpfer
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland
| | - Jacques S Beckmann
- Department of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland
| | - Fabienne Maurer
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland.
| | - Sven Bergmann
- Department of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
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17
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Corley SM, Canales CP, Carmona-Mora P, Mendoza-Reinosa V, Beverdam A, Hardeman EC, Wilkins MR, Palmer SJ. RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome. BMC Genomics 2016; 17:450. [PMID: 27295951 PMCID: PMC4907016 DOI: 10.1186/s12864-016-2801-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/26/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Williams-Beuren Syndrome (WBS) is a genetic disorder associated with multisystemic abnormalities, including craniofacial dysmorphology and cognitive defects. It is caused by a hemizygous microdeletion involving up to 28 genes in chromosome 7q11.23. Genotype/phenotype analysis of atypical microdeletions implicates two evolutionary-related transcription factors, GTF2I and GTF2IRD1, as prime candidates for the cause of the facial dysmorphology. RESULTS Using a targeted Gtf2ird1 knockout mouse, we employed massively-parallel sequencing of mRNA (RNA-Seq) to understand changes in the transcriptional landscape associated with inactivation of Gtf2ird1 in lip tissue. We found widespread dysregulation of genes including differential expression of 78 transcription factors or coactivators, several involved in organ development including Hey1, Myf6, Myog, Dlx2, Gli1, Gli2, Lhx2, Pou3f3, Sox2, Foxp3. We also found that the absence of GTF2IRD1 is associated with increased expression of genes involved in cellular proliferation, including growth factors consistent with the observed phenotype of extreme thickening of the epidermis. At the same time, there was a decrease in the expression of genes involved in other signalling mechanisms, including the Wnt pathway, indicating dysregulation in the complex networks necessary for epidermal differentiation and facial skin patterning. Several of the differentially expressed genes have known roles in both tissue development and neurological function, such as the transcription factor Lhx2 which regulates several genes involved in both skin and brain development. CONCLUSIONS Gtf2ird1 inactivation results in widespread gene dysregulation, some of which may be due to the secondary consequences of gene regulatory network disruptions involving several transcription factors and signalling molecules. Genes involved in growth factor signalling and cell cycle progression were identified as particularly important for explaining the skin dysmorphology observed in this mouse model. We have noted that a number of the dysregulated genes have known roles in brain development as well as epidermal differentiation and maintenance. Therefore, this study provides clues as to the underlying mechanisms that may be involved in the broader profile of WBS.
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Affiliation(s)
- Susan M Corley
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, NSW, Australia.
| | - Cesar P Canales
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Paulina Carmona-Mora
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | | | | | - Edna C Hardeman
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Stephen J Palmer
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
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18
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Khattak S, Brimble E, Zhang W, Zaslavsky K, Strong E, Ross PJ, Hendry J, Mital S, Salter MW, Osborne LR, Ellis J. Human induced pluripotent stem cell derived neurons as a model for Williams-Beuren syndrome. Mol Brain 2015; 8:77. [PMID: 26603386 PMCID: PMC4657290 DOI: 10.1186/s13041-015-0168-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/13/2015] [Indexed: 12/16/2022] Open
Abstract
Background Williams-Beuren Syndrome (WBS) is caused by the microdeletion of approximately 25 genes on chromosome 7q11.23, and is characterized by a spectrum of cognitive and behavioural features. Results We generated cortical neurons from a WBS individual and unaffected (WT) control by directed differentiation of induced pluripotent stem cells (iPSCs). Single cell mRNA analyses and immunostaining demonstrated very efficient production of differentiated cells expressing markers of mature neurons of mixed subtypes and from multiple cortical layers. We found that there was a profound alteration in action potentials, with significantly prolonged WBS repolarization times and a WBS deficit in voltage-activated K+ currents. Miniature excitatory synaptic currents were normal, indicating that unitary excitatory synaptic transmission was not altered. Gene expression profiling identified 136 negatively enriched gene sets in WBS compared to WT neurons including gene sets involved in neurotransmitter receptor activity, synaptic assembly, and potassium channel complexes. Conclusions Our findings provide insight into gene dysregulation and electrophysiological defects in WBS patient neurons. Electronic supplementary material The online version of this article (doi:10.1186/s13041-015-0168-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shahryar Khattak
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.
| | - Elise Brimble
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Wenbo Zhang
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Physiology, University of Toronto, Toronto, ON, Canada. .,University of Toronto Centre for the Study of Pain, University of Toronto, Toronto, ON, Canada.
| | - Kirill Zaslavsky
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Emma Strong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - P Joel Ross
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.
| | - Jason Hendry
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.
| | - Seema Mital
- Department of Pediatrics, Hospital for Sick Children, Toronto, ON, Canada.
| | - Michael W Salter
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Physiology, University of Toronto, Toronto, ON, Canada. .,University of Toronto Centre for the Study of Pain, University of Toronto, Toronto, ON, Canada.
| | - Lucy R Osborne
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - James Ellis
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Developmental and Stem Cell Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay St, 16th Floor - Room 9705, Toronto, ON, M5G 0A4, Canada.
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A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology. Am J Hum Genet 2015; 96:784-96. [PMID: 25937446 DOI: 10.1016/j.ajhg.2015.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
The 16p11.2 600 kb copy-number variants (CNVs) are associated with mirror phenotypes on BMI, head circumference, and brain volume and represent frequent genetic lesions in autism spectrum disorders (ASDs) and schizophrenia. Here we interrogated the transcriptome of individuals carrying reciprocal 16p11.2 CNVs. Transcript perturbations correlated with clinical endophenotypes and were enriched for genes associated with ASDs, abnormalities of head size, and ciliopathies. Ciliary gene expression was also perturbed in orthologous mouse models, raising the possibility that ciliary dysfunction contributes to 16p11.2 pathologies. In support of this hypothesis, we found structural ciliary defects in the CA1 hippocampal region of 16p11.2 duplication mice. Moreover, by using an established zebrafish model, we show genetic interaction between KCTD13, a key driver of the mirrored neuroanatomical phenotypes of the 16p11.2 CNV, and ciliopathy-associated genes. Overexpression of BBS7 rescues head size and neuroanatomical defects of kctd13 morphants, whereas suppression or overexpression of CEP290 rescues phenotypes induced by KCTD13 under- or overexpression, respectively. Our data suggest that dysregulation of ciliopathy genes contributes to the clinical phenotypes of these CNVs.
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20
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Haas BW, Smith AK. Oxytocin, vasopressin, and Williams syndrome: epigenetic effects on abnormal social behavior. Front Genet 2015; 6:28. [PMID: 25741359 PMCID: PMC4330921 DOI: 10.3389/fgene.2015.00028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/20/2015] [Indexed: 11/13/2022] Open
Abstract
Williams syndrome (WS) is a condition caused by a deletion of ∼26-28 genes on chromosome 7q11.23 often characterized by abnormal social behavior and disrupted oxytocin (OT) and vasopressin (AVP) functioning. The observation that individuals with WS exhibit OT and AVP dysregulation is compelling. There is currently a lack of evidence that any of the genes typically deleted in WS have any direct effect on either OT or AVP. In this perspective article, we present a novel epigenetic model describing how DNA methylation may impact the expression of key genes within the OT and AVP systems, which may ultimately influence the social behavior observed in WS. We draw support from data pooled from a prior empirical research study (Henrichsen et al., 2011), demonstrating that OXTR is overexpressed in WS. These preliminary findings may create new opportunities to target the OT and AVP systems with the specific goal of improving outcomes in WS and other psychiatric conditions.
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Affiliation(s)
- Brian W Haas
- Department of Psychology, University of Georgia , Athens, GA, USA ; Interdisciplinary Neuroscience Graduate Program, University of Georgia , Athens, GA, USA
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University , Atlanta, GA, USA
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21
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Kloosterman WP, Hochstenbach R. Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease. Mol Cytogenet 2014; 7:100. [PMID: 25606056 PMCID: PMC4299681 DOI: 10.1186/s13039-014-0100-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/08/2014] [Indexed: 01/14/2023] Open
Abstract
Chromosomal aberrations include translocations, deletions, duplications, inversions, aneuploidies and complex rearrangements. They underlie genetic disease in roughly 15% of patients with multiple congenital abnormalities and/or mental retardation (MCA/MR). In genetic diagnostics, the pathogenicity of chromosomal aberrations in these patients is typically assessed based on criteria such as phenotypic similarity to other patients with the same or overlapping aberration, absence in healthy individuals, de novo occurrence, and protein coding gene content. However, a thorough understanding of the molecular mechanisms that lead to MCA/MR as a result of chromosome aberrations is often lacking. Chromosome aberrations can affect one or more genes in a complex manner, such as by changing the regulation of gene expression, by disrupting exons, and by creating fusion genes. The precise delineation of breakpoints by whole-genome sequencing enables the construction of local genomic architecture and facilitates the prediction of the molecular determinants of the patient's phenotype. Here, we review current methods for breakpoint identification and their impact on the interpretation of chromosome aberrations in patients with MCA/MR. In addition, we discuss opportunities to dissect disease mechanisms based on large-scale genomic technologies and studies in model organisms.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, P.O. Box 85060, 3508 AB Utrecht, The Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Genome Diagnostics, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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22
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The developmental transcriptome of the human brain: implications for neurodevelopmental disorders. Curr Opin Neurol 2014; 27:149-56. [PMID: 24565942 DOI: 10.1097/wco.0000000000000069] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW Recent characterizations of the transcriptome of the developing human brain by several groups have generated comprehensive datasets on coding and noncoding RNAs that will be instrumental for illuminating the underlying biology of complex neurodevelopmental disorders. This review summarizes recent studies successfully utilizing these data to increase our understanding of the molecular mechanisms of pathogenesis. RECENT FINDINGS Several approaches have successfully integrated developmental transcriptome data with gene discovery to generate testable hypotheses about when and where in the developing human brain disease-associated genes converge. Specifically, these include the projection neurons in the prefrontal and primary motor--somatosensory cortex during mid-fetal development in autism spectrum disorder and the frontal cortex during fetal development in schizophrenia. SUMMARY Developmental transcriptome data is a key to interpreting disease-associated mutations and transcriptional changes. Novel approaches integrating the spatial and temporal dimensions of these data have increased our understanding of when and where disease occurs. Refinement of spatial and temporal properties and expanding these findings to other neurodevelopmental disorders will provide critical insights for understanding disease biology.
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The human WBSCR22 protein is involved in the biogenesis of the 40S ribosomal subunits in mammalian cells. PLoS One 2013; 8:e75686. [PMID: 24086612 PMCID: PMC3781059 DOI: 10.1371/journal.pone.0075686] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 08/19/2013] [Indexed: 11/29/2022] Open
Abstract
The human WBSCR22 protein was previously shown to be up-regulated in invasive breast cancer and its ectopic expression enhances tumor cell survival in the vasculature. In the current study, we show that the WBSCR22 protein is important for cell growth. Knock-down of WBSCR22 with siRNA results in slower growth of WBSCR22-depleted cells. Treatment with siWBSCR22 causes defects in the processing of pre-rRNAs and reduces the level of free 40S ribosomal subunit, suggesting that WBSCR22 is involved in ribosome small subunit biosynthesis. The human WBSCR22 partially complements the growth of WBSCR22 yeast homologue, bud23 deletion mutant suggesting that the human WBSCR22 is a functional homologue of yeast Bud23. WBSCR22 is localized throughout the cell nucleus and is not stably associated with ribosomal subunits within the cell nucleus. We also show that the WBSCR22 protein level is decreased in lymphoblastoid cell lines derived from William-Beuren Syndrome (WBS) patients compared to healthy controls. Our data suggest that the WBSCR22 protein is a ribosome biogenesis factor involved in the biosynthesis of 40S ribosomal particles in mammalian cells.
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Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Mol Syst Biol 2013; 9:662. [PMID: 23632384 PMCID: PMC3658274 DOI: 10.1038/msb.2013.20] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/28/2013] [Indexed: 12/14/2022] Open
Abstract
Drug-induced transcriptional modules (biclusters) were identified and annotated in three human cell lines and rat liver. These were used to assess conservation across systems and to infer and experimentally validate novel drug effects and gene functions. ![]()
Biclustering of drug-induced gene expression profiles resulted in modules of drugs and genes, which were enriched in both drug and gene annotations. Identifying drug-induced transcriptional modules separately in three human cell lines and rat liver allows assessment of their conservation across model systems. About 70% of modules are conserved across cell lines, a lower bound of 15% was estimated for their conservation across organisms, and between the in vitro and in vivo systems. Drug-induced transcriptional modules can predict novel gene functions. A conserved module associated with (chole)sterol metabolism revealed novel regulators of cellular cholesterol homeostasis; 10 of them were validated in functional imaging assays. Analysis of drugs clustered into modules can give new insights into their mechanisms of action and provide leads for drug repositioning. We predicted and experimentally validated novel cell cycle inhibitors and modulators of PPARγ, estrogen and adrenergic receptors, with potential for developing new therapies against diabetes and cancer.
In pharmacology, it is crucial to understand the complex biological responses that drugs elicit in the human organism and how well they can be inferred from model organisms. We therefore identified a large set of drug-induced transcriptional modules from genome-wide microarray data of drug-treated human cell lines and rat liver, and first characterized their conservation. Over 70% of these modules were common for multiple cell lines and 15% were conserved between the human in vitro and the rat in vivo system. We then illustrate the utility of conserved and cell-type-specific drug-induced modules by predicting and experimentally validating (i) gene functions, e.g., 10 novel regulators of cellular cholesterol homeostasis and (ii) new mechanisms of action for existing drugs, thereby providing a starting point for drug repositioning, e.g., novel cell cycle inhibitors and new modulators of α-adrenergic receptor, peroxisome proliferator-activated receptor and estrogen receptor. Taken together, the identified modules reveal the conservation of transcriptional responses towards drugs across cell types and organisms, and improve our understanding of both the molecular basis of drug action and human biology.
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Segura-Puimedon M, Borralleras C, Pérez-Jurado LA, Campuzano V. TFII-I regulates target genes in the PI-3K and TGF-β signaling pathways through a novel DNA binding motif. Gene 2013; 527:529-36. [DOI: 10.1016/j.gene.2013.06.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 06/10/2013] [Accepted: 06/21/2013] [Indexed: 11/17/2022]
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Vilardell M, Civit S, Herwig R. An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21. Biol Open 2013; 2:771-8. [PMID: 23951402 PMCID: PMC3744068 DOI: 10.1242/bio.20134408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/18/2013] [Indexed: 11/20/2022] Open
Abstract
Although approximately 50% of Down Syndrome (DS) patients have heart abnormalities, they exhibit an overprotection against cardiac abnormalities related with the connective tissue, for example a lower risk of coronary artery disease. A recent study reported a case of a person affected by DS who carried mutations in FBN1, the gene causative for a connective tissue disorder called Marfan Syndrome (MFS). The fact that the person did not have any cardiac alterations suggested compensation effects due to DS. This observation is supported by a previous DS meta-analysis at the molecular level where we have found an overall upregulation of FBN1 (which is usually downregulated in MFS). Additionally, that result was cross-validated with independent expression data from DS heart tissue. The aim of this work is to elucidate the role of FBN1 in DS and to establish a molecular link to MFS and MFS-related syndromes using a computational approach. To reach that, we conducted different analytical approaches over two DS studies (our previous meta-analysis and independent expression data from DS heart tissue) and revealed expression alterations in the FBN1 interaction network, in FBN1 co-expressed genes and FBN1-related pathways. After merging the significant results from different datasets with a Bayesian approach, we prioritized 85 genes that were able to distinguish control from DS cases. We further found evidence for several of these genes (47%), such as FBN1, DCN, and COL1A2, being dysregulated in MFS and MFS-related diseases. Consequently, we further encourage the scientific community to take into account FBN1 and its related network for the study of DS cardiovascular characteristics.
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Affiliation(s)
- Mireia Vilardell
- Department of Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63–73, D-14195 Berlin, Germany
| | - Sergi Civit
- Department of Statistics, University of Barcelona, Avenida Diagonal 645, Barcelona, 08028, Spain
| | - Ralf Herwig
- Department of Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63–73, D-14195 Berlin, Germany
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Lord CC, Thomas G, Brown JM. Mammalian alpha beta hydrolase domain (ABHD) proteins: Lipid metabolizing enzymes at the interface of cell signaling and energy metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:792-802. [PMID: 23328280 DOI: 10.1016/j.bbalip.2013.01.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/07/2012] [Accepted: 01/02/2013] [Indexed: 11/16/2022]
Abstract
Dysregulation of lipid metabolism underlies many chronic diseases such as obesity, diabetes, cardiovascular disease, and cancer. Therefore, understanding enzymatic mechanisms controlling lipid synthesis and degradation is imperative for successful drug discovery for these human diseases. Genes encoding α/β hydrolase fold domain (ABHD) proteins are present in virtually all reported genomes, and conserved structural motifs shared by these proteins predict common roles in lipid synthesis and degradation. However, the physiological substrates and products for these lipid metabolizing enzymes and their broader role in metabolic pathways remain largely uncharacterized. Recently, mutations in several members of the ABHD protein family have been implicated in inherited inborn errors of lipid metabolism. Furthermore, studies in cell and animal models have revealed important roles for ABHD proteins in lipid metabolism, lipid signal transduction, and metabolic disease. The purpose of this review is to provide a comprehensive summary surrounding the current state of knowledge regarding mammalian ABHD protein family members. In particular, we will discuss how ABHD proteins are ideally suited to act at the interface of lipid metabolism and signal transduction. Although, the current state of knowledge regarding mammalian ABHD proteins is still in its infancy, this review highlights the potential for the ABHD enzymes as being attractive targets for novel therapies targeting metabolic disease.
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Affiliation(s)
- Caleb C Lord
- Department of Pathology, Section on Lipid Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Gwynneth Thomas
- Department of Pathology, Section on Lipid Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - J Mark Brown
- Department of Pathology, Section on Lipid Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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Vandeweyer G, Van der Aa N, Reyniers E, Kooy RF. The contribution of CLIP2 haploinsufficiency to the clinical manifestations of the Williams-Beuren syndrome. Am J Hum Genet 2012; 90:1071-8. [PMID: 22608712 DOI: 10.1016/j.ajhg.2012.04.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 03/16/2012] [Accepted: 04/10/2012] [Indexed: 11/16/2022] Open
Abstract
Williams-Beuren syndrome is a rare contiguous gene syndrome, characterized by intellectual disability, facial dysmorphisms, connective-tissue abnormalities, cardiac defects, structural brain abnormalities, and transient infantile hypercalcemia. Genes lying telomeric to RFC2, including CLIP2, GTF2I and GTF2IRD1, are currently thought to be the most likely major contributors to the typical Williams syndrome cognitive profile, characterized by a better-than-expected auditory rote-memory ability, a relative sparing of language capabilities, and a severe visual-spatial constructive impairment. Atypical deletions in the region have helped to establish genotype-phenotype correlations. So far, however, hardly any deletions affecting only a single gene in the disease region have been described. We present here two healthy siblings with a pure, hemizygous deletion of CLIP2. A putative role in the cognitive and behavioral abnormalities seen in Williams-Beuren patients has been suggested for this gene on the basis of observations in a knock-out mouse model. The presented siblings did not show any of the clinical features associated with the syndrome. Cognitive testing showed an average IQ for both and no indication of the Williams syndrome cognitive profile. This shows that CLIP2 haploinsufficiency by itself does not lead to the physical or cognitive characteristics of the Williams-Beuren syndrome, nor does it lead to the Williams syndrome cognitive profile. Although contribution of CLIP2 to the phenotype cannot be excluded when it is deleted in combination with other genes, our results support the hypothesis that GTF2IRD1 and GTF2I are the main genes causing the cognitive defects associated with Williams-Beuren syndrome.
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Affiliation(s)
- Geert Vandeweyer
- Department of Medical Genetics, University Hospital of Antwerp, University of Antwerp, Edegem, Belgium
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