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Corrêa T, Santos-Rebouças CB, Mayndra M, Schinzel A, Riegel M. Shared Neurodevelopmental Perturbations Can Lead to Intellectual Disability in Individuals with Distinct Rare Chromosome Duplications. Genes (Basel) 2021; 12:genes12050632. [PMID: 33922640 PMCID: PMC8146713 DOI: 10.3390/genes12050632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Chromosomal duplications are associated with a large group of human diseases that arise mainly from dosage imbalance of genes within the rearrangements. Phenotypes range widely but are often associated with global development delay, intellectual disability, autism spectrum disorders, and multiple congenital abnormalities. How different contiguous genes from a duplicated genomic region interact and dynamically affect the expression of each other remains unclear in most cases. Here, we report a genomic comparative delineation of genes located in duplicated chromosomal regions 8q24.13q24.3, 18p11.32p11.21, and Xq22.3q27.2 in three patients followed up at our genetics service who has the intellectual disability (ID) as a common phenotype. We integrated several genomic data levels by identification of gene content within the duplications, protein-protein interactions, and functional analysis on specific tissues. We found functional relationships among genes from three different duplicated chromosomal regions, reflecting interactions of protein-coding genes and their involvement in common cellular subnetworks. Furthermore, the sharing of common significant biological processes associated with ID has been demonstrated between proteins from the different chromosomal regions. Finally, we elaborated a shared model of pathways directly or indirectly related to the central nervous system (CNS), which could perturb cognitive function and lead to ID in the three duplication conditions.
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Affiliation(s)
- Thiago Corrêa
- Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul UFRGS, Porto Alegre 91501-970, Brazil;
| | - Cíntia B. Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro 20511-010, Brazil;
| | - Maytza Mayndra
- Children’s Hospital Jeser Amarante Faria, Joinville 89204-310, Brazil;
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland;
| | - Mariluce Riegel
- Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul UFRGS, Porto Alegre 91501-970, Brazil;
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, Brazil
- Correspondence:
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Jorquera R, González C, Clausen PTLC, Petersen B, Holmes DS. SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6122466. [PMID: 33507271 PMCID: PMC7904048 DOI: 10.1093/database/baab002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/01/2020] [Accepted: 01/05/2021] [Indexed: 11/27/2022]
Abstract
Single-exon coding sequences (CDSs), also known as ‘single-exon genes’ (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases. Database URL:http://v2.sinex.cl/
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Affiliation(s)
- R Jorquera
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Zañartu 1482, Ñuñoa Santiago 7780132, Chile
- Laboratorio Medicina Traslacional, Fundación Arturo López Pérez, José Manuel Infante 805, Providencia, Santiago 7500691, Chile
| | - C González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Zañartu 1482, Ñuñoa Santiago 7780132, Chile
- Centro de Genómica y Bioinformática, Universidad Mayor, Camino la pirámide 5750, Huechuraba, Santiago 8580745, Chile
| | - P T L C Clausen
- Department of Global Surveillance, Technical University of Denmark, Kemitorvet building 204, 2800 Kgs. Lyngby, Denmark
| | - B Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Hovedstaden, Øster Voldgade 5–7, Copenhagen 1350, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Batu 3 1/2, Jalan Bukit Air Nasi, 08100 Bedong, Kedah, Malaysia
| | - D S Holmes
- *Corresponding author: Tel: +56 2 22398969;
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Wang LL, Gschwandtner M, Eckhart L, Tschachler E. Cerebellar Degeneration-related Antigen 1 Is Ubiquitously Expressed in Human Epidermis and Dermis. Curr Med Sci 2020; 40:570-573. [PMID: 32681261 DOI: 10.1007/s11596-020-2192-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 03/19/2020] [Indexed: 10/23/2022]
Abstract
Cerebellar degeneration-related antigen 1 (CDR1) was described to be expressed in the nervous system and in different types of cancer tissues. In the present study, we demonstrate that CDR1 is in addition ubiquitously expressed in human epidermis, dermis and isolated skin cells. Both CDR1 mRNA and protein were detected in human skin-derived mast cells, melanocytes, fibroblasts and keratinocytes, suggesting that CDR1 does not have a neuron-specific function.
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Affiliation(s)
- Lu-Lu Wang
- Department of Dermatology, Research Division of Biology and Pathobiology of the Skin, Medical University of Vienna, Vienna, A-1090, Austria.,Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, 518053, China
| | - Maria Gschwandtner
- Department of Dermatology, Research Division of Biology and Pathobiology of the Skin, Medical University of Vienna, Vienna, A-1090, Austria
| | - Leopold Eckhart
- Department of Dermatology, Research Division of Biology and Pathobiology of the Skin, Medical University of Vienna, Vienna, A-1090, Austria
| | - Erwin Tschachler
- Department of Dermatology, Research Division of Biology and Pathobiology of the Skin, Medical University of Vienna, Vienna, A-1090, Austria.
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Salemi M, Rappazzo G, Ridolfo F, Salluzzo MG, Cannarella R, Castiglione R, Caniglia S, Tirolo C, Calogero AE, Romano C. Cerebellar degeneration-related protein 1 expression in fibroblasts of patients affected by down syndrome. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1832922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
| | - Giancarlo Rappazzo
- Laboratory of Molecular Genetics, Department of Biological Geological Environmental Sciences, University of Catania, Catania, Italy
| | - Federico Ridolfo
- UOSD of Clinical Pathology, ASUR Marche – AV2, Hospital of Senigallia, Senigallia, Italy
| | | | - Rossella Cannarella
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
| | - Roberto Castiglione
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
| | | | | | - Aldo E. Calogero
- Section of Endocrinology, Andrology and Internal Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania. Italy
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FUS(1-359) transgenic mice as a model of ALS: pathophysiological and molecular aspects of the proteinopathy. Neurogenetics 2018; 19:189-204. [DOI: 10.1007/s10048-018-0553-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022]
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Expression of the onconeural protein CDR1 in cerebellum and ovarian cancer. Oncotarget 2018; 9:23975-23986. [PMID: 29844866 PMCID: PMC5963614 DOI: 10.18632/oncotarget.25252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 04/04/2018] [Indexed: 12/23/2022] Open
Abstract
Cerebellar degeneration related protein 1 (CDR1) is expressed in the cerebellum, and CDR1 antibodies have been associated with paraneoplastic cerebellar degeneration (PCD). In this study, we examined CDR1 expression in cerebellum and in ovarian and breast tumors, as well as the intracellular localization of CDR1 in cancer cells in culture. CDR1 was strongly expressed in the cytosol and dendrites of Purkinje cells and in interneurons of the molecular layer in cerebellum. CDR1 was also present in ovarian and breast tumors, as well as in ovarian and breast cancer cell lines, but was not present in normal breast or ovarian tissue. In cells overexpressing CDR1, CDR1 localized close to the plasma membrane in a polarized pattern at one edge. CDR1 was strongly expressed on the outer surface, apparently in filopodias or lamellipodias, in cells endogenously expressing CDR1. Overexpression of CDR1 showed a 37 and a 45 kDa band in western blot. The 37-kDa isoform was present in 16 ovarian cancer lysates, while the 45-kDa isoform was only found in three ovarian cancer patients. The presence of CDR1 in ovarian cancer was not associated with PCD. CDR1 antibodies were only found in serum from one patient with PCD and ovarian tumor with metastases. Therefore, CDR1 is probably not a marker for PCD. However, CDR1 may be associated with cell migration and differentiation.
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Abstract
The emerging complexity of the transcriptional landscape poses great challenges to our conventional preconceptions of how the genome regulates brain function and dysfunction. Non-protein-coding RNAs (ncRNAs) confer a high level of intricate and dynamic regulation of various molecular processes in the CNS and they have been implicated in neurodevelopment and brain ageing, as well as in synapse function and cognitive performance, in both health and disease. ncRNA-mediated processes may be involved in various aspects of the pathogenesis of neurodegenerative disorders. Understanding these events may help to develop novel diagnostic and therapeutic tools. Here, we provide an overview of the complex mechanisms that are affected by the diverse ncRNA classes that have been implicated in neurodegeneration.
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