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Zucker R, Kovalerchik M, Stern A, Kaufman H, Linial M. Revealing the genetic complexity of hypothyroidism: integrating complementary association methods. Front Genet 2024; 15:1409226. [PMID: 38919955 PMCID: PMC11196612 DOI: 10.3389/fgene.2024.1409226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/16/2024] [Indexed: 06/27/2024] Open
Abstract
Hypothyroidism is a common endocrine disorder whose prevalence increases with age. The disease manifests itself when the thyroid gland fails to produce sufficient thyroid hormones. The disorder includes cases of congenital hypothyroidism (CH), but most cases exhibit hormonal feedback dysregulation and destruction of the thyroid gland by autoantibodies. In this study, we sought to identify causal genes for hypothyroidism in large populations. The study used the UK-Biobank (UKB) database, reporting on 13,687 cases of European ancestry. We used GWAS compilation from Open Targets (OT) and tuned protocols focusing on genes and coding regions, along with complementary association methods of PWAS (proteome-based) and TWAS (transcriptome-based). Comparing summary statistics from numerous GWAS revealed a limited number of variants associated with thyroid development. The proteome-wide association study method identified 77 statistically significant genes, half of which are located within the Chr6-MHC locus and are enriched with autoimmunity-related genes. While coding GWAS and PWAS highlighted the centrality of immune-related genes, OT and transcriptome-wide association study mostly identified genes involved in thyroid developmental programs. We used independent populations from Finland (FinnGen) and the Taiwan cohort to validate the PWAS results. The higher prevalence in females relative to males is substantiated as the polygenic risk score prediction of hypothyroidism relied mostly from the female group genetics. Comparing results from OT, TWAS, and PWAS revealed the complementary facets of hypothyroidism's etiology. This study underscores the significance of synthesizing gene-phenotype association methods for this common, intricate disease. We propose that the integration of established association methods enhances interpretability and clinical utility.
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Affiliation(s)
- Roei Zucker
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Kovalerchik
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amos Stern
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hadasa Kaufman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Huang HYR, Wireko AA, Miteu GD, Khan A, Roy S, Ferreira T, Garg T, Aji N, Haroon F, Zakariya F, Alshareefy Y, Pujari AG, Madani D, Papadakis M. Advancements and progress in juvenile idiopathic arthritis: A Review of pathophysiology and treatment. Medicine (Baltimore) 2024; 103:e37567. [PMID: 38552102 PMCID: PMC10977530 DOI: 10.1097/md.0000000000037567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024] Open
Abstract
Juvenile idiopathic arthritis (JIA) is a chronic clinical condition characterized by arthritic features in children under the age of 16, with at least 6 weeks of active symptoms. The etiology of JIA remains unknown, and it is associated with prolonged synovial inflammation and structural joint damage influenced by environmental and genetic factors. This review aims to enhance the understanding of JIA by comprehensively analyzing relevant literature. The focus lies on current diagnostic and therapeutic approaches and investigations into the pathoaetiologies using diverse research modalities, including in vivo animal models and large-scale genome-wide studies. We aim to elucidate the multifactorial nature of JIA with a strong focus towards genetic predilection, while proposing potential strategies to improve therapeutic outcomes and enhance diagnostic risk stratification in light of recent advancements. This review underscores the need for further research due to the idiopathic nature of JIA, its heterogeneous phenotype, and the challenges associated with biomarkers and diagnostic criteria. Ultimately, this contribution seeks to advance the knowledge and promote effective management strategies in JIA.
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Affiliation(s)
- Helen Ye Rim Huang
- Faculty of Medicine and Health Science, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Goshen David Miteu
- School of Biosciences, Biotechnology, University of Nottingham, Nottingham, UK
- Department of Biochemistry, Caleb University Lagos, Lagos, Nigeria
| | - Adan Khan
- Kent and Medway Medical School, Canterbury, Kent, UK
| | - Sakshi Roy
- School of Medicine, Queen’s University Belfast, Belfast, Northern Ireland, UK
| | - Tomas Ferreira
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Tulika Garg
- Government Medical College and Hospital Chandigarh, Chandigarh, India
| | - Narjiss Aji
- Faculty of Medicine and Pharmacy of Rabat, Rabat, Morocco
| | - Faaraea Haroon
- Faculty of Public Health, Health Services Academy, Islamabad, Pakistan
| | - Farida Zakariya
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University Zaria, Zaria, Nigeria
| | - Yasir Alshareefy
- School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Anushka Gurunath Pujari
- Faculty of Medicine and Health Science, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Kinesiology, Faculty of Science, McMaster University, Hamilton, Ontario, Canada
| | - Djabir Madani
- UCD Lochlann Quinn School of Business and Sutherland School of Law, University College Dublin, Dublin, Ireland
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Wuppertal, Germany
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Tsare EPG, Klapa MI, Moschonas NK. Protein-protein interaction network-based integration of GWAS and functional data for blood pressure regulation analysis. Hum Genomics 2024; 18:15. [PMID: 38326862 DOI: 10.1186/s40246-023-00565-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/12/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND It is valuable to analyze the genome-wide association studies (GWAS) data for a complex disease phenotype in the context of the protein-protein interaction (PPI) network, as the related pathophysiology results from the function of interacting polyprotein pathways. The analysis may include the design and curation of a phenotype-specific GWAS meta-database incorporating genotypic and eQTL data linking to PPI and other biological datasets, and the development of systematic workflows for PPI network-based data integration toward protein and pathway prioritization. Here, we pursued this analysis for blood pressure (BP) regulation. METHODS The relational scheme of the implemented in Microsoft SQL Server BP-GWAS meta-database enabled the combined storage of: GWAS data and attributes mined from GWAS Catalog and the literature, Ensembl-defined SNP-transcript associations, and GTEx eQTL data. The BP-protein interactome was reconstructed from the PICKLE PPI meta-database, extending the GWAS-deduced network with the shortest paths connecting all GWAS-proteins into one component. The shortest-path intermediates were considered as BP-related. For protein prioritization, we combined a new integrated GWAS-based scoring scheme with two network-based criteria: one considering the protein role in the reconstructed by shortest-path (RbSP) interactome and one novel promoting the common neighbors of GWAS-prioritized proteins. Prioritized proteins were ranked by the number of satisfied criteria. RESULTS The meta-database includes 6687 variants linked with 1167 BP-associated protein-coding genes. The GWAS-deduced PPI network includes 1065 proteins, with 672 forming a connected component. The RbSP interactome contains 1443 additional, network-deduced proteins and indicated that essentially all BP-GWAS proteins are at most second neighbors. The prioritized BP-protein set was derived from the union of the most BP-significant by any of the GWAS-based or the network-based criteria. It included 335 proteins, with ~ 2/3 deduced from the BP PPI network extension and 126 prioritized by at least two criteria. ESR1 was the only protein satisfying all three criteria, followed in the top-10 by INSR, PTN11, CDK6, CSK, NOS3, SH2B3, ATP2B1, FES and FINC, satisfying two. Pathway analysis of the RbSP interactome revealed numerous bioprocesses, which are indeed functionally supported as BP-associated, extending our understanding about BP regulation. CONCLUSIONS The implemented workflow could be used for other multifactorial diseases.
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Affiliation(s)
- Evridiki-Pandora G Tsare
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece.
| | - Nicholas K Moschonas
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece.
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece.
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Tekielak A, Pietrauszka K, Miziołek B, Bergler-Czop B. Vitiligo and insulin resistance as a component of metabolic syndrome: an analysis. Postepy Dermatol Alergol 2023; 40:529-533. [PMID: 37692261 PMCID: PMC10485765 DOI: 10.5114/ada.2023.126871] [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: 01/16/2023] [Accepted: 02/11/2023] [Indexed: 09/12/2023] Open
Abstract
There have been many studies on the association between vitiligo and metabolic syndrome, while only few scientific papers on vitiligo and insulin resistance. In recent years, there have been significant developments in research to trace and understand the aetiology of both conditions. In this article we have analysed pathophysiological mechanisms and the association of insulin resistance (as a component of metabolic syndrome) and vitiligo.
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Affiliation(s)
- Anna Tekielak
- Students’ Scientific Association at the Department of Dermatology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Kornelia Pietrauszka
- Department of Dermatology, Andrzej Mielêcki Independent Public Clinical Hospital of the Silesian Medical University, Katowice, Poland
| | - Bartosz Miziołek
- Department of Dermatology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Beata Bergler-Czop
- Department of Dermatology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
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Albiñana C, Zhu Z, Borbye-Lorenzen N, Boelt SG, Cohen AS, Skogstrand K, Wray NR, Revez JA, Privé F, Petersen LV, Bulik CM, Plana-Ripoll O, Musliner KL, Agerbo E, Børglum AD, Hougaard DM, Nordentoft M, Werge T, Mortensen PB, Vilhjálmsson BJ, McGrath JJ. Genetic correlates of vitamin D-binding protein and 25-hydroxyvitamin D in neonatal dried blood spots. Nat Commun 2023; 14:852. [PMID: 36792583 PMCID: PMC9932173 DOI: 10.1038/s41467-023-36392-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023] Open
Abstract
The vitamin D binding protein (DBP), encoded by the group-specific component (GC) gene, is a component of the vitamin D system. In a genome-wide association study of DBP concentration in 65,589 neonates we identify 26 independent loci, 17 of which are in or close to the GC gene, with fine-mapping identifying 2 missense variants on chromosomes 12 and 17 (within SH2B3 and GSDMA, respectively). When adjusted for GC haplotypes, we find 15 independent loci distributed over 10 chromosomes. Mendelian randomization analyses identify a unidirectional effect of higher DBP concentration and (a) higher 25-hydroxyvitamin D concentration, and (b) a reduced risk of multiple sclerosis and rheumatoid arthritis. A phenome-wide association study confirms that higher DBP concentration is associated with a reduced risk of vitamin D deficiency. Our findings provide valuable insights into the influence of DBP on vitamin D status and a range of health outcomes.
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Affiliation(s)
- Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Zhihong Zhu
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Nis Borbye-Lorenzen
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Sanne Grundvad Boelt
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Clinical Mass Spectrometry, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Arieh S Cohen
- Testcenter Denmark, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Kristin Skogstrand
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Joana A Revez
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Florian Privé
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Liselotte V Petersen
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
| | - Cynthia M Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Oleguer Plana-Ripoll
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Katherine L Musliner
- Department of Affective Disorders, Aarhus University and Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Esben Agerbo
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- CIRRAU - Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Center, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Department for Congenital Disorders, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen N, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Preben Bo Mortensen
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- CIRRAU - Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus C, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark.
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia.
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, 4076, Australia.
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Carmo-Silva S, Ferreira-Marques M, Nóbrega C, Botelho M, Costa D, Aveleira CA, Pulst SM, Pereira de Almeida L, Cavadas C. Ataxin-2 in the hypothalamus at the crossroads between metabolism and clock genes. J Mol Endocrinol 2023; 70:JME-21-0272. [PMID: 36103139 DOI: 10.1530/jme-21-0272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/14/2022] [Indexed: 01/19/2023]
Abstract
ATXN2 gene, encoding for ataxin-2, is located in a trait locus for obesity. Atxn2 knockout (KO) mice are obese and insulin resistant; however, the cause for this phenotype is still unknown. Moreover, several findings suggest ataxin-2 as a metabolic regulator, but the role of this protein in the hypothalamus was never studied before. The aim of this work was to understand if ataxin-2 modulation in the hypothalamus could play a role in metabolic regulation. Ataxin-2 was overexpressed/re-established in the hypothalamus of C57Bl6/Atxn2 KO mice fed either a chow or a high-fat diet (HFD). This delivery was achieved through stereotaxic injection of lentiviral vectors encoding for ataxin-2. We show, for the first time, that HFD decreases ataxin-2 levels in mouse hypothalamus and liver. Specific hypothalamic ataxin-2 overexpression prevents HFD-induced obesity and insulin resistance. Ataxin-2 re-establishment in Atxn2 KO mice improved metabolic dysfunction without changing body weight. Furthermore, we observed altered clock gene expression in Atxn2 KO that might be causative of metabolic dysfunction. Interestingly, ataxin-2 hypothalamic re-establishment rescued these circadian alterations. Thus, ataxin-2 in the hypothalamus is a determinant for weight, insulin sensitivity and clock gene expression. Ataxin-2's potential role in the circadian clock, through the regulation of clock genes, might be a relevant mechanism to regulate metabolism. Overall, this work shows hypothalamic ataxin-2 as a new player in metabolism regulation, which might contribute to the development of new strategies for metabolic disorders.
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Affiliation(s)
- Sara Carmo-Silva
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- MIA - Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Marisa Ferreira-Marques
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Clévio Nóbrega
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- ABC-RI, Algarve Biomedical Center Research Institute, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, Faro, Portugal
| | - Mariana Botelho
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Daniela Costa
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Célia A Aveleira
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- MIA - Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, Utah, USA
| | - Luís Pereira de Almeida
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Claudia Cavadas
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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7
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Schaschl H, Göllner T, Morris DL. Positive selection acts on regulatory genetic variants in populations of European ancestry that affect ALDH2 gene expression. Sci Rep 2022; 12:4563. [PMID: 35296751 PMCID: PMC8927298 DOI: 10.1038/s41598-022-08588-0] [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: 10/21/2021] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
ALDH2 is a key enzyme in alcohol metabolism that protects cells from acetaldehyde toxicity. Using iHS, iSAFE and FST statistics, we identified regulatory acting variants affecting ALDH2 gene expression under positive selection in populations of European ancestry. Several SNPs (rs3184504, rs4766578, rs10774625, rs597808, rs653178, rs847892, rs2013002) that function as eQTLs for ALDH2 in various tissues showed evidence of strong positive selection. Very large pairwise FST values indicated high genetic differentiation at these loci between populations of European ancestry and populations of other global ancestries. Estimating the timing of positive selection on the beneficial alleles suggests that these variants were recently adapted approximately 3000-3700 years ago. The derived beneficial alleles are in complete linkage disequilibrium with the derived ALDH2 promoter variant rs886205, which is associated with higher transcriptional activity. The SNPs rs4766578 and rs847892 are located in binding sequences for the transcription factor HNF4A, which is an important regulatory element of ALDH2 gene expression. In contrast to the missense variant ALDH2 rs671 (ALDH2*2), which is common only in East Asian populations and is associated with greatly reduced enzyme activity and alcohol intolerance, the beneficial alleles of the regulatory variants identified in this study are associated with increased expression of ALDH2. This suggests adaptation of Europeans to higher alcohol consumption.
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Affiliation(s)
- Helmut Schaschl
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Tobias Göllner
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - David L Morris
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, Great Maze Pond, London, SE1 9RT, UK
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The Missing LNK: Evolution from Cytosis to Chronic Myelomonocytic Leukemia in a Patient with Multiple Sclerosis and Germline SH2B3 Mutation. Case Rep Genet 2022; 2022:6977041. [PMID: 35281324 PMCID: PMC8904908 DOI: 10.1155/2022/6977041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
Chronic myelomonocytic leukemia (CMML) is a rare but distinct hematological neoplasm with overlapping features of myelodysplastic syndrome (MDS) and myeloproliferative neoplasm (MPN). Individuals with CMML have persistent monocytosis and bone marrow dyspoiesis associated with various constitutional symptoms like fevers, unintentional weight loss, or night sweats. It is established that there is a strong association of CMML with preceding or coexisting autoimmune diseases and systemic inflammatory syndromes affecting around 20% of patients. Various molecular abnormalities like TET2, SRSF2, ASXL1, and RAS are reported in the pathogenesis of CMML, but no such mutations have been described to explain the strong association of autoimmune diseases and severe inflammatory phenotype seen in CMML. Germline mutation in SH2B adaptor protein 3 (SH2B3) had been reported before to affect a family with autoimmune disorders and acute lymphoblastic leukemia. In this report, we describe the first case of a female subject with many years of preceding history of multiple sclerosis before the diagnosis of CMML. We outline the evidence supporting the pathogenic role of SH2B3 p.E395K germline mutation, connecting the dots of association between autoimmune diseases and CMML genesis.
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Rajabi F, Abdollahimajd F, Jabalameli N, Nassiri Kashani M, Firooz A. The Immunogenetics of Alopecia areata. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:19-59. [DOI: 10.1007/978-3-030-92616-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Jiao H, Zhang M, Zhang Y, Wang Y, Li WD. Pathway Association Studies Reveal Gene Loci and Pathway Networks that Associated With Plasma Cystatin C Levels. Front Genet 2021; 12:711155. [PMID: 34899825 PMCID: PMC8656399 DOI: 10.3389/fgene.2021.711155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/09/2021] [Indexed: 01/09/2023] Open
Abstract
As a marker for glomerular filtration, plasma cystatin C level is used to evaluate kidney function. To decipher genetic factors that control the plasma cystatin C level, we performed genome-wide association and pathway association studies using United Kingdom Biobank data. One hundred fifteen loci yielded p values less than 1 × 10−100, three genes (clusters) showed the most significant associations, including the CST8-CST9 cluster on chromosome 20, the SH2B3-ATXN2 gene region on chromosome 12, and the SHROOM3-CCDC158 gene region on chromosome 4. In pathway association studies, forty significant pathways had FDR (false discovery rate) and or FWER (family-wise error rate) ≤ 0.001: spermatogenesis, leukocyte trans-endothelial migration, cell adhesion, glycoprotein, membrane lipid, steroid metabolic process, and insulin signaling pathways were among the most significant pathways that associated with the plasma cystatin C levels. We also performed Genome-wide association studies for eGFR, top associated genes were largely overlapped with those for cystatin C.
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Affiliation(s)
- Hongxiao Jiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaomiao Zhang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuan Zhang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,College of Public Health, Tianjin Medical University, Tianjin, China
| | - Yaogang Wang
- College of Public Health, Tianjin Medical University, Tianjin, China
| | - Wei-Dong Li
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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11
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Misicka E, Davis MF, Kim W, Brugger SW, Beales J, Loomis S, Bronson PG, Briggs FB. A higher burden of multiple sclerosis genetic risk confers an earlier onset. Mult Scler 2021; 28:1189-1197. [PMID: 34709090 DOI: 10.1177/13524585211053155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Age at onset of multiple sclerosis (MS) is an objective, influential predictor of the evolution of MS independent of disease duration. OBJECTIVES Determine the influence of MS genetic predisposition on age of onset. METHODS We conducted a comprehensive investigation of MS risk variants and age at onset in 3495 non-Latinx white individuals, including for combinations of HLA-DRB1*15:01 alleles and quintiles of an unweighted genetic risk score (GRS) for 198 of 200 autosomal MS risk variants that reside outside the major histocompatibility complex. RESULTS The mean age at onset was 32 years, 29% were male, and 46% were HLA-DRB1*15:01 carriers. For those with the greatest genetic risk burden (the highest GRS quintile with two HLA-DRB1*15:01 alleles) were on average 5 years younger at onset (p = 0.002) than those with the lowest genetic risk burden (the lowest GRS quintile with no HLA-DRB1*15:01 alleles). There was a strong inverse relationship between the MS genetic risk burden and age at onset of MS (p < 5 × 10-8). CONCLUSION We demonstrate a significant gradient between elevated MS genetic risk burden and an earlier onset of MS, suggesting that a higher MS genetic risk burden accelerates onset of the disease.
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Affiliation(s)
- Elina Misicka
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mary F Davis
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA/Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Woori Kim
- Human Target Validation Core, Translational Biology, Biogen, Boston, MA, USA
| | - Steven W Brugger
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Jeremy Beales
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Stephanie Loomis
- Human Target Validation Core, Translational Biology, Biogen, Boston, MA, USA
| | - Paola G Bronson
- Human Target Validation Core, Translational Biology, Biogen, Boston, MA, USA
| | - Farren Bs Briggs
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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12
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Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gestational diabetes mellitus. Biosci Rep 2021; 41:228450. [PMID: 33890634 PMCID: PMC8145272 DOI: 10.1042/bsr20210617] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/08/2023] Open
Abstract
Gestational diabetes mellitus (GDM) is the metabolic disorder that appears during pregnancy. The current investigation aimed to identify central differentially expressed genes (DEGs) in GDM. The transcription profiling by array data (E-MTAB-6418) was obtained from the ArrayExpress database. The DEGs between GDM samples and non-GDM samples were analyzed. Functional enrichment analysis were performed using ToppGene. Then we constructed the protein–protein interaction (PPI) network of DEGs by the Search Tool for the Retrieval of Interacting Genes database (STRING) and module analysis was performed. Subsequently, we constructed the miRNA–hub gene network and TF–hub gene regulatory network. The validation of hub genes was performed through receiver operating characteristic curve (ROC). Finally, the candidate small molecules as potential drugs to treat GDM were predicted by using molecular docking. Through transcription profiling by array data, a total of 869 DEGs were detected including 439 up-regulated and 430 down-regulated genes. Functional enrichment analysis showed these DEGs were mainly enriched in reproduction, cell adhesion, cell surface interactions at the vascular wall and extracellular matrix organization. Ten genes, HSP90AA1, EGFR, RPS13, RBX1, PAK1, FYN, ABL1, SMAD3, STAT3 and PRKCA were associated with GDM, according to ROC analysis. Finally, the most significant small molecules were predicted based on molecular docking. This investigation identified hub genes, signal pathways and therapeutic agents, which might help us, enhance our understanding of the mechanisms of GDM and find some novel therapeutic agents for GDM.
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13
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Smyth LJ, Kilner J, Nair V, Liu H, Brennan E, Kerr K, Sandholm N, Cole J, Dahlström E, Syreeni A, Salem RM, Nelson RG, Looker HC, Wooster C, Anderson K, McKay GJ, Kee F, Young I, Andrews D, Forsblom C, Hirschhorn JN, Godson C, Groop PH, Maxwell AP, Susztak K, Kretzler M, Florez JC, McKnight AJ. Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study. Clin Epigenetics 2021; 13:99. [PMID: 33933144 PMCID: PMC8088646 DOI: 10.1186/s13148-021-01081-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence suggests epigenetic changes in DNA methylation may have a causal role in both T1DM and DKD. The aim of this exploratory investigation was to assess differences in blood-derived DNA methylation patterns between individuals with T1DM-ESKD and individuals with long-duration T1DM but no evidence of kidney disease upon repeated testing to identify potential blood-based biomarkers. Blood-derived DNA from individuals (107 cases, 253 controls and 14 experimental controls) were bisulphite treated before DNA methylation patterns from both groups were generated and analysed using Illumina's Infinium MethylationEPIC BeadChip arrays (n = 862,927 sites). Differentially methylated CpG sites (dmCpGs) were identified (false discovery rate adjusted p ≤ × 10-8 and fold change ± 2) by comparing methylation levels between ESKD cases and T1DM controls at single site resolution. Gene annotation and functionality was investigated to enrich and rank methylated regions associated with ESKD in T1DM. RESULTS Top-ranked genes within which several dmCpGs were located and supported by functional data with methylation look-ups in other cohorts include: AFF3, ARID5B, CUX1, ELMO1, FKBP5, HDAC4, ITGAL, LY9, PIM1, RUNX3, SEPTIN9 and UPF3A. Top-ranked enrichment pathways included pathways in cancer, TGF-β signalling and Th17 cell differentiation. CONCLUSIONS Epigenetic alterations provide a dynamic link between an individual's genetic background and their environmental exposures. This robust evaluation of DNA methylation in carefully phenotyped individuals has identified biomarkers associated with ESKD, revealing several genes and implicated key pathways associated with ESKD in individuals with T1DM.
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Affiliation(s)
- L J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
| | - J Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - V Nair
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - H Liu
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E Brennan
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - K Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - N Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J Cole
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - E Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - A Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R M Salem
- Department of Family Medicine and Public Health, UC San Diego, San Diego, CA, USA
| | - R G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - H C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - C Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - K Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - F Kee
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - I Young
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - D Andrews
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - C Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J N Hirschhorn
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C Godson
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - P H Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - A P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.,Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - K Susztak
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - M Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - J C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - A J McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
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14
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Vasta R, D'Ovidio F, Logroscino G, Chiò A. The links between diabetes mellitus and amyotrophic lateral sclerosis. Neurol Sci 2021; 42:1377-1387. [PMID: 33544228 PMCID: PMC7955983 DOI: 10.1007/s10072-021-05099-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/28/2021] [Indexed: 02/06/2023]
Abstract
ALS etiology and prognostic factors are mostly unknown. Metabolic diseases and especially diabetes mellitus (DM) have been variously related to ALS. However, pieces of evidence have been variegated and often conflicting so far. This review aims to give an overview of recent contributions focusing on the relationship between DM and ALS. DM seems to reduce the risk of developing ALS if diagnosed at a younger age; conversely, when diagnosed at an older age, DM seems protective against ALS. Such a relationship was not confirmed in Asian countries where DM increases the risk of ALS independently of the age of onset. Interestingly, DM does not affect ALS prognosis, possibly weakening the potential causal relationship between the two diseases. However, since most studies are observational, it is difficult to state the exact nature of such a relationship and several hypotheses have been made. A recent study using Mendelian randomization suggested that DM is indeed protective against ALS in the European population. However, these analyses are not without limits and further evidence is needed. DM is usually the core of a larger metabolic syndrome. Thus, other metabolic changes such as dyslipidemia, body mass index, and cardiovascular diseases should be collectively considered. Finally, hypermetabolism usually found in ALS patients should be considered too since all these metabolic changes could be compensation (or the cause) of the higher energy expenditure.
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Affiliation(s)
- Rosario Vasta
- ALS Center, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy.
| | - Fabrizio D'Ovidio
- ALS Center, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy
| | - Giancarlo Logroscino
- Department of Clinical Research in Neurology, Center for Neurodegenerative Diseases and the Aging Brain, University of Bari "Aldo Moro", "Pia Fondazione Cardinale G. Panico", Tricase, Italy
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Chiò
- ALS Center, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy
- Neurology 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
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15
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GWAS for autoimmune Addison's disease identifies multiple risk loci and highlights AIRE in disease susceptibility. Nat Commun 2021; 12:959. [PMID: 33574239 PMCID: PMC7878795 DOI: 10.1038/s41467-021-21015-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Autoimmune Addison's disease (AAD) is characterized by the autoimmune destruction of the adrenal cortex. Low prevalence and complex inheritance have long hindered successful genetic studies. We here report the first genome-wide association study on AAD, which identifies nine independent risk loci (P < 5 × 10-8). In addition to loci implicated in lymphocyte function and development shared with other autoimmune diseases such as HLA, BACH2, PTPN22 and CTLA4, we associate two protein-coding alterations in Autoimmune Regulator (AIRE) with AAD. The strongest, p.R471C (rs74203920, OR = 3.4 (2.7-4.3), P = 9.0 × 10-25) introduces an additional cysteine residue in the zinc-finger motif of the second PHD domain of the AIRE protein. This unbiased elucidation of the genetic contribution to development of AAD points to the importance of central immunological tolerance, and explains 35-41% of heritability (h2).
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16
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Canet-Pons J, Sen NE, Arsović A, Almaguer-Mederos LE, Halbach MV, Key J, Döring C, Kerksiek A, Picchiarelli G, Cassel R, René F, Dieterlé S, Fuchs NV, König R, Dupuis L, Lütjohann D, Gispert S, Auburger G. Atxn2-CAG100-KnockIn mouse spinal cord shows progressive TDP43 pathology associated with cholesterol biosynthesis suppression. Neurobiol Dis 2021; 152:105289. [PMID: 33577922 DOI: 10.1016/j.nbd.2021.105289] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/11/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Large polyglutamine expansions in Ataxin-2 (ATXN2) cause multi-system nervous atrophy in Spinocerebellar Ataxia type 2 (SCA2). Intermediate size expansions carry a risk for selective motor neuron degeneration, known as Amyotrophic Lateral Sclerosis (ALS). Conversely, the depletion of ATXN2 prevents disease progression in ALS. Although ATXN2 interacts directly with RNA, and in ALS pathogenesis there is a crucial role of RNA toxicity, the affected functional pathways remain ill defined. Here, we examined an authentic SCA2 mouse model with Atxn2-CAG100-KnockIn for a first definition of molecular mechanisms in spinal cord pathology. Neurophysiology of lower limbs detected sensory neuropathy rather than motor denervation. Triple immunofluorescence demonstrated cytosolic ATXN2 aggregates sequestrating TDP43 and TIA1 from the nucleus. In immunoblots, this was accompanied by elevated CASP3, RIPK1 and PQBP1 abundance. RT-qPCR showed increase of Grn, Tlr7 and Rnaset2 mRNA versus Eif5a2, Dcp2, Uhmk1 and Kif5a decrease. These SCA2 findings overlap well with known ALS features. Similar to other ataxias and dystonias, decreased mRNA levels for Unc80, Tacr1, Gnal, Ano3, Kcna2, Elovl5 and Cdr1 contrasted with Gpnmb increase. Preterminal stage tissue showed strongly activated microglia containing ATXN2 aggregates, with parallel astrogliosis. Global transcriptome profiles from stages of incipient motor deficit versus preterminal age identified molecules with progressive downregulation, where a cluster of cholesterol biosynthesis enzymes including Dhcr24, Msmo1, Idi1 and Hmgcs1 was prominent. Gas chromatography demonstrated a massive loss of crucial cholesterol precursor metabolites. Overall, the ATXN2 protein aggregation process affects diverse subcellular compartments, in particular stress granules, endoplasmic reticulum and receptor tyrosine kinase signaling. These findings identify new targets and potential biomarkers for neuroprotective therapies.
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Affiliation(s)
- Júlia Canet-Pons
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Nesli-Ece Sen
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany; Faculty of Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Aleksandar Arsović
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Luis-Enrique Almaguer-Mederos
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany; Center for Investigation and Rehabilitation of Hereditary Ataxias (CIRAH), Holguín, Cuba
| | - Melanie V Halbach
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Jana Key
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany; Faculty of Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Anja Kerksiek
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Nordrhein-Westfalen, Germany
| | - Gina Picchiarelli
- UMRS-1118 INSERM, Faculty of Medicine, University of Strasbourg, 67000 Strasbourg, France
| | - Raphaelle Cassel
- UMRS-1118 INSERM, Faculty of Medicine, University of Strasbourg, 67000 Strasbourg, France
| | - Frédérique René
- UMRS-1118 INSERM, Faculty of Medicine, University of Strasbourg, 67000 Strasbourg, France
| | - Stéphane Dieterlé
- UMRS-1118 INSERM, Faculty of Medicine, University of Strasbourg, 67000 Strasbourg, France
| | - Nina V Fuchs
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Luc Dupuis
- UMRS-1118 INSERM, Faculty of Medicine, University of Strasbourg, 67000 Strasbourg, France
| | - Dieter Lütjohann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Nordrhein-Westfalen, Germany
| | - Suzana Gispert
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany
| | - Georg Auburger
- Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany.
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17
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Type 1 diabetes: genes associated with disease development. Cent Eur J Immunol 2021; 45:439-453. [PMID: 33658892 PMCID: PMC7882399 DOI: 10.5114/ceji.2020.103386] [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: 03/27/2019] [Accepted: 01/02/2020] [Indexed: 11/17/2022] Open
Abstract
Type 1 diabetes (T1D) is the third most common autoimmune disease which develops due to genetic and environmental risk factors. Based on the World Health Organization (WHO) report from 2014 the number of people suffering from all types of diabetes ascended to 422 million, compared to 108 million in 1980. It was calculated that this number will double by the end of 2030. In 2015 American Diabetes Association (ADA) announced that 30.3 million Americans (that is 9.4% of the overall population) had diabetes of which only approximately 1.25 million had T1D. Nowadays, T1D represents roughly 10% of adult diabetes cases total. Multiple genetic abnormalities at different loci have been found to contribute to type 1 diabetes development. The analysis of genome-wide association studies (GWAS) of T1D has identified over 50 susceptible regions (and genes within these regions). Many of these regions are defined by single nucleotide polymorphisms (SNPs) but molecular mechanisms through which they increase or lower the risk of diabetes remain unknown. Genetic factors (in existence since birth) can be detected long before the emergence of immunological or clinical markers. Therefore, a comprehensive understanding of the multiple genetic factors underlying T1D is extremely important for further clinical trials and development of personalized medicine for diabetic patients. We present an overview of current studies and information about regions in the human genome associated with T1D. Moreover, we also put forward information about epigenetic modifications, non-coding RNAs and environmental factors involved in T1D development and onset.
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Abstract
PURPOSE OF REVIEW Diabetes is a spectrum of clinical manifestations, including latent autoimmune diabetes in adults (LADA). However, it has been questioned whether LADA exists or simply is a group of misclassified type 1 diabetes (T1D) and type 2 diabetes (T2D) patients. This review will provide an updated overview of the genetics of LADA, highlight what genetics tell us about LADA as a diabetes subtype, and point to future directions in the study of LADA. RECENT FINDINGS Recent studies have verified the genetic overlap between LADA and both T1D and T2D and have contributed identification of a novel LADA-specific locus, namely, PFKFB3, and subtype-specific signatures in the HLA region. Genetic risk scores comprising T1D-risk variants have been shown to be a promising tool for discriminating diabetes subtypes and identifying patients rapidly progressing to insulin dependence. Genetic data support the existence of LADA, but further studies are needed to fully determine the place of LADA in the diabetes spectrum.
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Affiliation(s)
- Mette K Andersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark.
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19
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Hansen M, Zeddies S, Meinders M, di Summa F, Rollmann E, van Alphen FP, Hoogendijk AJ, Moore KS, Halbach M, Gutiérrez L, van den Biggelaar M, Thijssen-Timmer DC, Auburger GW, van den Akker E, von Lindern M. The RNA-Binding Protein ATXN2 is Expressed during Megakaryopoiesis and May Control Timing of Gene Expression. Int J Mol Sci 2020; 21:ijms21030967. [PMID: 32024018 PMCID: PMC7037754 DOI: 10.3390/ijms21030967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 12/13/2022] Open
Abstract
Megakaryopoiesis is the process during which megakaryoblasts differentiate to polyploid megakaryocytes that can subsequently shed thousands of platelets in the circulation. Megakaryocytes accumulate mRNA during their maturation, which is required for the correct spatio-temporal production of cytoskeletal proteins, membranes and platelet-specific granules, and for the subsequent shedding of thousands of platelets per cell. Gene expression profiling identified the RNA binding protein ATAXIN2 (ATXN2) as a putative novel regulator of megakaryopoiesis. ATXN2 expression is high in CD34+/CD41+ megakaryoblasts and sharply decreases upon maturation to megakaryocytes. ATXN2 associates with DDX6 suggesting that it may mediate repression of mRNA translation during early megakaryopoiesis. Comparative transcriptome and proteome analysis on megakaryoid cells (MEG-01) with differential ATXN2 expression identified ATXN2 dependent gene expression of mRNA and protein involved in processes linked to hemostasis. Mice deficient for Atxn2 did not display differences in bleeding times, but the expression of key surface receptors on platelets, such as ITGB3 (carries the CD61 antigen) and CD31 (PECAM1), was deregulated and platelet aggregation upon specific triggers was reduced.
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Affiliation(s)
- Marten Hansen
- Department Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, 1066CX Amsterdam, The Netherlands; (M.H.); (S.Z.); (F.d.S.); (K.S.M.); (D.C.T.-T.); (E.v.d.A.)
| | - Sabrina Zeddies
- Department Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, 1066CX Amsterdam, The Netherlands; (M.H.); (S.Z.); (F.d.S.); (K.S.M.); (D.C.T.-T.); (E.v.d.A.)
| | - Marjolein Meinders
- Department Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam,1066CX Amsterdam, The Netherlands; (M.M.); (L.G.)
| | - Franca di Summa
- Department Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, 1066CX Amsterdam, The Netherlands; (M.H.); (S.Z.); (F.d.S.); (K.S.M.); (D.C.T.-T.); (E.v.d.A.)
| | - Ewa Rollmann
- Experimental Neurology, Goethe University Medical School, 60528 Frankfurt am Main, Germany; (E.R.); (M.H.)
| | - Floris P.J. van Alphen
- Department of Molecular and Cellular Hemostasis, Sanquin Research, 1066CX Amsterdam, The Netherlands (A.J.H.); (M.v.d.B.)
| | - Arjan J. Hoogendijk
- Department of Molecular and Cellular Hemostasis, Sanquin Research, 1066CX Amsterdam, The Netherlands (A.J.H.); (M.v.d.B.)
| | - Kat S. Moore
- Department Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, 1066CX Amsterdam, The Netherlands; (M.H.); (S.Z.); (F.d.S.); (K.S.M.); (D.C.T.-T.); (E.v.d.A.)
| | - Melanie Halbach
- Experimental Neurology, Goethe University Medical School, 60528 Frankfurt am Main, Germany; (E.R.); (M.H.)
| | - Laura Gutiérrez
- Department Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam,1066CX Amsterdam, The Netherlands; (M.M.); (L.G.)
| | - Maartje van den Biggelaar
- Department of Molecular and Cellular Hemostasis, Sanquin Research, 1066CX Amsterdam, The Netherlands (A.J.H.); (M.v.d.B.)
| | - Daphne C. Thijssen-Timmer
- Department Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, 1066CX Amsterdam, The Netherlands; (M.H.); (S.Z.); (F.d.S.); (K.S.M.); (D.C.T.-T.); (E.v.d.A.)
| | - Georg W.J. Auburger
- Experimental Neurology, Goethe University Medical School, 60528 Frankfurt am Main, Germany; (E.R.); (M.H.)
| | - Emile van den Akker
- Department Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, 1066CX Amsterdam, The Netherlands; (M.H.); (S.Z.); (F.d.S.); (K.S.M.); (D.C.T.-T.); (E.v.d.A.)
| | - Marieke von Lindern
- Department Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, 1066CX Amsterdam, The Netherlands; (M.H.); (S.Z.); (F.d.S.); (K.S.M.); (D.C.T.-T.); (E.v.d.A.)
- Correspondence: ; Tel.: +31-6-1203-7801
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Sen NE, Arsovic A, Meierhofer D, Brodesser S, Oberschmidt C, Canet-Pons J, Kaya ZE, Halbach MV, Gispert S, Sandhoff K, Auburger G. In Human and Mouse Spino-Cerebellar Tissue, Ataxin-2 Expansion Affects Ceramide-Sphingomyelin Metabolism. Int J Mol Sci 2019; 20:E5854. [PMID: 31766565 PMCID: PMC6928749 DOI: 10.3390/ijms20235854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Ataxin-2 (human gene symbol ATXN2) acts during stress responses, modulating mRNA translation and nutrient metabolism. Ataxin-2 knockout mice exhibit progressive obesity, dyslipidemia, and insulin resistance. Conversely, the progressive ATXN2 gain of function due to the fact of polyglutamine (polyQ) expansions leads to a dominantly inherited neurodegenerative process named spinocerebellar ataxia type 2 (SCA2) with early adipose tissue loss and late muscle atrophy. We tried to understand lipid dysregulation in a SCA2 patient brain and in an authentic mouse model. Thin layer chromatography of a patient cerebellum was compared to the lipid metabolome of Atxn2-CAG100-Knockin (KIN) mouse spinocerebellar tissue. The human pathology caused deficits of sulfatide, galactosylceramide, cholesterol, C22/24-sphingomyelin, and gangliosides GM1a/GD1b despite quite normal levels of C18-sphingomyelin. Cerebellum and spinal cord from the KIN mouse showed a consistent decrease of various ceramides with a significant elevation of sphingosine in the more severely affected spinal cord. Deficiency of C24/26-sphingomyelins contrasted with excess C18/20-sphingomyelin. Spinocerebellar expression profiling revealed consistent reductions of CERS protein isoforms, Sptlc2 and Smpd3, but upregulation of Cers2 mRNA, as prominent anomalies in the ceramide-sphingosine metabolism. Reduction of Asah2 mRNA correlated to deficient S1P levels. In addition, downregulations for the elongase Elovl1, Elovl4, Elovl5 mRNAs and ELOVL4 protein explain the deficit of very long-chain sphingomyelin. Reduced ASMase protein levels correlated to the accumulation of long-chain sphingomyelin. Overall, a deficit of myelin lipids was prominent in SCA2 nervous tissue at prefinal stage and not compensated by transcriptional adaptation of several metabolic enzymes. Myelination is controlled by mTORC1 signals; thus, our human and murine observations are in agreement with the known role of ATXN2 yeast, nematode, and mouse orthologs as mTORC1 inhibitors and autophagy promoters.
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Affiliation(s)
- Nesli-Ece Sen
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Aleksandar Arsovic
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany;
| | - Susanne Brodesser
- Membrane Biology and Lipid Biochemistry Unit, Life and Medical Sciences Institute, University of Bonn, 53121 Bonn, Germany;
| | - Carola Oberschmidt
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
| | - Júlia Canet-Pons
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
| | - Zeynep-Ece Kaya
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
- Cerrahpasa School of Medicine, Istanbul University, 34098 Istanbul, Turkey
| | - Melanie-Vanessa Halbach
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
| | - Suzana Gispert
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
| | - Konrad Sandhoff
- Membrane Biology and Lipid Biochemistry Unit, Life and Medical Sciences Institute, University of Bonn, 53121 Bonn, Germany;
| | - Georg Auburger
- Experimental Neurology, Building 89, Goethe University Medical Faculty, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany; (N.-E.S.); (A.A.); (C.O.); (J.C.-P.); (Z.-E.K.); (M.-V.H.); (S.G.)
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21
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Sen NE, Canet-Pons J, Halbach MV, Arsovic A, Pilatus U, Chae WH, Kaya ZE, Seidel K, Rollmann E, Mittelbronn M, Meierhofer D, De Zeeuw CI, Bosman LWJ, Gispert S, Auburger G. Generation of an Atxn2-CAG100 knock-in mouse reveals N-acetylaspartate production deficit due to early Nat8l dysregulation. Neurobiol Dis 2019; 132:104559. [PMID: 31376479 DOI: 10.1016/j.nbd.2019.104559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder caused by CAG-expansion mutations in the ATXN2 gene, mainly affecting motor neurons in the spinal cord and Purkinje neurons in the cerebellum. While the large expansions were shown to cause SCA2, the intermediate length expansions lead to increased risk for several atrophic processes including amyotrophic lateral sclerosis and Parkinson variants, e.g. progressive supranuclear palsy. Intense efforts to pioneer a neuroprotective therapy for SCA2 require longitudinal monitoring of patients and identification of crucial molecular pathways. The ataxin-2 (ATXN2) protein is mainly involved in RNA translation control and regulation of nutrient metabolism during stress periods. The preferential mRNA targets of ATXN2 are yet to be determined. In order to understand the molecular disease mechanism throughout different prognostic stages, we generated an Atxn2-CAG100-knock-in (KIN) mouse model of SCA2 with intact murine ATXN2 expression regulation. Its characterization revealed somatic mosaicism of the expansion, with shortened lifespan, a progressive spatio-temporal pattern of pathology with subsequent phenotypes, and anomalies of brain metabolites such as N-acetylaspartate (NAA), all of which mirror faithfully the findings in SCA2 patients. Novel molecular analyses from stages before the onset of motor deficits revealed a strong selective effect of ATXN2 on Nat8l mRNA which encodes the enzyme responsible for NAA synthesis. This metabolite is a prominent energy store of the brain and a well-established marker for neuronal health. Overall, we present a novel authentic rodent model of SCA2, where in vivo magnetic resonance imaging was feasible to monitor progression and where the definition of earliest transcriptional abnormalities was possible. We believe that this model will not only reveal crucial insights regarding the pathomechanism of SCA2 and other ATXN2-associated disorders, but will also aid in developing gene-targeted therapies and disease prevention.
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Affiliation(s)
- Nesli-Ece Sen
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Júlia Canet-Pons
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Melanie V Halbach
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Aleksandar Arsovic
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Ulrich Pilatus
- Institute of Neuroradiology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Woon-Hyung Chae
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt am Main, Germany
| | - Zeynep-Ece Kaya
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany; Department of Neurology, Cerrahpasa School of Medicine, Istanbul University, 34098 Istanbul, Turkey
| | - Kay Seidel
- Department of Anatomy II, Institute of Clinical Neuroanatomy, Goethe University, 60590 Frankfurt am Main, Germany
| | - Ewa Rollmann
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Michel Mittelbronn
- Neurological Institute (Edinger Institute), Goethe University, 60590 Frankfurt am Main, Germany; Luxembourg Centre of Neuropathology (LCNP), Luxembourg; Department of Pathology, Laboratoire National de Santé (LNS), Dudelange, Luxembourg; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg; Department of Oncology, NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Chris I De Zeeuw
- Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, 1105 BA Amsterdam, the Netherlands; Department of Neuroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Laurens W J Bosman
- Department of Neuroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany.
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22
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Librado P, Orlando L. Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD. Mol Biol Evol 2019; 35:1520-1535. [PMID: 29617830 PMCID: PMC5967574 DOI: 10.1093/molbev/msy053] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within single populations and population pairs, the increasing wealth of high-throughput sequencing data requires improved methods capable of handling multiple, and ideally large number of, populations in a single analysis. In this study, we introduce LSD (levels of exclusively shared differences), a fast and flexible framework to perform genome-wide selection scans, along the internal and external branches of a given population tree. We use forward simulations to demonstrate that LSD can identify branches targeted by positive selection with remarkable sensitivity and specificity. We illustrate a range of potential applications by analyzing data from the 1000 Genomes Project and uncover a list of adaptive candidates accompanying the expansion of anatomically modern humans out of Africa and their spread to Europe.
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
- Corresponding author: E-mail:
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
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23
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Sun D, Liu M, Huang F, Huang F. [Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:215-221. [PMID: 30890511 DOI: 10.12122/j.issn.1673-4254.2019.02.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To investigate the differentially expressed genes between gastric cancer and normal gastric mucosa by bioinformatics analysis, identify the important gene participating in the occurrence and progression of gastric cancer, and predict the functions of these genes. METHODS The gene expression microarray data GSE100935 (including 18 gastric cancer samples and normal gastric mucosal tissues) downloaded from the GEO expression profile database were analyzed using Morpheus to obtain the differentially expressed genes in gastric cancer, and a cluster analysis heat map was constructed. The online database UALCAN was used to obtain the expression levels of these differentially expressed genes in gastric cancer and normal gastric mucosa. The prognostic value of the differentially expressed genes in gastric cancer was evaluated with Kaplan-Meier survival analysis. GO functional enrichment analysis was performed using Fun-Rich software, and the STRING database was exploited to establish a PPI network for the differentially expressed genes. RESULTS A total of 45119 differentially expressed genes were identified from GSE100935 microarray data. Analysis with UALCAN showed an obvious high expression of EXD3 gene in gastric cancer, and survival analysis suggested that a high expression level of EXD3 was associated with a poorer prognosis of the patients with gastric cancer. GO functional enrichment analysis found that the differentially expressed genes in gastric cancer were involved mainly in the regulation of nucleotide metabolism and the activity of transcription factors in the cancer cells. CONCLUSIONS EXD3 may be a potential oncogene in gastric cancer possibly in relation to DNA damage repair. The up-regulation of EXD3 plays an important role in the development and prognosis of gastric cancer, and may serve as an important indicator for prognostic evaluation of the patients.
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Affiliation(s)
- Dengzhong Sun
- Department of Gastrointestinal Surgery, Bengbu Medical College, Bengbu 233003, China
| | - Mulin Liu
- Department of Gastrointestinal Surgery, Bengbu Medical College, Bengbu 233003, China
| | - Fuxin Huang
- First Affiliated Hospital, Department of Biological Sciences, Bengbu Medical College, Bengbu 233003, China
| | - Fuxin Huang
- First Affiliated Hospital, Department of Biological Sciences, Bengbu Medical College, Bengbu 233003, China
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24
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Abstract
The mechanistic target of rapamycin (mTOR) is an evolutionary conserved protein with a serine/threonine kinase activity that regulates cell growth, proliferation, motility, survival, protein synthesis, autophagy and transcription. It is embedded in 2 large protein complexes: mTORC1 and mTORC2. Regulation of specific mTOR pathway functions depends on multiple GTPases, that act either as regulators of mTOR protein complexes, coupling energy availability with mTORC1 activity, or as downstream effectors of both mTORC1 and mTORC2. In this commentary, we highlight the advantages of studying the mTOR pathway in C. elegans, including the subcellular localization of the signaling pathway components and the animal phenotypes following tissue specific protein over-expression or knockdown. One important regulator that is not limited to the mTOR pathway is RHEB. We discuss in vitro and in vivo data suggesting that RHEB can function as an inhibitor of mTOR when not bound to GTP. RHEB-1 itself is regulated by Rab GDP dissociation inhibitor β, which directly binds to ATX-2. We also highlight the roles of these proteins in dietary restriction-depended reduction in animal size and fat content.
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Affiliation(s)
- Daniel Z Bar
- a National Human Genome Research Institute, National Institutes of Health , Bethesda , MD , USA
| | - Chayki Charar
- b Department of Genetics , Institute of Life Sciences, Hebrew University of Jerusalem , Jerusalem , Israel
| | - Yosef Gruenbaum
- b Department of Genetics , Institute of Life Sciences, Hebrew University of Jerusalem , Jerusalem , Israel
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25
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Genetic Polymorphisms Associated with the Neutrophil⁻Lymphocyte Ratio and Their Clinical Implications for Metabolic Risk Factors. J Clin Med 2018; 7:jcm7080204. [PMID: 30096757 PMCID: PMC6111840 DOI: 10.3390/jcm7080204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Background: The neutrophil–lymphocyte ratio (NLR) is a valuable prognostic or predictive biomarker in various diseases, but the genetic factors that underlie the NLR have not been studied. We attempted to investigate polymorphisms related to NLR phenotype and analyze their ability to predict metabolic risks. Methods: A genome-wide association study was performed with log-transformed NLR using an Affymetrix Axiom™ KORV1.1-96 Array. Regression models for metabolic risk status were designed using the identified significant single-nucleotide polymorphisms (SNPs). Results: We identified four SNPs near the TMEM116, NAA25, and PTPN11 genes that were associated with the NLR. The top SNP associated with the log-transformed NLR was rs76181728 in TMEM116. A case–control study was performed to analyze the metabolic risks associated with each SNP after adjusting for age, sex, and body mass index (BMI). Three SNPs displayed significant odds ratios (ORs) for increased blood pressure and increased waist circumference. In the regression model for metabolic syndrome, rs76181728 showed a significant association (OR = 1.465, 95% confidence interval (CI) = 1.091–1.969, P = 0.011) after adjustment for the NLR phenotype. Conclusions: We identified four novel SNPs that are associated with the NLR in healthy Koreans. SNPs in relevant genes might therefore serve as biomarkers for metabolic risks.
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26
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Barić A, Brčić L, Gračan S, Torlak Lovrić V, Gunjača I, Šimunac M, Brekalo M, Boban M, Polašek O, Barbalić M, Zemunik T, Punda A, Boraska Perica V. Association of established hypothyroidism-associated genetic variants with Hashimoto's thyroiditis. J Endocrinol Invest 2017; 40:1061-1067. [PMID: 28382505 DOI: 10.1007/s40618-017-0660-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/21/2017] [Indexed: 12/26/2022]
Abstract
PURPOSE Hashimoto's thyroiditis (HT) as a chronic autoimmune disease of the thyroid gland is the most common cause of hypothyroidism. Since HT and hypothyroidism are closely related, the main aim of this study was to explore the association of established hypothyroidism single-nucleotide polymorphisms (SNPs) with HT. METHODS The case-control dataset included 200 HT cases and 304 controls. Diagnosis of HT cases was based on clinical examination, measurement of thyroid antibodies (TgAb, TPOAb), hormones (TSH and FT4) and ultrasound examination. We genotyped and analysed 11 known hypothyroidism-associated genetic variants. Case-control association analysis was performed in order to test each SNP for the association with HT using logistic regression model. Additionally, each SNP was tested for the association with thyroid-related quantitative traits (TPOAb levels, TgAb levels and thyroid volume) in HT cases only using linear regression. RESULTS We identified two genetic variants nominally associated with HT rs3184504 in SH2B3 gene (P = 0.0135, OR = 0.74, 95% CI = 0.57-0.95) and rs4704397 in PDE8B gene (P = 0.0383, OR = 1.32, 95% CI = 1.01-1.74). The SH2B3 genetic variant also showed nominal association with TPOAb levels (P = 0.0163, β = -0.46) and rs4979402 inside DFNB31 gene was nominally associated with TgAb levels (P = 0.0443, β = 0.41). CONCLUSIONS SH2B3 gene has previously been associated with susceptibility to several autoimmune diseases, whereas PDE8B has been associated with TSH levels and suggested to modulate thyroid physiology that may influence the manifestation of thyroid disease. Identified loci are novel and biologically plausible candidates for HT development and represent good basis for further exploration of HT susceptibility.
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Affiliation(s)
- A Barić
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - L Brčić
- Department of Medical Biology, School of Medicine, University of Split, Split, Croatia
| | - S Gračan
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - V Torlak Lovrić
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - I Gunjača
- Department of Medical Biology, School of Medicine, University of Split, Split, Croatia
| | - M Šimunac
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - M Brekalo
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - M Boban
- Department of Pharmacology, School of Medicine, University of Split, Split, Croatia
| | - O Polašek
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - M Barbalić
- Department of Medical Biology, School of Medicine, University of Split, Split, Croatia
| | - T Zemunik
- Department of Medical Biology, School of Medicine, University of Split, Split, Croatia
| | - A Punda
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - V Boraska Perica
- Department of Medical Biology, School of Medicine, University of Split, Split, Croatia.
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27
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Halbach MV, Gispert S, Stehning T, Damrath E, Walter M, Auburger G. Atxn2 Knockout and CAG42-Knock-in Cerebellum Shows Similarly Dysregulated Expression in Calcium Homeostasis Pathway. THE CEREBELLUM 2017; 16:68-81. [PMID: 26868665 PMCID: PMC5243904 DOI: 10.1007/s12311-016-0762-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominantly inherited neurodegenerative disorder with preferential affection of Purkinje neurons, which are known as integrators of calcium currents. The expansion of a polyglutamine (polyQ) domain in the RNA-binding protein ataxin-2 (ATXN2) is responsible for this disease, but the causal roles of deficient ATXN2 functions versus aggregation toxicity are still under debate. Here, we studied mouse mutants with Atxn2 knockout (KO) regarding their cerebellar global transcriptome by microarray and RT-qPCR, in comparison with data from Atxn2-CAG42-knock-in (KIN) mouse cerebellum. Global expression downregulations involved lipid and growth signaling pathways in good agreement with previous data. As a novel effect, downregulations of key factors in calcium homeostasis pathways (the transcription factor Rora, transporters Itpr1 and Atp2a2, as well as regulator Inpp5a) were observed in the KO cerebellum, and some of them also occurred subtly early in KIN cerebellum. The ITPR1 protein levels were depleted from soluble fractions of cerebellum in both mutants, but accumulated in its membrane-associated form only in the SCA2 model. Coimmunoprecipitation demonstrated no association of ITPR1 with Q42-expanded or with wild-type ATXN2. These findings provide evidence that the physiological functions and protein interactions of ATXN2 are relevant for calcium-mediated excitation of Purkinje cells as well as for ATXN2-triggered neurotoxicity. These insights may help to understand pathogenesis and tissue specificity in SCA2 and other polyQ ataxias like SCA1, where inositol regulation of calcium flux and RORalpha play a role.
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Affiliation(s)
- Melanie Vanessa Halbach
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590, Frankfurt am Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590, Frankfurt am Main, Germany
| | - Tanja Stehning
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590, Frankfurt am Main, Germany
| | - Ewa Damrath
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590, Frankfurt am Main, Germany
| | - Michael Walter
- Institute for Medical Genetics, Eberhard-Karls-University of Tuebingen, 72076, Tuebingen, Germany
| | - Georg Auburger
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590, Frankfurt am Main, Germany.
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28
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Auburger G, Sen NE, Meierhofer D, Başak AN, Gitler AD. Efficient Prevention of Neurodegenerative Diseases by Depletion of Starvation Response Factor Ataxin-2. Trends Neurosci 2017; 40:507-516. [DOI: 10.1016/j.tins.2017.06.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022]
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29
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Maslah N, Cassinat B, Verger E, Kiladjian JJ, Velazquez L. The role of LNK/SH2B3 genetic alterations in myeloproliferative neoplasms and other hematological disorders. Leukemia 2017; 31:1661-1670. [PMID: 28484264 DOI: 10.1038/leu.2017.139] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/10/2017] [Accepted: 04/24/2017] [Indexed: 12/11/2022]
Abstract
Malignant hematological diseases are mainly because of the occurrence of molecular abnormalities leading to the deregulation of signaling pathways essential for precise cell behavior. High-resolution genome analysis using microarray and large-scale sequencing have helped identify several important acquired gene mutations that are responsible for such signaling deregulations across different hematological malignancies. In particular, the genetic landscape of classical myeloproliferative neoplasms (MPNs) has been in large part completed with the identification of driver mutations (targeting the cytokine receptor/Janus-activated kinase 2 (JAK2) pathway) that determine MPN phenotype, as well as additional mutations mainly affecting the regulation of gene expression (epigenetics or splicing regulators) and signaling. At present, most efforts concentrate in understanding how all these genetic alterations intertwine together to influence disease evolution and/or dictate clinical phenotype in order to use them to personalize diagnostic and clinical care. However, it is now evident that factors other than somatic mutations also play an important role in MPN disease initiation and progression, among which germline predisposition (single-nucleotide polymorphisms and haplotypes) may strongly influence the occurrence of MPNs. In this context, the LNK inhibitory adaptor protein encoded by the LNK/SH2B adaptor protein 3 (SH2B3) gene is the target of several genetic variations, acquired or inherited in MPNs, lymphoid leukemia and nonmalignant hematological diseases, underlying its importance in these pathological processes. As LNK adaptor is a key regulator of normal hematopoiesis, understanding the consequences of LNK variants on its protein functions and on driver or other mutations could be helpful to correlate genotype and phenotype of patients and to develop therapeutic strategies to target this molecule. In this review we summarize the current knowledge of LNK function in normal hematopoiesis, the different SH2B3 mutations reported to date and discuss how these genetic variations may influence the development of hematological malignancies.
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Affiliation(s)
- N Maslah
- APHP, Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Paris, France.,Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France
| | - B Cassinat
- APHP, Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Paris, France.,Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France
| | - E Verger
- APHP, Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Paris, France.,Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France
| | - J-J Kiladjian
- Inserm UMRS 1131, IUH, Université Paris-Diderot, Paris, France.,APHP, Centre d'investigations Cliniques, Hôpital Saint-Louis, Paris, France
| | - L Velazquez
- INSERM UMRS-MD1197, Institut André Lwoff/Université Paris XI, Hôpital Paul Brousse, Villejuif, France
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30
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Carmo-Silva S, Nobrega C, Pereira de Almeida L, Cavadas C. Unraveling the Role of Ataxin-2 in Metabolism. Trends Endocrinol Metab 2017; 28:309-318. [PMID: 28117213 DOI: 10.1016/j.tem.2016.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/14/2016] [Accepted: 12/23/2016] [Indexed: 12/21/2022]
Abstract
Ataxin-2 is a polyglutamine protein implicated in several biological processes such as RNA metabolism and cytoskeleton reorganization. Ataxin-2 is highly expressed in various tissues including the hypothalamus, a brain region that controls food intake and energy balance. Ataxin-2 expression is influenced by nutritional status. Emerging studies discussed here now show that ataxin-2 deficiency correlates with insulin resistance and dyslipidemia, an action mediated via the mTOR pathway, suggesting that ataxin-2 might play key roles in metabolic homeostasis including body weight regulation, insulin sensitivity, and cellular stress responses. In this review we also discuss the relevance of ataxin-2 in the hypothalamic regulation of energy balance, and its potential as a therapeutic target in metabolic disorders such as obesity.
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Affiliation(s)
- Sara Carmo-Silva
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Clevio Nobrega
- Department of Biomedical Sciences and Medicine, Center for Biomedical Research (CBMR), University of Algarve, Faro, Portugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Claudia Cavadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
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Affiliation(s)
- Nesli E Sen
- Department of Neurology, Goethe University Medical School, Frankfurt am Main, Germany
| | - Suzana Gispert
- Department of Neurology, Goethe University Medical School, Frankfurt am Main, Germany
| | - Georg Auburger
- Department of Neurology, Goethe University Medical School, Frankfurt am Main, Germany
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Seidel G, Meierhofer D, Şen NE, Guenther A, Krobitsch S, Auburger G. Quantitative Global Proteomics of Yeast PBP1 Deletion Mutants and Their Stress Responses Identifies Glucose Metabolism, Mitochondrial, and Stress Granule Changes. J Proteome Res 2016; 16:504-515. [PMID: 27966978 DOI: 10.1021/acs.jproteome.6b00647] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The yeast protein PBP1 is implicated in very diverse pathways. Intriguingly, its deletion mitigates the toxicity of human neurodegeneration factors. Here, we performed label-free quantitative global proteomics to identify crucial downstream factors, either without stress or under cell stress conditions (heat and NaN3). Compared to the wildtype BY4741 strain, PBP1 deletion always triggered downregulation of the key bioenergetics enzyme KGD2 and the prion protein RNQ1 as well as upregulation of the leucine biosynthesis enzyme LEU1. Without stress, enrichment of stress response factors was consistently detected for both deletion mutants; upon stress, these factors were more pronounced. The selective analysis of components of stress granules and P-bodies revealed a prominent downregulation of GIS2. Our yeast data are in good agreement with a global proteomics and metabolomics publication that the PBP1 ortholog ATAXIN-2 (ATXN2) knockout (KO) in mouse results in mitochondrial deficits in leucine/fatty acid catabolism and bioenergetics, with an obesity phenotype. Furthermore, our data provide the completely novel insight that PBP1 mutations in stress periods involve GIS2, a plausible scenario in view of previous data that both PBP1 and GIS2 relocalize from ribosomes to stress granules, interact with poly(A)-binding protein in translation regulation and prevent mitochondrial precursor overaccumulation stress (mPOS). This may be relevant for human diseases like spinocerebellar ataxias, amyotrophic lateral sclerosis, and the metabolic syndrome.
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Affiliation(s)
- Gunnar Seidel
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Nesli-Ece Şen
- Experimental Neurology, Goethe University Medical School , Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Anika Guenther
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Sylvia Krobitsch
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School , Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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Alves-Cruzeiro JMDC, Mendonça L, Pereira de Almeida L, Nóbrega C. Motor Dysfunctions and Neuropathology in Mouse Models of Spinocerebellar Ataxia Type 2: A Comprehensive Review. Front Neurosci 2016; 10:572. [PMID: 28018166 PMCID: PMC5156697 DOI: 10.3389/fnins.2016.00572] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022] Open
Abstract
Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant ataxia caused by an expansion of CAG repeats in the exon 1 of the gene ATXN2, conferring a gain of toxic function that triggers the appearance of the disease phenotype. SCA2 is characterized by several symptoms including progressive gait ataxia and dysarthria, slow saccadic eye movements, sleep disturbances, cognitive impairments, and psychological dysfunctions such as insomnia and depression, among others. The available treatments rely on palliative care, which mitigate some of the major symptoms but ultimately fail to block the disease progression. This persistent lack of effective therapies led to the development of several models in yeast, C. elegans, D. melanogaster, and mice to serve as platforms for testing new therapeutic strategies and to accelerate the research on the complex disease mechanisms. In this work, we review 4 transgenic and 1 knock-in mouse that exhibit a SCA2-related phenotype and discuss their usefulness in addressing different scientific problems. The knock-in mice are extremely faithful to the human disease, with late onset of symptoms and physiological levels of mutant ataxin-2, while the other transgenic possess robust and well-characterized motor impairments and neuropathological features. Furthermore, a new BAC model of SCA2 shows promise to study the recently explored role of non-coding RNAs as a major pathogenic mechanism in this devastating disorder. Focusing on specific aspects of the behavior and neuropathology, as well as technical aspects, we provide a highly practical description and comparison of all the models with the purpose of creating a useful resource for SCA2 researchers worldwide.
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Affiliation(s)
| | - Liliana Mendonça
- Center for Neuroscience and Cell Biology, University of Coimbra Coimbra, Portugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal; Faculty of Pharmacy, University of CoimbraCoimbra, Portugal
| | - Clévio Nóbrega
- Department of Biomedical Sciences and Medicine and Center for Biomedical Research, University of Algarve Faro, Portugal
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Hao M, Yuan F, Jin C, Zhou Z, Cao Q, Xu L, Wang G, Huang H, Yang D, Xie M, Zhao X. Overexpression of Lnk in the Ovaries Is Involved in Insulin Resistance in Women With Polycystic Ovary Syndrome. Endocrinology 2016; 157:3709-3718. [PMID: 27459314 PMCID: PMC5045500 DOI: 10.1210/en.2016-1234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Polycystic ovary syndrome (PCOS) progression involves abnormal insulin signaling. SH2 domain-containing adaptor protein (Lnk) may be an important regulator of the insulin signaling pathway. We investigated whether Lnk was involved in insulin resistance (IR). Thirty-seven women due to receive laparoscopic surgery from June 2011 to February 2012 were included from the gynecologic department of the Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University. Samples of polycystic and normal ovary tissues were examined by immunohistochemistry. Ovarian cell lines underwent insulin stimulation and Lnk overexpression. Expressed Lnk underwent coimmunoprecipitation tests with green fluorescent protein-labeled insulin receptor and His-tagged insulin receptor substrate 1 (IRS1), and their colocalization in HEK293T cells was examined. Ovarian tissues from PCOS patients with IR exhibited higher expression of Lnk than ovaries from normal control subjects and PCOS patients without IR; mainly in follicular granulosa cells, the follicular fluid and plasma of oocytes in secondary follicles, and atretic follicles. Lnk was coimmunoprecipitated with insulin receptor and IRS1. Lnk and insulin receptor/IRS1 locations overlapped around the nucleus. IR, protein kinase B (Akt), and ERK1/2 activities were inhibited by Lnk overexpression and inhibited further after insulin stimulation, whereas IRS1 serine activity was increased. Insulin receptor (Tyr1150/1151), Akt (Thr308), and ERK1/2 (Thr202/Tyr204) phosphorylation was decreased, whereas IRS1 (Ser307) phosphorylation was increased with Lnk overexpression. In conclusion, Lnk inhibits the phosphatidylinositol 3 kinase-AKT and MAPK-ERK signaling response to insulin. Higher expression of Lnk in PCOS suggests that Lnk probably plays a role in the development of IR.
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Affiliation(s)
- Meihua Hao
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Feng Yuan
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Chenchen Jin
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Zehong Zhou
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Qi Cao
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Ling Xu
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Guanlei Wang
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Hui Huang
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Dongzi Yang
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Meiqing Xie
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
| | - Xiaomiao Zhao
- Department of Obstetrics and Gynecology (M.H., H.H., D.Y., M.X., X.Z.), Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Pharmacology (F.Y., C.J., G.W.), Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510120 China; Department of Obstetrics and Gynecology (Z.Z.), Reproductive Medical Center, Peking University Third Hospital, Haidian District, Beijing, China; Division of Hematology/Oncology (Q.C.), Cedar-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California; and Cedar-Sinai Medical Center (L.X.), University of California, Los Angeles School of Medicine, Los Angeles, California
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Sen NE, Drost J, Gispert S, Torres-Odio S, Damrath E, Klinkenberg M, Hamzeiy H, Akdal G, Güllüoğlu H, Başak AN, Auburger G. Search for SCA2 blood RNA biomarkers highlights Ataxin-2 as strong modifier of the mitochondrial factor PINK1 levels. Neurobiol Dis 2016; 96:115-126. [PMID: 27597528 DOI: 10.1016/j.nbd.2016.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/24/2016] [Accepted: 09/01/2016] [Indexed: 12/13/2022] Open
Abstract
Ataxin-2 (ATXN2) polyglutamine domain expansions of large size result in an autosomal dominantly inherited multi-system-atrophy of the nervous system named spinocerebellar ataxia type 2 (SCA2), while expansions of intermediate size act as polygenic risk factors for motor neuron disease (ALS and FTLD) and perhaps also for Levodopa-responsive Parkinson's disease (PD). In view of the established role of ATXN2 for RNA processing in periods of cell stress and the expression of ATXN2 in blood cells such as platelets, we investigated whether global deep RNA sequencing of whole blood from SCA2 patients identifies a molecular profile which might serve as diagnostic biomarker. The bioinformatic analysis of SCA2 blood global transcriptomics revealed various significant effects on RNA processing pathways, as well as the pathways of Huntington's disease and PD where mitochondrial dysfunction is crucial. Notably, an induction of PINK1 and PARK7 expression was observed. Conversely, expression of Pink1 was severely decreased upon global transcriptome profiling of Atxn2-knockout mouse cerebellum and liver, in parallel to strong effects on Opa1 and Ghitm, which encode known mitochondrial dynamics regulators. These results were validated by quantitative PCR and immunoblots. Starvation stress of human SH-SY5Y neuroblastoma cells led to a transcriptional phasic induction of ATXN2 in parallel to PINK1, and the knockdown of one enhanced the expression of the other during stress response. These findings suggest that ATXN2 may modify the known PINK1 roles for mitochondrial quality control and autophagy during cell stress. Given that PINK1 is responsible for autosomal recessive juvenile PD, this genetic interaction provides a concept how the degeneration of nigrostriatal dopaminergic neurons and the Parkinson phenotype may be triggered by ATXN2 mutations.
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Affiliation(s)
- Nesli Ece Sen
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt/Main, Germany; Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Boğaziçi University, 34342 Istanbul, Turkey
| | - Jessica Drost
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt/Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt/Main, Germany
| | - Sylvia Torres-Odio
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt/Main, Germany
| | - Ewa Damrath
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt/Main, Germany
| | - Michael Klinkenberg
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt/Main, Germany
| | - Hamid Hamzeiy
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Boğaziçi University, 34342 Istanbul, Turkey
| | - Gülden Akdal
- Department of Neurology, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - Halil Güllüoğlu
- Department of Neurology, Faculty of Medicine, Izmir University, Izmir, Turkey
| | - A Nazlı Başak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Boğaziçi University, 34342 Istanbul, Turkey.
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt/Main, Germany.
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Lastres-Becker I, Nonis D, Eich F, Klinkenberg M, Gorospe M, Kötter P, Klein FAC, Kedersha N, Auburger G. Mammalian ataxin-2 modulates translation control at the pre-initiation complex via PI3K/mTOR and is induced by starvation. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1862:1558-69. [PMID: 27240544 PMCID: PMC4967000 DOI: 10.1016/j.bbadis.2016.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/11/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Ataxin-2 is a cytoplasmic protein, product of the ATXN2 gene, whose deficiency leads to obesity, while its gain-of-function leads to neural atrophy. Ataxin-2 affects RNA homeostasis, but its effects are unclear. Here, immunofluorescence analysis suggested that ataxin-2 associates with 48S pre-initiation components at stress granules in neurons and mouse embryonic fibroblasts, but is not essential for stress granule formation. Coimmunoprecipitation analysis showed associations of ataxin-2 with initiation factors, which were concentrated at monosome fractions of polysome gradients like ataxin-2, unlike its known interactor PABP. Mouse embryonic fibroblasts lacking ataxin-2 showed increased phosphorylation of translation modulators 4E-BP1 and ribosomal protein S6 through the PI3K-mTOR pathways. Indeed, human neuroblastoma cells after trophic deprivation showed a strong induction of ATXN2 transcript via mTOR inhibition. Our results support the notion that ataxin-2 is a nutritional stress-inducible modulator of mRNA translation at the pre-initiation complex.
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Affiliation(s)
- Isabel Lastres-Becker
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany.
| | - David Nonis
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Florian Eich
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Michael Klinkenberg
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Peter Kötter
- Center of Excellence Macromolecular Complexes, Institute of Molecular Biosciences, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Fabrice A C Klein
- Translational Medicine and Neurogenetics Department, Institut de Génétique et Biologie Moléculaire et Cellulaire, UMR7104-CNRS/U964-INSERM/UDS, BP10142, 67404 Illkirch Cédex, France
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, One Jimmy Fund Way, Boston, MA 02115, USA
| | - Georg Auburger
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany.
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Yu F, Guo Y, Wang H, Feng J, Jin Z, Chen Q, Liu Y, He J. Type 2 diabetes mellitus and risk of colorectal adenoma: a meta-analysis of observational studies. BMC Cancer 2016; 16:642. [PMID: 27535548 PMCID: PMC4989384 DOI: 10.1186/s12885-016-2685-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 08/05/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND To summarize the relationship between type 2 diabetes mellitus (T2DM) and risk of colorectal adenomas (CRA), we performed a meta-analysis of observational studies. METHODS To find studies, we searched PubMed, Embase, the Cochrane Library, Web of Science and conference abstracts and related publications for American Society of Clinical Oncology and the European Society of Medical Oncology. Studies that reported relative risks (RRs) or odds ratios (ORs) with 95 % confidence intervals (CIs) for the association between T2DM and risk of CRA were included. The meta-analysis assessed the relationships between T2DM and risk of CRA. Sensitivity analyses were performed in two ways: (1) by omitting each study iteratively and (2) by keeping high-quality studies only. Publication bias was detected by Egger's and Begg's tests and corrected using the trim and fill method. RESULTS This meta-analysis included 17 studies with 28,999 participants and 6798 CRA cases. We found that T2DM was a risk factor for CRA (RR: 1.52; 95 % CI: 1.29-1.80), and also for the advanced adenoma (RR: 1.41; 95 % CI: 1.06-1.87). Patients with existing T2DM (RR: 1.56; 95 % CI: 1.16-2.08) or newly diagnosed T2DM (RR: 1.51; 95 % CI: 1.16-1.97) have a risk of CRA. Similar significant results were found in retrospective studies (RR: 1.57; 95 % CI: 1.30-1.89) and population based cross-sectional studies (RR: 1.46; 95 % CI: 1.21-1.89), but not in prospective studies (RR: 1.27; 95 % CI: 0.77-2.10). CONCLUSIONS Our results suggested that T2DM plays a risk role in the risk of developing CRA. Consequently, medical workers should increase the rate of CRA screening for T2DM patients so that they can benefit from behavioural interventions that can help prevent the development of colorectal cancer. Additional, large prospective cohort studies are needed to make a more convincing case for these associations.
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Affiliation(s)
- Feifei Yu
- Medical Service Research Division, Navy Medical Research Institute, Shanghai, China
| | - Yibin Guo
- Department of Health Statistics, Second Military Medical University, No. 800 Xiangyin Road, Shanghai, 200433, China
| | - Hao Wang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Jian Feng
- Department of Health Statistics, Second Military Medical University, No. 800 Xiangyin Road, Shanghai, 200433, China
| | - Zhichao Jin
- Department of Health Statistics, Second Military Medical University, No. 800 Xiangyin Road, Shanghai, 200433, China
| | - Qi Chen
- Department of Health Statistics, Second Military Medical University, No. 800 Xiangyin Road, Shanghai, 200433, China
| | - Yu Liu
- College of Art & Science, University of San Francisco, San Francisco, USA
| | - Jia He
- Department of Health Statistics, Second Military Medical University, No. 800 Xiangyin Road, Shanghai, 200433, China.
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Bar DZ, Charar C, Dorfman J, Yadid T, Tafforeau L, Lafontaine DLJ, Gruenbaum Y. Cell size and fat content of dietary-restricted Caenorhabditis elegans are regulated by ATX-2, an mTOR repressor. Proc Natl Acad Sci U S A 2016; 113:E4620-9. [PMID: 27457958 PMCID: PMC4987808 DOI: 10.1073/pnas.1512156113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dietary restriction (DR) is a metabolic intervention that extends the lifespan of multiple species, including yeast, flies, nematodes, rodents, and, arguably, rhesus monkeys and humans. Hallmarks of lifelong DR are reductions in body size, fecundity, and fat accumulation, as well as slower development. We have identified atx-2, the Caenorhabditis elegans homolog of the human ATXN2L and ATXN2 genes, as the regulator of these multiple DR phenotypes. Down-regulation of atx-2 increases the body size, cell size, and fat content of dietary-restricted animals and speeds animal development, whereas overexpression of atx-2 is sufficient to reduce the body size and brood size of wild-type animals. atx-2 regulates the mechanistic target of rapamycin (mTOR) pathway, downstream of AMP-activated protein kinase (AMPK) and upstream of ribosomal protein S6 kinase and mTOR complex 1 (TORC1), by its direct association with Rab GDP dissociation inhibitor β, which likely regulates RHEB shuttling between GDP-bound and GTP-bound forms. Taken together, this work identifies a previously unknown mechanism regulating multiple aspects of DR, as well as unknown regulators of the mTOR pathway. They also extend our understanding of diet-dependent growth retardation, and offers a potential mechanism to treat obesity.
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Affiliation(s)
- Daniel Z Bar
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Chayki Charar
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Jehudith Dorfman
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Tam Yadid
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel
| | - Lionel Tafforeau
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), BioPark Campus, Gosselies B-6041, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), BioPark Campus, Gosselies B-6041, Belgium
| | - Yosef Gruenbaum
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 9190401, Israel;
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Effect of Associated Autoimmune Diseases on Type 1 Diabetes Mellitus Incidence and Metabolic Control in Children and Adolescents. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6219730. [PMID: 27525273 PMCID: PMC4971288 DOI: 10.1155/2016/6219730] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 04/06/2016] [Accepted: 04/19/2016] [Indexed: 02/06/2023]
Abstract
Type 1 diabetes mellitus (T1DM) is one of the most common chronic diseases developing in childhood. The incidence of the disease in children increases for unknown reasons at a rate from 3 to 5% every year worldwide. The background of T1DM is associated with the autoimmune process of pancreatic beta cell destruction, which leads to absolute insulin deficiency and organ damage. Complex interactions between environmental and genetic factors contribute to the development of T1DM in genetically predisposed patients. The T1DM-inducing autoimmune process can also affect other organs, resulting in development of additional autoimmune diseases in the patient, thereby impeding diabetes control. The most common T1DM comorbidities include autoimmune thyroid diseases, celiac disease, and autoimmune gastritis; additionally, diabetes can be a component of PAS (Polyglandular Autoimmune Syndrome). The aim of this review is to assess the prevalence of T1DM-associated autoimmune diseases in children and adolescents and their impact on the course of T1DM. We also present suggestions concerning screening tests.
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Brčić L, Barić A, Gračan S, Brdar D, Torlak Lovrić V, Vidan N, Zemunik T, Polašek O, Barbalić M, Punda A, Boraska Perica V. Association of established thyroid peroxidase autoantibody (TPOAb) genetic variants with Hashimoto’s thyroiditis. Autoimmunity 2016; 49:480-485. [DOI: 10.1080/08916934.2016.1191475] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Genome-wide association study of cognitive functions and educational attainment in UK Biobank (N=112 151). Mol Psychiatry 2016; 21:758-67. [PMID: 27046643 PMCID: PMC4879186 DOI: 10.1038/mp.2016.45] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/14/2016] [Accepted: 02/11/2016] [Indexed: 12/13/2022]
Abstract
People's differences in cognitive functions are partly heritable and are associated with important life outcomes. Previous genome-wide association (GWA) studies of cognitive functions have found evidence for polygenic effects yet, to date, there are few replicated genetic associations. Here we use data from the UK Biobank sample to investigate the genetic contributions to variation in tests of three cognitive functions and in educational attainment. GWA analyses were performed for verbal-numerical reasoning (N=36 035), memory (N=112 067), reaction time (N=111 483) and for the attainment of a college or a university degree (N=111 114). We report genome-wide significant single-nucleotide polymorphism (SNP)-based associations in 20 genomic regions, and significant gene-based findings in 46 regions. These include findings in the ATXN2, CYP2DG, APBA1 and CADM2 genes. We report replication of these hits in published GWA studies of cognitive function, educational attainment and childhood intelligence. There is also replication, in UK Biobank, of SNP hits reported previously in GWA studies of educational attainment and cognitive function. GCTA-GREML analyses, using common SNPs (minor allele frequency>0.01), indicated significant SNP-based heritabilities of 31% (s.e.m.=1.8%) for verbal-numerical reasoning, 5% (s.e.m.=0.6%) for memory, 11% (s.e.m.=0.6%) for reaction time and 21% (s.e.m.=0.6%) for educational attainment. Polygenic score analyses indicate that up to 5% of the variance in cognitive test scores can be predicted in an independent cohort. The genomic regions identified include several novel loci, some of which have been associated with intracranial volume, neurodegeneration, Alzheimer's disease and schizophrenia.
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Rodríguez-Labrada R, Velázquez-Pérez L, Auburger G, Ziemann U, Canales-Ochoa N, Medrano-Montero J, Vázquez-Mojena Y, González-Zaldivar Y. Spinocerebellar ataxia type 2: Measures of saccade changes improve power for clinical trials. Mov Disord 2016; 31:570-8. [DOI: 10.1002/mds.26532] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/19/2015] [Accepted: 12/13/2015] [Indexed: 11/11/2022] Open
Affiliation(s)
- Roberto Rodríguez-Labrada
- Department of Clinical Neurophysiology; Center for the Research and Rehabilitation of Hereditary Ataxias; Holguín Cuba
| | - Luis Velázquez-Pérez
- Department of Clinical Neurophysiology; Center for the Research and Rehabilitation of Hereditary Ataxias; Holguín Cuba
| | - Georg Auburger
- Section of Experimental Neurology, Department of Neurology; Goethe University Medical School; Frankfurt am Main Germany
| | - Ulf Ziemann
- Department of Neurology & Stroke, and Hertie Institute for Clinical Brain Research; University Tübingen; Tübingen Germany
| | - Nalia Canales-Ochoa
- Department of Clinical Neurophysiology; Center for the Research and Rehabilitation of Hereditary Ataxias; Holguín Cuba
| | - Jacqueline Medrano-Montero
- Department of Clinical Neurophysiology; Center for the Research and Rehabilitation of Hereditary Ataxias; Holguín Cuba
| | - Yaimeé Vázquez-Mojena
- Department of Molecular Neurobiology; Center for the Research and Rehabilitation of Hereditary Ataxias; Holguín Cuba
| | - Yanetza González-Zaldivar
- Department of Molecular Neurobiology; Center for the Research and Rehabilitation of Hereditary Ataxias; Holguín Cuba
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Meierhofer D, Halbach M, Şen NE, Gispert S, Auburger G. Ataxin-2 (Atxn2)-Knock-Out Mice Show Branched Chain Amino Acids and Fatty Acids Pathway Alterations. Mol Cell Proteomics 2016; 15:1728-39. [PMID: 26850065 DOI: 10.1074/mcp.m115.056770] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 12/13/2022] Open
Abstract
Human Ataxin-2 (ATXN2) gene locus variants have been associated with obesity, diabetes mellitus type 1,and hypertension in genome-wide association studies, whereas mouse studies showed the knock-out of Atxn2 to lead to obesity, insulin resistance, and dyslipidemia. Intriguingly, the deficiency of ATXN2 protein orthologs in yeast and flies rescues the neurodegeneration process triggered by TDP-43 and Ataxin-1 toxicity. To understand the molecular effects of ATXN2 deficiency by unbiased approaches, we quantified the global proteome and metabolome of Atxn2-knock-out mice with label-free mass spectrometry. In liver tissue, significant downregulations of the proteins ACADS, ALDH6A1, ALDH7A1, IVD, MCCC2, PCCA, OTC, together with bioinformatic enrichment of downregulated pathways for branched chain and other amino acid metabolism, fatty acids, and citric acid cycle were observed. Statistical trends in the cerebellar proteome and in the metabolomic profiles supported these findings. They are in good agreement with recent claims that PBP1, the yeast ortholog of ATXN2, sequestrates the nutrient sensor TORC1 in periods of cell stress. Overall, ATXN2 appears to modulate nutrition and metabolism, and its activity changes are determinants of growth excess or cell atrophy.
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Affiliation(s)
- David Meierhofer
- From the ‡Max Planck Institute for Molecular Genetics, Ihnestraβe 63-73, 14195 Berlin, Germany;
| | - Melanie Halbach
- §Experimental Neurology, Building 89, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Nesli Ece Şen
- §Experimental Neurology, Building 89, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Suzana Gispert
- §Experimental Neurology, Building 89, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Georg Auburger
- §Experimental Neurology, Building 89, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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Replication of GWAS Coding SNPs Implicates MMEL1 as a Potential Susceptibility Locus among Saudi Arabian Celiac Disease Patients. DISEASE MARKERS 2015; 2015:351673. [PMID: 26843707 PMCID: PMC4710944 DOI: 10.1155/2015/351673] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023]
Abstract
Celiac disease (CD), a gluten intolerance disorder, was implicated to have 57 genetic susceptibility loci for Europeans but not for culturally and geographically distinct ethnic populations like Saudi Arabian CD patients. Therefore, we genotyped Saudi CD patients and healthy controls for three polymorphisms, that is, Phe196Ser in IRAK1, Trp262Arg in SH2B3, and Met518Thr in MMEL1 genes. Single locus analysis identified that carriers of the 518 Thr/Thr (MMEL1) genotype conferred a 1.6-fold increased disease risk compared to the noncarriers (OR = 2.6; 95% CI: 1.22-5.54; P < 0.01). This significance persisted even under allelic (OR = 1.55; 95% CI: 1.05-2.28; P = 0.02) and additive (OR = 0.35; 95% CI: 0.17-0.71; P = 0.03) genetic models. However, frequencies for Trp262Arg (SH2B3) and Phe196Ser (IRAK1) polymorphisms were not significantly different between patients and controls. The overall best MDR model included Met518Thr and Trp262Arg polymorphisms, with a maximal testing accuracy of 64.1% and a maximal cross-validation consistency of 10 out of 10 (P = 0.0156). Allelic distribution of the 518 Thr/Thr polymorphism in MMEL1 primarily suggests its independent and synergistic contribution towards CD susceptibility among Saudi patients. Lack of significant association of IRAK and SH2B3 gene polymorphisms in Saudi patients but their association in European groups suggests the genetic heterogeneity of CD.
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Kakleas K, Soldatou A, Karachaliou F, Karavanaki K. Associated autoimmune diseases in children and adolescents with type 1 diabetes mellitus (T1DM). Autoimmun Rev 2015; 14:781-97. [DOI: 10.1016/j.autrev.2015.05.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 12/16/2022]
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Genetic variants associated with celiac disease and the risk for coronary artery disease. Mol Genet Genomics 2015; 290:1911-7. [PMID: 25893417 DOI: 10.1007/s00438-015-1045-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/02/2015] [Indexed: 02/07/2023]
Abstract
Epidemiological evidence suggests that patients with celiac disease are at increased risk for coronary artery disease (CAD). Genetic-epidemiological analyses identified many single nucleotide polymorphisms (SNPs) associated with celiac disease. If there is a causal relation between celiac disease and CAD, one might expect that risk alleles primarily associated with celiac disease also increase the risk of CAD. In this study we identified from literature 41 SNPs that have been previously described to be genome-wide associated with celiac disease (p < 5 × 10(-08)). These SNPs were evaluated for their association with CAD in the Coronary ARtery DIsease Genome-wide Replication and Meta-analysis (CARDIoGRAM) dataset, a meta-analysis comprising genome-wide SNP association data from 22,233 CAD cases and 64,762 controls. 24 out of 41 (58.5 %) risk alleles for celiac disease displayed a positive association with CAD (CAD-OR range 1.001-1.081). The remaining risk alleles for celiac disease (n = 16) revealed CAD-ORs of ≤1.0 (range 0.951-1.0). The proportion of CAD associated alleles was greater but did not differ significantly from the proportion of 50 % expected by chance (p = 0.069). One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically significant association with CAD with directionality consistent effects on celiac disease and CAD. However, the effect of this locus is most likely driven by pleiotropic effects on multiple other diseases. In conclusion, this genetically based approach provided no convincing evidence that SNPs associated with celiac disease contribute to the risk of CAD. Hence, common non-genetic factors may play a more important role explaining the coincidence of these two complex disease conditions.
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Both ubiquitin ligases FBXW8 and PARK2 are sequestrated into insolubility by ATXN2 PolyQ expansions, but only FBXW8 expression is dysregulated. PLoS One 2015; 10:e0121089. [PMID: 25790475 PMCID: PMC4366354 DOI: 10.1371/journal.pone.0121089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/27/2015] [Indexed: 12/13/2022] Open
Abstract
The involvement of the ubiquitin-proteasome system (UPS) in the course of various age-associated neurodegenerative diseases is well established. The single RING finger type E3 ubiquitin-protein ligase PARK2 is mutated in a Parkinson’s disease (PD) variant and was found to interact with ATXN2, a protein where polyglutamine expansions cause Spinocerebellar ataxia type 2 (SCA2) or increase the risk for Levodopa-responsive PD and for the motor neuron disease Amyotrophic lateral sclerosis (ALS). We previously reported evidence for a transcriptional induction of the multi-subunit RING finger Skp1/Cul/F-box (SCF) type E3 ubiquitin-protein ligase complex component FBXW8 in global microarray profiling of ATXN2-expansion mouse cerebellum and demonstrated its role for ATXN2 degradation in vitro. Now, we documented co-localization in vitro and co-immunoprecipitations both in vitro and in vivo, which indicate associations of FBXW8 with ATXN2 and PARK2. Both FBXW8 and PARK2 proteins are driven into insolubility by expanded ATXN2. Whereas the FBXW8 transcript upregulation by ATXN2- expansion was confirmed also in qPCR of skin fibroblasts and blood samples of SCA2 patients, a FBXW8 expression dysregulation was not observed in ATXN2-deficient mice, nor was a PARK2 transcript dysregulation observed in any samples. Jointly, all available data suggest that the degradation of wildtype and mutant ATXN2 is dependent on FBXW8, and that ATXN2 accumulation selectively modulates FBXW8 levels, while PARK2 might act indirectly through FBXW8. The effects of ATXN2-expansions on FBXW8 expression in peripheral tissues like blood may become useful for clinical diagnostics.
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48
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Horton WB, Taylor JS, Ragland TJ, Subauste AR. Diabetic muscle infarction: a systematic review. BMJ Open Diabetes Res Care 2015; 3:e000082. [PMID: 25932331 PMCID: PMC4410119 DOI: 10.1136/bmjdrc-2015-000082] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 02/07/2023] Open
Abstract
CONTEXT Diabetic muscle infarction (DMI) is a rare complication associated with poorly controlled diabetes mellitus. Less than 200 cases have been reported in the literature since it was first described over 45 years ago. There is no clear 'standard of care' for managing these patients. EVIDENCE ACQUISITION PubMed searches were conducted for 'diabetic muscle infarction' and 'diabetic myonecrosis' from database inception through July 2014. All articles identified by these searches were reviewed in detail if the article text was available in English. EVIDENCE SYNTHESIS The current literature exists as case reports or small case series, with no prospective or higher-order treatment studies available. Thus, an evidence-based approach to data synthesis was difficult. The available literature is presented objectively with an attempt to describe clinically relevant trends and findings in the diagnosis and management of DMI. CONCLUSIONS Early recognition of DMI is key, so appropriate treatment can be initiated. MRI is the radiological study of choice. A combination of bed rest, glycemic control, and non-steroidal anti-inflammatory drug therapy appears to yield the shortest time to symptom resolution and the lowest risk of recurrence.
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Affiliation(s)
- William B Horton
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Jeremy S Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Timothy J Ragland
- Department of Radiology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Angela R Subauste
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Division of Endocrinology, University of Mississippi Medical Center, Jackson, Mississippi, USA
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