1
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Negrutskii BS, Porubleva LV, Malinowska A, Novosylna OV, Dadlez M, Knudsen CR. Understanding functions of eEF1 translation elongation factors beyond translation. A proteomic approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:67-99. [PMID: 38220433 DOI: 10.1016/bs.apcsb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Mammalian translation elongation factors eEF1A1 and eEF1A2 are 92% homologous isoforms whose mutually exclusive tissue-specific expression is regulated during development. The isoforms have similar translation functionality, but show differences in spatial organization and participation in various processes, such as oncogenesis and virus reproduction. The differences may be due to their ability to interact with isoform-specific partner proteins. We used the identified sets of eEF1A1 or eEF1A2 partner proteins to identify cell complexes and/or processes specific to one particular isoform. As a result, we found isoform-specific interactions reflecting the involvement of different eEF1A isoforms in different cellular processes, including actin-related, chromatin-remodeling, ribonuclease H2, adenylyl cyclase, and Cul3-RING ubiquitin ligase complexes as well as initiation of mitochondrial transcription. An essential by-product of our analysis is the elucidation of a number of cellular processes beyond protein biosynthesis, where both isoforms appear to participate such as large ribosomal subunit biogenesis, mRNA splicing, DNA mismatch repair, 26S proteasome activity, P-body and exosomes formation, protein targeting to the membrane. This information suggests that a relatively high content of eEF1A in the cell may be necessary not only to maintain efficient translation, but also to ensure its participation in various cellular processes, where some roles of eEF1A have not yet been described. We believe that the data presented here will be useful for deciphering new auxiliary functions of eEF1A and its isoforms, and provide a new look at the known non-canonical functions of this main component of the human translation-elongation machinery.
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Affiliation(s)
- Boris S Negrutskii
- Institute of Molecular Biology and Genetics, Kyiv, Ukraine; Aarhus Institute of Advanced Sciences, Høegh-Guldbergs, Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark.
| | | | - Agata Malinowska
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | | | - Michal Dadlez
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | - Charlotte R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark
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2
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Kurosaki T, Ashizawa T. The genetic and molecular features of the intronic pentanucleotide repeat expansion in spinocerebellar ataxia type 10. Front Genet 2022; 13:936869. [PMID: 36199580 PMCID: PMC9528567 DOI: 10.3389/fgene.2022.936869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is characterized by progressive cerebellar neurodegeneration and, in many patients, epilepsy. This disease mainly occurs in individuals with Indigenous American or East Asian ancestry, with strong evidence supporting a founder effect. The mutation causing SCA10 is a large expansion in an ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene. The ATTCT repeat is highly unstable, expanding to 280–4,500 repeats in affected patients compared with the 9–32 repeats in normal individuals, one of the largest repeat expansions causing neurological disorders identified to date. However, the underlying molecular basis of how this huge repeat expansion evolves and contributes to the SCA10 phenotype remains largely unknown. Recent progress in next-generation DNA sequencing technologies has established that the SCA10 repeat sequence has a highly heterogeneous structure. Here we summarize what is known about the structure and origin of SCA10 repeats, discuss the potential contribution of variant repeats to the SCA10 disease phenotype, and explore how this information can be exploited for therapeutic benefit.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
- Center for RNA Biology, University of Rochester, Rochester, NY, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
| | - Tetsuo Ashizawa
- Stanley H. Appel Department of Neurology, Houston Methodist Research Institute and Weil Cornell Medical College at Houston Methodist Houston, TX, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
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3
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Blasco Tavares Pereira Lopes F, Schlatzer D, Wang R, Li X, Feng E, Koyutürk M, Qi X, Chance MR. Temporal and Sex-Linked Protein Expression Dynamics in a Familial Model of Alzheimer's Disease. Mol Cell Proteomics 2022; 21:100280. [PMID: 35944844 PMCID: PMC9483563 DOI: 10.1016/j.mcpro.2022.100280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Mouse models of Alzheimer's disease (AD) show progression through stages reflective of human pathology. Proteomics identification of temporal and sex-linked factors driving AD-related pathways can be used to dissect initiating and propagating events of AD stages to develop biomarkers or design interventions. In the present study, we conducted label-free proteome measurements of mouse hippocampus tissue with variables of time (3, 6, and 9 months), genetic background (5XFAD versus WT), and sex (equal males and females). These time points are associated with well-defined phenotypes with respect to the following: Aβ42 plaque deposition, memory deficits, and neuronal loss, allowing correlation of proteome-based molecular signatures with the mouse model stages. Our data show 5XFAD mice exhibit increases in known human AD biomarkers as amyloid-beta peptide, APOE, GFAP, and ITM2B are upregulated across all time points/stages. At the same time, 23 proteins are here newly associated with Alzheimer's pathology as they are also dysregulated in 5XFAD mice. At a pathways level, the 5XFAD-specific upregulated proteins are significantly enriched for DNA damage and stress-induced senescence at 3-month only, while at 6-month, the AD-specific proteome signature is altered and significantly enriched for membrane trafficking and vesicle-mediated transport protein annotations. By 9-month, AD-specific dysregulation is also characterized by significant neuroinflammation with innate immune system, platelet activation, and hyper-reactive astrocyte-related enrichments. Aside from these temporal changes, analysis of sex-linked differences in proteome signatures uncovered novel sex and AD-associated proteins. Pathway analysis revealed sex-linked differences in the 5XFAD model to be involved in the regulation of well-known human AD-related processes of amyloid fibril formation, wound healing, lysosome biogenesis, and DNA damage. Verification of the discovery results by Western blot and parallel reaction monitoring confirm the fundamental conclusions of the study and poise the 5XFAD model for further use as a molecular tool for understanding AD.
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Affiliation(s)
- Filipa Blasco Tavares Pereira Lopes
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Daniela Schlatzer
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rihua Wang
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiaolin Li
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Emily Feng
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mehmet Koyutürk
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Department of Computer and Data Sciences, Case School of Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xin Qi
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark R Chance
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
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4
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Bentley-Ford MR, Andersen RS, Croyle MJ, Haycraft CJ, Clearman KR, Foote JB, Reiter JF, Yoder BK. ATXN10 Is Required for Embryonic Heart Development and Maintenance of Epithelial Cell Phenotypes in the Adult Kidney and Pancreas. Front Cell Dev Biol 2021; 9:705182. [PMID: 34970537 PMCID: PMC8712648 DOI: 10.3389/fcell.2021.705182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Atxn10 is a gene known for its role in cytokinesis and is associated with spinocerebellar ataxia (SCA10), a slowly progressing cerebellar syndrome caused by an intragenic pentanucleotide repeat expansion. Atxn10 is also implicated in the ciliopathy syndromes nephronophthisis (NPHP) and Joubert syndrome (JBTS), which are caused by the disruption of cilia function leading to nephron loss, impaired renal function, and cerebellar hypoplasia. How Atxn10 disruption contributes to these disorders remains unknown. Here, we generated Atxn10 congenital and conditional mutant mouse models. Our data indicate that while ATXN10 protein can be detected around the base of the cilium as well as in the cytosol, its loss does not cause overt changes in cilia formation or morphology. Congenital loss of Atxn10 results in embryonic lethality around E10.5 associated with pericardial effusion and loss of trabeculation. Similarly, tissue-specific loss of ATXN10 in the developing endothelium (Tie2-Cre) and myocardium (cTnT-Cre) also results in embryonic lethality with severe cardiac malformations occurring in the latter. Using an inducible Cagg-CreER to disrupt ATXN10 systemically at postnatal stages, we show that ATXN10 is also required for survival in adult mice. Loss of ATXN10 results in severe pancreatic and renal abnormalities leading to lethality within a few weeks post ATXN10 deletion in adult mice. Evaluation of these phenotypes further identified rapid epithelial-to-mesenchymal transition (EMT) in these tissues. In the pancreas, the phenotype includes signs of both acinar to ductal metaplasia and EMT with aberrant cilia formation and severe defects in glucose homeostasis related to pancreatic insufficiency or defects in feeding or nutrient intake. Collectively, this study identifies ATXN10 as an essential protein for survival.
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Affiliation(s)
- Melissa R. Bentley-Ford
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Reagan S. Andersen
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mandy J. Croyle
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney J. Haycraft
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kelsey R. Clearman
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy B. Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, University of Alabama at Birmingham, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, United States
| | - Bradley K. Yoder
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
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5
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Ataxin-10 Inhibits TNF- α-Induced Endothelial Inflammation via Suppressing Interferon Regulatory Factor-1. Mediators Inflamm 2021; 2021:7042148. [PMID: 34858081 PMCID: PMC8632433 DOI: 10.1155/2021/7042148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/01/2021] [Indexed: 02/08/2023] Open
Abstract
Endothelial inflammation is a crucial event in the initiation of atherosclerosis. Here, we identify Ataxin-10 protein as a novel negative modulator of endothelial activation by suppressing IRF-1 transcription activity. The protein level of Ataxin-10 is relatively higher in human vascular endothelial cells, which can be significantly suppressed by TNF-α in both HUVECs and HLMECs. Overexpression of Ataxin-10 markedly inhibited the mRNA expressions of VCAM-1 and several cytokines including MCP-1, CXCL-1, CCL-5, and TNF-α; thus, it can also suppress monocyte adhesion to endothelial cells. Accordingly, Ataxin-10 silencing promoted endothelial inflammation. However, Ataxin-10 did not affect the MAPK/NF-κB signaling pathway stimulated by TNF-α in HUVECs. Using the yeast two-hybrid assay, we found that Ataxin-10 can directly bind to interferon regulatory factor-1 (IRF-1). Upon TNF-α stimulation, Ataxin-10 promoted the cytoplasmic localization of IRF-1, which inhibited the transcription of VCAM-1. Moreover, knockdown of IRF-1 can eliminate the effect of Ataxin-10 on the expression of VCAM-1 in HUVECs induced by TNF-α. Taken together, these results indicate that Ataxin-10 inhibits endothelial cell activation and may serve as a promising therapeutic target for some vascular inflammatory-related diseases such as atherosclerosis.
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6
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Guichard M, Dainat B, Eynard S, Vignal A, Servin B, Neuditschko M. Two quantitative trait loci are associated with recapping of Varroa destructor-infested brood cells in Apis mellifera mellifera. Anim Genet 2021; 53:156-160. [PMID: 34729804 PMCID: PMC9297925 DOI: 10.1111/age.13150] [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] [Accepted: 10/10/2021] [Indexed: 11/30/2022]
Abstract
Recapping of Varroa destructor-infested brood cells is a trait that has recently attracted interest in honey bee breeding to select mite-resistant Apis mellifera colonies. To investigate the genetic architecture of this trait, we evaluated a sample of A. mellifera mellifera colonies (N = 155) from Switzerland and France and performed a genome-wide association study, using a pool of 500 workers per colony for next-generation sequencing. The results revealed that two QTL were significantly (P < 0.05) associated with recapping of V. destructor-infested brood cells. The best-associated QTL is located on chromosome 5 in a region previously found to be associated with grooming behaviour, a resistance trait against V. destructor, in A. mellifera and Apis cerana. The second best-associated QTL is located on chromosome 4 in an intron of the Dscam gene, which is involved in neuronal wiring. Previous research demonstrated that genes involved in neuronal wiring are associated with recapping and varroa sensitive hygiene. Therefore, our study confirms the role of a gene region on chromosome 5 in social immunity and simultaneously provides novel insights into genetic interactions between common mite resistance traits in honey bees.
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Affiliation(s)
- M Guichard
- Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, Bern, 3003, Switzerland.,Agroscope, Animal GenoPhenomics, Rte de la Tioleyre 4, Posieux, 1725, Switzerland
| | - B Dainat
- Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, Bern, 3003, Switzerland
| | - S Eynard
- GenPhySE, INRA, INPT, INPENVT, Université de Toulouse, Castanet-Tolosan, 31320, France.,UMT PrADE, Protection des Abeilles Dans l'Environnement, Avignon, 84914, France
| | - A Vignal
- GenPhySE, INRA, INPT, INPENVT, Université de Toulouse, Castanet-Tolosan, 31320, France.,UMT PrADE, Protection des Abeilles Dans l'Environnement, Avignon, 84914, France
| | - B Servin
- GenPhySE, INRA, INPT, INPENVT, Université de Toulouse, Castanet-Tolosan, 31320, France.,UMT PrADE, Protection des Abeilles Dans l'Environnement, Avignon, 84914, France
| | -
- Labogena, Domaine de Vilvert Bat 224 CS80009, Jouy-en-Josas CEDEX, 78353, France
| | - M Neuditschko
- Agroscope, Animal GenoPhenomics, Rte de la Tioleyre 4, Posieux, 1725, Switzerland
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7
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Ichhaporia VP, Hendershot LM. Role of the HSP70 Co-Chaperone SIL1 in Health and Disease. Int J Mol Sci 2021; 22:ijms22041564. [PMID: 33557244 PMCID: PMC7913895 DOI: 10.3390/ijms22041564] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/30/2021] [Accepted: 01/30/2021] [Indexed: 12/04/2022] Open
Abstract
Cell surface and secreted proteins provide essential functions for multicellular life. They enter the endoplasmic reticulum (ER) lumen co-translationally, where they mature and fold into their complex three-dimensional structures. The ER is populated with a host of molecular chaperones, associated co-factors, and enzymes that assist and stabilize folded states. Together, they ensure that nascent proteins mature properly or, if this process fails, target them for degradation. BiP, the ER HSP70 chaperone, interacts with unfolded client proteins in a nucleotide-dependent manner, which is tightly regulated by eight DnaJ-type proteins and two nucleotide exchange factors (NEFs), SIL1 and GRP170. Loss of SIL1′s function is the leading cause of Marinesco-Sjögren syndrome (MSS), an autosomal recessive, multisystem disorder. The development of animal models has provided insights into SIL1′s functions and MSS-associated pathologies. This review provides an in-depth update on the current understanding of the molecular mechanisms underlying SIL1′s NEF activity and its role in maintaining ER homeostasis and normal physiology. A precise understanding of the underlying molecular mechanisms associated with the loss of SIL1 may allow for the development of new pharmacological approaches to treat MSS.
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8
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Singh S, Bano A, Saraya A, Das P, Sharma R. iTRAQ-based analysis for the identification of MARCH8 targets in human esophageal squamous cell carcinoma. J Proteomics 2021; 236:104125. [PMID: 33540066 DOI: 10.1016/j.jprot.2021.104125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 12/04/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
MARCH8 is an E3 ligase, primarily involved in immune-modulation. Recently, we reported its aberrant expression in human esophageal squamous cell carcinoma. However, exact mechanisms by which it regulates cancer have been poorly understood. We applied high-throughput quantitative proteomics approach to identify downstream protein targets of MARCH8. Silencing of endogenous MARCH8 in ESCC cells followed by LC-MS/MS analysis led to identification of 1,029 unique proteins showing altered expression post MARCH8 knockdown. Several previously reported MARCH8 target proteins viz. TFR1, syntaxin-4, e-cadherin and CD44 were found to be upregulated. Furthermore, new putative targets of MARCH8, including β2M, were identified in the present study. We demonstrated that MARCH8 interacts with and ubiquitinates CDH1 and β2M. Inhibiting proteasome activity with MG132 prevented CDH1 and β2M degradation, indicating that MARCH8 might be targeting CDH1 and β2M for proteasomal degradation. Further, loss of β2M and CDH1 expression significantly and inversely correlated with MARCH8 expression in ESCC tissues (r = -0.737 and - 0.651, respectively; p < 0.01). In conclusion, our present study has led to identification of new targets of MARCH8 and suggests the role of MARCH8 in regulating CDH1 and β2M turnover in esophageal cancer cells. SIGNIFICANCE: The use of quantitative proteomics carried out has led to the recognition of new targets of MARCH8. The present study gives a broad understanding of the molecular remodeling arising in the ESCC after MARCH8 knockdown. The study also solidifies the idea that role of MARCH8 is not just limited to immunomodulation as silencing of MARCH8 affects various other processes such as protein processing and localization. This study might help in understanding the regulation of MARCH8 in ESCCs and the mechanism by which MARCH8 might be facilitating cancer cells to evade immune surveillance.
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Affiliation(s)
- Shivam Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector-16(C), Dwarka, New Delhi 110078, India
| | - Arjumand Bano
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector-16(C), Dwarka, New Delhi 110078, India
| | - Anoop Saraya
- Department of Gastroenterology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Prasenjit Das
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rinu Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector-16(C), Dwarka, New Delhi 110078, India.
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9
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Ng SS, Park JE, Meng W, Chen CP, Kalaria RN, McCarthy NE, Sze SK. Pulsed SILAM Reveals In Vivo Dynamics of Murine Brain Protein Translation. ACS OMEGA 2020; 5:13528-13540. [PMID: 32566817 PMCID: PMC7301365 DOI: 10.1021/acsomega.9b04439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Identification of proteins that are synthesized de novo in response to specific microenvironmental cues is critical for understanding molecular mechanisms that underpin vital physiological processes and pathologies. Here, we report that a brief period of SILAM (Stable Isotope Labeling of Mammals) diet enables the determination of biological functions corresponding to actively translating proteins in the mouse brain. Our results demonstrate that the synapse, dendrite, and myelin sheath are highly active neuronal structures that display rapid protein synthesis, producing key mediators of chemical signaling as well as nutrient sensing, lipid metabolism, and amyloid precursor protein processing/stability. Together, these findings confirm that protein metabolic activity varies significantly between brain functional units in vivo. Our data indicate that pulsed SILAM approaches can unravel complex protein expression dynamics in the murine brain and identify active synthetic pathways and associated functions that are likely impaired in neurodegenerative diseases.
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Affiliation(s)
- Ser Sue Ng
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
| | - Jung Eun Park
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
| | - Wei Meng
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
| | - Christopher P. Chen
- Memory,
Aging and Cognition Centre, National University
Health System, 1E Kent
Ridge Road, 119228 Singapore
- Department
of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD3, 16 Medical Drive, 117600 Singapore
| | - Raj N. Kalaria
- Institute
of Neuroscience, Campus for Ageing and Vitality, Newcastle University, Newcastle
upon Tyne NE4 5PL, U.K.
| | - Neil E. McCarthy
- Centre
for Immunobiology, The Blizard Institute, Bart’s and The London
School of Medicine and Dentistry, Queen
Mary University of London, 4 Newark St, London E1
2AT, U.K.
| | - Siu Kwan Sze
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
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10
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Tian J, Shi Y, Nai S, Geng Q, Zhang L, Wei GH, Xu X, Li J. Ataxin-10 is involved in Golgi membrane dynamics. J Genet Genomics 2017; 44:549-552. [PMID: 29169923 DOI: 10.1016/j.jgg.2017.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/18/2022]
Affiliation(s)
- Jie Tian
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China; Molecular & Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Yingxin Shi
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Shanshan Nai
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Leiliang Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu 90014, Finland
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China; Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen 518060, China.
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China.
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11
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Maass PG, Glažar P, Memczak S, Dittmar G, Hollfinger I, Schreyer L, Sauer AV, Toka O, Aiuti A, Luft FC, Rajewsky N. A map of human circular RNAs in clinically relevant tissues. J Mol Med (Berl) 2017; 95:1179-1189. [PMID: 28842720 PMCID: PMC5660143 DOI: 10.1007/s00109-017-1582-9] [Citation(s) in RCA: 252] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 08/03/2017] [Accepted: 08/18/2017] [Indexed: 01/09/2023]
Abstract
Abstract Cellular circular RNAs (circRNAs) are generated by head-to-tail splicing and are present in all multicellular organisms studied so far. Recently, circRNAs have emerged as a large class of RNA which can function as post-transcriptional regulators. It has also been shown that many circRNAs are tissue- and stage-specifically expressed. Moreover, the unusual stability and expression specificity make circRNAs important candidates for clinical biomarker research. Here, we present a circRNA expression resource of 20 human tissues highly relevant to disease-related research: vascular smooth muscle cells (VSMCs), human umbilical vein cells (HUVECs), artery endothelial cells (HUAECs), atrium, vena cava, neutrophils, platelets, cerebral cortex, placenta, and samples from mesenchymal stem cell differentiation. In eight different samples from a single donor, we found highly tissue-specific circRNA expression. Circular-to-linear RNA ratios revealed that many circRNAs were expressed higher than their linear host transcripts. Among the 71 validated circRNAs, we noticed potential biomarkers. In adenosine deaminase-deficient, severe combined immunodeficiency (ADA-SCID) patients and in Wiskott-Aldrich-Syndrome (WAS) patients’ samples, we found evidence for differential circRNA expression of genes that are involved in the molecular pathogenesis of both phenotypes. Our findings underscore the need to assess circRNAs in mechanisms of human disease. Key messages circRNA resource catalog of 20 clinically relevant tissues. circRNA expression is highly tissue-specific. circRNA transcripts are often more abundant than their linear host RNAs. circRNAs can be differentially expressed in disease-associated genes.
Electronic supplementary material The online version of this article (10.1007/s00109-017-1582-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philipp G Maass
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany. .,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany. .,Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA, 02138, USA.
| | - Petar Glažar
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Sebastian Memczak
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Irene Hollfinger
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Luisa Schreyer
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Aisha V Sauer
- Scientific Institute HS Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), 20132, Milan, Italy
| | - Okan Toka
- Department of Pediatric Cardiology, Children's Hospital, Friedrich-Alexander University Erlangen, Loschge Strasse 15, 91054, Erlangen, Germany.,The German Registry for Congenital Heart Defects, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Alessandro Aiuti
- Scientific Institute HS Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), 20132, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Nikolaus Rajewsky
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
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Giannakopoulos A, Fryssira H, Tzetis M, Xaidara A, Kanaka-Gantenbein C. Central precocious puberty in a boy with 22q13 deletion syndrome and NOTCH-1 gene duplication. J Pediatr Endocrinol Metab 2016; 29:1307-1311. [PMID: 27235670 DOI: 10.1515/jpem-2015-0484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/19/2016] [Indexed: 12/25/2022]
Abstract
The 22q13 deletion syndrome or Phelan-McDermid syndrome is a neurodevelopmental disorder associated with developmental delay, hypotonia, delayed or absent speech, autistic-like behavior, normal to accelerated growth and dysmorphic faces. We report the occurrence of central precocious puberty in a boy diagnosed with Phelan-McDermid syndrome. At the age of 1 year, our patient presented with increased testicular volume for his age, bone age advancement and growth acceleration. Stimulated gonadotropin levels demonstrated a premature activation of the hypothalamic-pituitary-gonadal (HPG) axis. Central precocious puberty was treated with gonadotropin-releasing hormone (GnRH) analog. Molecular diagnosis with array-comparative genomic hybridization (CGH) revealed a major deletion of 5.8 Mb at the 22q13 chromosomal region and a 25 kb duplication at the 9q34.3 region that included the NOTCH-1 gene. On the background of 22q13 deletion syndrome and data from animals on the effect of abnormal NOTCH-1 gene expression on kisspeptin neuron formation, we discuss the probable role of Notch signaling in the premature activation of the HPG axis.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/drug therapy
- Abnormalities, Multiple/genetics
- Chromosome Deletion
- Chromosome Disorders/diagnosis
- Chromosomes, Human, Pair 22
- Chromosomes, Human, Pair 9
- Cytogenetic Analysis
- Delayed Diagnosis
- Drug Monitoring
- Gene Duplication
- Gonadotropin-Releasing Hormone/adverse effects
- Gonadotropin-Releasing Hormone/analogs & derivatives
- Gonadotropin-Releasing Hormone/therapeutic use
- Greece
- Humans
- Infant, Newborn
- Male
- Puberty, Precocious/diagnosis
- Puberty, Precocious/drug therapy
- Puberty, Precocious/genetics
- Receptor, Notch1/genetics
- Reproductive Control Agents/adverse effects
- Reproductive Control Agents/therapeutic use
- Treatment Outcome
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Tian J, Tian C, Ding Y, Li Z, Geng Q, Xiahou Z, Wang J, Hou W, Liao J, Dong MQ, Xu X, Li J. Aurora B-dependent phosphorylation of Ataxin-10 promotes the interaction between Ataxin-10 and Plk1 in cytokinesis. Sci Rep 2015; 5:8360. [PMID: 25666058 PMCID: PMC4322367 DOI: 10.1038/srep08360] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/19/2015] [Indexed: 11/09/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurologic disorder caused by ATTCT expansion in the ATXN10 gene. Previous investigations have identified that depletion of Ataxin-10, the gene product, leads to cellular apoptosis and cytokinesis failure. Herein we identify the mitotic kinase Aurora B as an Ataxin-10 interacting partner. Aurora B interacts with and phosphorylates Ataxin-10 at S12, as evidenced by in vitro kinase and mass spectrometry analysis. Both endogenous and S12-phosphorylated Ataxin-10 localizes to the midbody during cytokinesis, and cytokinetic defects induced by inhibition of ATXN10 expression is not rescued by the S12A mutant. Inhibition of Aurora B or expression of the S12A mutant renders reduced interaction between Ataxin-10 and polo-like kinase 1 (Plk1), a kinase previously identified to regulate Ataxin-10 in cytokinesis. Taken together, we propose a model that Aurora B phosphorylates Ataxin-10 at S12 to promote the interaction between Ataxin-10 and Plk1 in cytokinesis. These findings identify an Aurora B-dependent mechanism that implicates Ataxin-10 in cytokinesis.
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Affiliation(s)
- Jie Tian
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Chuan Tian
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhe Li
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhikai Xiahou
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jue Wang
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Wenya Hou
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ji Liao
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
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Abstract
Heredoataxias are a group of genetic disorders with a cerebellar syndrome as the leading clinical manifestation. The current classification distinguishes heredoataxias according to the trait of inheritance into autosomal dominant, autosomal recessive, X-linked, and maternally inherited heredoataxias. The autosomal dominant heredoataxias are separated into spinocerebellar ataxias (SCA1-8, 10-15, 17-23, 25-30, and dentato-rubro-pallido-luysian atrophy), episodic ataxias (EA1-7), and autosomal dominant mitochondrial heredoataxias (Leigh syndrome, MIRAS, ADOAD, and AD-CPEO). The autosomal recessive ataxias are separated into Friedreich ataxia, ataxia due to vitamin E deficiency, ataxia due to Abeta-lipoproteinemia, Refsum disease, late-onset Tay-Sachs disease, cerebrotendineous xanthomatosis, spinocerebellar ataxia with axonal neuropathy, ataxia telangiectasia, ataxia telangiectasia-like disorder, ataxia with oculomotor apraxia 1 and 2, spastic ataxia of Charlevoix-Saguenay, Cayman ataxia, Marinesco-Sjögren syndrome, and autosomal recessive mitochondrial ataxias (AR-CPEO, SANDO, SCAE, AHS, IOSCA, MEMSA, LBSL CoQ-deficiency, PDC-deficiency). Only two of the heredoataxias, fragile X/tremor/ataxia syndrome, and XLSA/A are transmitted via an X-linked trait. Maternally inherited heredoataxias are due to point mutations in genes encoding for tRNAs, rRNAs, respiratory chain subunits or single large scale deletions/duplications of the mitochondrial DNA and include MELAS, MERRF, KSS, PS, MILS, NARP, and non-syndromic mitochondrial disorders. Treatment of heredoataxias is symptomatic and supportive and may have a beneficial effect in single patients.**Please see page 424 for abbreviation list.
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15
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Ma L, Aslanian A, Sun H, Jin M, Shi Y, Yates JR, Hunter T. Identification of small ubiquitin-like modifier substrates with diverse functions using the Xenopus egg extract system. Mol Cell Proteomics 2014; 13:1659-75. [PMID: 24797264 DOI: 10.1074/mcp.m113.035626] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Post-translational modification by SUMO is a highly conserved pathway in eukaryotes that plays very important regulatory roles in many cellular processes. Deregulation of the SUMO pathway contributes to the development and progression of many diseases including cancer. Therefore, identifying additional SUMO substrates and studying how their cellular and biological functions are regulated by sumoylation should provide new insights. Our studies showed that sumoylation activity was significant in Xenopus egg extracts, and that a high level of sumoylation was associated with sperm chromatin when SUMO was incubated with Xenopus egg extracts. By isolating SUMO-conjugated substrates using His-tagged SUMO1 or SUMO2 proteins under denaturing conditions, we identified 346 proteins by mass spectrometry analysis that were not present in control pull-downs. Among them, 167 proteins were identified from interphase egg extracts, 86 proteins from mitotic phase egg extracts, and 93 proteins from both. Thirty-three proteins were pulled down by SUMO1, 85 proteins by SUMO2, and 228 proteins by both. We validated the sumoylation of five candidates, CKB, ATXN10, BTF3, HABP4, and BZW1, by co-transfecting them along with SUMO in HEK293T cells. Gene ontology analysis showed that SUMO substrates identified in this study were involved in diverse biological processes. Additionally, SUMO substrates identified from different cell cycle stages or pulled down by different SUMO homologs were enriched for distinct cellular components and functional categories. Our results comprehensively profile the sumoylation occurring in the Xenopus egg extract system.
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Affiliation(s)
- Li Ma
- From the ‡Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Aaron Aslanian
- From the ‡Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA; §Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Huaiyu Sun
- From the ‡Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Mingji Jin
- From the ‡Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Yu Shi
- From the ‡Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - John R Yates
- §Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Tony Hunter
- From the ‡Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA;
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16
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Kobilo T, Guerrieri D, Zhang Y, Collica SC, Becker KG, van Praag H. AMPK agonist AICAR improves cognition and motor coordination in young and aged mice. Learn Mem 2014; 21:119-26. [PMID: 24443745 PMCID: PMC3895225 DOI: 10.1101/lm.033332.113] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Normal aging can result in a decline of memory and muscle function. Exercise may prevent or delay these changes. However, aging-associated frailty can preclude physical activity. In young sedentary animals, pharmacological activation of AMP-activated protein kinase (AMPK), a transcriptional regulator important for muscle physiology, enhanced spatial memory function, and endurance. In the present study we investigated effects of AMPK agonist 5-aminoimidazole-4-carboxamide riboside (AICAR) on memory and motor function in young (5- to 7-wk-old) and aged (23-mo-old) female C57Bl/6 mice, and in young (4- to 6-wk-old) transgenic mice with muscle-specific mutated AMPK α2-subunit (AMPK-DN). Mice were injected with AICAR (500 mg/kg) for 3–14 d. Two weeks thereafter animals were tested in the Morris water maze, rotarod, and open field. Improved water maze performance and motor function were observed, albeit at longer duration of administration, in aged (14-d AICAR) than in young (3-d AICAR) mice. In the AMPK-DN mice, the compound did not enhance behavior, providing support for a muscle-mediated mechanism. In addition, microarray analysis of muscle and hippocampal tissue derived from aged mice treated with AICAR revealed changes in gene expression in both tissues, which correlated with behavioral effects in a dose-dependent manner. Pronounced up-regulation of mitochondrial genes in muscle was observed. In the hippocampus, genes relevant to neuronal development and plasticity were enriched. Altogether, endurance-related factors may mediate both muscle and brain health in aging, and could play a role in new therapeutic interventions.
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Affiliation(s)
- Tali Kobilo
- Neuroplasticity and Behavior Unit, Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
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17
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Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J. Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. PLoS One 2013; 8:e76194. [PMID: 24098440 PMCID: PMC3789819 DOI: 10.1371/journal.pone.0076194] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/20/2013] [Indexed: 12/03/2022] Open
Abstract
Recent findings have revealed the complexity of the transcriptional landscape in mammalian cells. One recently described class of novel transcripts are the Cytoplasmic Intron-sequence Retaining Transcripts (CIRTs), hypothesized to confer post-transcriptional regulatory function. For instance, the neuronal CIRT KCNMA1i16 contributes to the firing properties of hippocampal neurons. Intronic sub-sequence retention within IL1-β mRNA in anucleate platelets has been implicated in activity-dependent splicing and translation. In a recent study, we showed CIRTs harbor functional SINE ID elements which are hypothesized to mediate dendritic localization in neurons. Based on these studies and others, we hypothesized that CIRTs may be present in a broad set of transcripts and comprise novel signals for post-transcriptional regulation. We carried out a transcriptome-wide survey of CIRTs by sequencing micro-dissected subcellular RNA fractions. We sequenced two batches of 150-300 individually dissected dendrites from primary cultures of hippocampal neurons in rat and three batches from mouse hippocampal neurons. After statistical processing to minimize artifacts, we found a broad prevalence of CIRTs in the neurons in both species (44-60% of the expressed transcripts). The sequence patterns, including stereotypical length, biased inclusion of specific introns, and intron-intron junctions, suggested CIRT-specific nuclear processing. Our analysis also suggested that these cytoplasmic intron-sequence retaining transcripts may serve as a primary transcript for ncRNAs. Our results show that retaining intronic sequences is not isolated to a few loci but may be a genome-wide phenomenon for embedding functional signals within certain mRNA. The results hypothesize a novel source of cis-sequences for post-transcriptional regulation. Our results hypothesize two potentially novel splicing pathways: one, within the nucleus for CIRT biogenesis; and another, within the cytoplasm for removing CIRT sequences before translation. We also speculate that release of CIRT sequences prior to translation may form RNA-based signals within the cell potentially comprising a novel class of signaling pathways.
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Affiliation(s)
- Mugdha Khaladkar
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Peter T. Buckley
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Miler T. Lee
- Department of Genetics, Yale University, New Haven, Connecticut, United States of America
| | - Chantal Francis
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mitra M. Eghbal
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tina Chuong
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sangita Suresh
- Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Bernhard Kuhn
- Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - James Eberwine
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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18
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Cheng X, Gan L, Zhao J, Chen M, Liu Y, Wang Y. Changes in Ataxin-10 Expression after Sciatic Nerve Crush in Adult Rats. Neurochem Res 2013; 38:1013-21. [DOI: 10.1007/s11064-013-1011-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/19/2013] [Accepted: 02/23/2013] [Indexed: 01/22/2023]
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Transgenic models of spinocerebellar ataxia type 10: modeling a repeat expansion disorder. Genes (Basel) 2012; 3:481-491. [PMID: 24533179 PMCID: PMC3899997 DOI: 10.3390/genes3030481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 01/01/2023] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disease with a spectrum of phenotypes. SCA10 is caused by a pentanucleotide repeat expansion of the ATTCT motif within intron 9 of ATAXIN 10 (ATXN10). Patients present with cerebellar ataxia; however, a subset also develops epileptic seizures which significantly contribute to the morbidity and mortality of the disease. Past research from our lab has demonstrated that epileptic SCA10 patients predominantly originate from or have ancestral ties to Mexico. In addition, a large proportion of epileptic SCA10 patients carry repeat interruptions within their SCA10 expansion. This paper outlines the variability in SCA10 phenotypes and our attempts to model these phenotypes using transgenic mouse models and highlights the benefits of using a transgenic model organism to understand the pathological mechanisms of a human disease.
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20
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21
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Affiliation(s)
- Tetsuo Ashizawa
- Department of Neurology, Evelyn & WIlliam L. McKinght Brain Institute, University of Florida, Gainesville, FL, USA.
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22
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White M, Xia G, Gao R, Wakamiya M, Sarkar PS, McFarland K, Ashizawa T. Transgenic mice with SCA10 pentanucleotide repeats show motor phenotype and susceptibility to seizure: a toxic RNA gain-of-function model. J Neurosci Res 2011; 90:706-14. [PMID: 22065565 DOI: 10.1002/jnr.22786] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 08/04/2011] [Accepted: 08/16/2011] [Indexed: 11/11/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disorder manifested by ataxia and seizure. SCA10 is caused by a large expansion of an intronic ATTCT pentanucleotide repeat in the ATXN10 gene. We have recently postulated a toxic RNA-mediated gain of function in the pathogenesis of spinal cerebellar ataxia type 10 (SCA10). The spliced intron-9 RNA containing the expanded AUUCU repeat aggregates in SCA10 cells and sequesters hnRNP K. hnRNP K sequestration triggers the translocation of protein kinase Cδ (PKCδ) to mitochondria, leading to activation of caspase-3 and apoptosis. To confirm the toxic RNA-mediated gain of function, we generated a new transgenic mouse model in which the expanded pentanucleotide repeats are constructed in the 3'-untranslated region (3'UTR) to ensure transcription without translation of the repeat. We constructed an artificial transgene containing the SCA10 (ATTCT)(500) track within the 3'UTR of the LacZ gene driven by the rat prion promoter (PrP) and used this to generate a new transgenic mouse model for SCA10. We then examined these mice for neurological phenotypes and histopathological, molecular, and cellular changes. The transgenic mice showed irregular gait and increased seizure susceptibility at the age of 6 months, resembling the clinical phenotype of SCA10. The cerebral cortex, hippocampus, and pontine nuclei showed neuronal loss. The brains of these animals also showed molecular and cellular changes similar to those previously found in an SCA10 cell model. Expression of the expanded SCA10 AUUCU repeat within the 3'UTR of a gene results in neuronal loss with associated gait abnormalities and increased seizure susceptibility phenotypes, which resemble those seen in SCA10 patients. Moreover, these results bolster the idea that the SCA10 disease mechanism is mediated by a toxic RNA gain-of-function mutation of the expanded AUUCU repeat.
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Affiliation(s)
- Misti White
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, USA
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23
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Rovillain E, Mansfield L, Lord CJ, Ashworth A, Jat PS. An RNA interference screen for identifying downstream effectors of the p53 and pRB tumour suppressor pathways involved in senescence. BMC Genomics 2011; 12:355. [PMID: 21740549 PMCID: PMC3161017 DOI: 10.1186/1471-2164-12-355] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 07/08/2011] [Indexed: 12/28/2022] Open
Abstract
Background Cellular senescence is an irreversible cell cycle arrest that normal cells undergo in response to progressive shortening of telomeres, changes in telomeric structure, oncogene activation or oxidative stress and acts as an important tumour suppressor mechanism. Results To identify the downstream effectors of the p53-p21 and p16-pRB tumour suppressor pathways crucial for mediating entry into senescence, we have carried out a loss-of-function RNA interference screen in conditionally immortalised human fibroblasts that can be induced to rapidly undergo senescence, whereas in primary cultures senescence is stochastic and occurs asynchronously. These cells are immortal but undergo a rapid irreversible arrest upon activation of the p53-p21 and p16-pRB pathways that can be readily bypassed upon their inactivation. The primary screen identified 112 known genes including p53 and another 29 shRNAmirs targetting as yet unidentified loci. Comparison of these known targets with genes known to be up-regulated upon senescence in these cells, by micro-array expression profiling, identified 4 common genes TMEM9B, ATXN10, LAYN and LTBP2/3. Direct silencing of these common genes, using lentiviral shRNAmirs, bypassed senescence in the conditionally immortalised cells. Conclusion The senescence bypass screen identified TMEM9B, ATXN10, LAYN and LTBP2/3 as novel downstream effectors of the p53-p21 and p16-pRB tumour suppressor pathways. Although none of them has previously been linked to cellular senescence, TMEM9B has been suggested to be an upstream activator of NF-κB signalling which has been found to have a causal role in promoting senescence. Future studies will focus on determining on how many of the other primary hits also have a casual role in senescence and what is the mechanism of action.
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Affiliation(s)
- Emilie Rovillain
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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Teive HAG, Munhoz RP, Arruda WO, Raskin S, Werneck LC, Ashizawa T. Spinocerebellar ataxia type 10 - A review. Parkinsonism Relat Disord 2011; 17:655-61. [PMID: 21531163 DOI: 10.1016/j.parkreldis.2011.04.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 04/02/2011] [Accepted: 04/03/2011] [Indexed: 10/18/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant inherited ataxia caused by an expanded ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene, on chromosome 22q13.3. SCA10 represents a rare form of SCA, until now only described in Latin America, particularly in Mexico, Brazil, Argentina and Venezuela. In Mexico and Brazil SCA10 represents the second most common type of autosomal dominant cerebellar ataxia. The phenotype described in Mexico, is characterized by the association of cerebellar ataxia with epilepsy, while in Brazil the SCA10 phenotype is that of a pure cerebellar ataxia. As yet unidentified genotypic variables may account for this phenotypic difference.
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Affiliation(s)
- Hélio A G Teive
- Movement Disorders Unit, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, PR, Brazil.
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Wilde IB, Brack M, Winget JM, Mayor T. Proteomic characterization of aggregating proteins after the inhibition of the ubiquitin proteasome system. J Proteome Res 2011; 10:1062-72. [PMID: 21204586 DOI: 10.1021/pr1008543] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein aggregation, which is associated with the impairment of the ubiquitin proteasome system, is a hallmark of many neurodegenerative diseases. To better understand the contribution of proteasome inhibition in aggregation, we analyzed which proteins may potentially localize in chemically induced aggregates in human neuroblastoma tissue culture cells. We enriched for proteins in high-density structures by using a sucrose gradient in combination with stable isotope labeling with amino acids in cell culture (SILAC). The quantitative analysis allowed us to distinguish which proteins were specifically affected by the proteasome inhibition. We identified 642 potentially aggregating proteins, including the p62/sequestosome 1 and NBR1 ubiquitin-binding proteins involved in aggregation. We also identified the ubiquitin-associated protein 2 like (UBAP2L). We verified that it cofractionated with ubiquitin in the high-density fraction and that it was colocalized in the ubiquitin-containing aggregates after proteasome inhibition. In addition, we identified several chaperone proteins and used data from protein interaction networks to show that they potentially interact with distinct subgroups of proteins within the aggregating structures. Several other proteins associated with neurodegenerative diseases, like UCHL1, were identified, further underlining the potential of our analysis to better understand the aggregation process and proteotoxic stress caused by proteasome inhibition.
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Affiliation(s)
- Inga B Wilde
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, V6T 1Z4, Canada
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26
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Boulisfane N, Choleza M, Rage F, Neel H, Soret J, Bordonné R. Impaired minor tri-snRNP assembly generates differential splicing defects of U12-type introns in lymphoblasts derived from a type I SMA patient. Hum Mol Genet 2010; 20:641-8. [PMID: 21098506 DOI: 10.1093/hmg/ddq508] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The survival of motor neuron (SMN) protein is essential for cytoplasmic assembly of spliceosomal snRNPs. Although the normal proportion of endogenous snRNAs is unevenly altered in spinal muscular atrophy (SMA) tissues, the biogenesis of individual snRNPs is not dramatically affected in SMN-deficient cells. The SMN protein is also required for normal Cajal body (CB) formation, but the functional consequences of CB disruption upon SMN deficiency have not yet been analyzed at the level of macromolecular snRNPs assembly. Here, we show that the SMN protein is required for tri-snRNPs formation and that the level of the minor U4atac/U6atac/U5 tri-snRNPs is dramatically decreased in lymphoblasts derived from a patient suffering from a severe form of SMA. We found also that splicing of some, but not all, minor introns is inhibited in these cells, demonstrating links between SMN deficiency and differential alterations of splicing events mediated by the minor spliceosome. Our results suggest that SMA might result from the inefficient splicing of one or only a few pre-mRNAs carrying minor introns and coding for proteins required for motor neurons function and/or organization.
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Affiliation(s)
- Nawal Boulisfane
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS UMR 5535/IFR122, Université Montpellier I and II,1919 route de Mende, 34293 Montpellier Cedex 5, France
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White MC, Gao R, Xu W, Mandal SM, Lim JG, Hazra TK, Wakamiya M, Edwards SF, Raskin S, Teive HAG, Zoghbi HY, Sarkar PS, Ashizawa T. Inactivation of hnRNP K by expanded intronic AUUCU repeat induces apoptosis via translocation of PKCdelta to mitochondria in spinocerebellar ataxia 10. PLoS Genet 2010; 6:e1000984. [PMID: 20548952 PMCID: PMC2883596 DOI: 10.1371/journal.pgen.1000984] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 05/12/2010] [Indexed: 01/20/2023] Open
Abstract
We have identified a large expansion of an ATTCT repeat within intron 9 of ATXN10 on chromosome 22q13.31 as the genetic mutation of spinocerebellar ataxia type 10 (SCA10). Our subsequent studies indicated that neither a gain nor a loss of function of ataxin 10 is likely the major pathogenic mechanism of SCA10. Here, using SCA10 cells, and transfected cells and transgenic mouse brain expressing expanded intronic AUUCU repeats as disease models, we show evidence for a key pathogenic molecular mechanism of SCA10. First, we studied the fate of the mutant repeat RNA by in situ hybridization. A Cy3-(AGAAU)10 riboprobe detected expanded AUUCU repeats aggregated in foci in SCA10 cells. Pull-down and co-immunoprecipitation data suggested that expanded AUUCU repeats within the spliced intronic sequence strongly bind to hnRNP K. Co-localization of hnRNP K and the AUUCU repeat aggregates in the transgenic mouse brain and transfected cells confirmed this interaction. To examine the impact of this interaction on hnRNP K function, we performed RT–PCR analysis of a splicing-regulatory target of hnRNP K, and found diminished hnRNP K activity in SCA10 cells. Cells expressing expanded AUUCU repeats underwent apoptosis, which accompanied massive translocation of PKCδ to mitochondria and activation of caspase 3. Importantly, siRNA–mediated hnRNP K deficiency also caused the same apoptotic event in otherwise normal cells, and over-expression of hnRNP K rescued cells expressing expanded AUUCU repeats from apoptosis, suggesting that the loss of function of hnRNP K plays a key role in cell death of SCA10. These results suggest that the expanded AUUCU–repeat in the intronic RNA undergoes normal transcription and splicing, but causes apoptosis via an activation cascade involving a loss of hnRNP K activities, massive translocation of PKCδ to mitochondria, and caspase 3 activation. In an earlier study, we showed that the mutation of spinocerebellar ataxia 10 (SCA10) is an enormous expansion of a gene segment, which contains a tandemly repeated 5-base (ATTCT) unit. Since SCA10 is the only known human disease that is proven to be caused by 5-base repeat expansion, it is important to learn how this novel class of mutation causes the disease. We found that the mutation produces an expanded RNA repeat, which aberrantly accumulates in SCA10 cells and interacts with a major RNA–binding protein. When we expressed expanded RNA repeats or decreased the RNA–binding protein level in cultured cells, either of these manipulations produced a specific type of cell death that is associated with a massive transfer of a key enzyme called protein kinase C delta to mitochondria. We also showed that either blocking the expanded AUUCU repeat or replenishing hnRNP K rescues cells from the cell death induced by the SCA10 mutation. Together, we conclude that the mutant RNA inactivates hnRNP K and kills cells by triggering the specific cell-death mechanism. Our data provide important clues for therapeutic intervention in SCA10.
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Affiliation(s)
- Misti C. White
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rui Gao
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Weidong Xu
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Santi M. Mandal
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jung G. Lim
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maki Wakamiya
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sharon F. Edwards
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Salmo Raskin
- Center for Health and Biological Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | | | - Huda Y. Zoghbi
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
| | - Partha S. Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Neurology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Keren B, Jacquette A, Depienne C, Leite P, Durr A, Carpentier W, Benyahia B, Ponsot G, Soubrier F, Brice A, Héron D. Evidence against haploinsuffiency of human ataxin 10 as a cause of spinocerebellar ataxia type 10. Neurogenetics 2009; 11:273-4. [PMID: 19936807 DOI: 10.1007/s10048-009-0227-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 10/23/2009] [Indexed: 11/29/2022]
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Kippert F, Gerloff DL. Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH. PLoS One 2009; 4:e7148. [PMID: 19777061 PMCID: PMC2744927 DOI: 10.1371/journal.pone.0007148] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Accepted: 08/21/2009] [Indexed: 11/19/2022] Open
Abstract
Background HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. Methodology and Principal Findings Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. Significance A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high sensitivity at a low false positive rate and will therefore greatly enhance the accuracy of predictions of HEAT and ARM domains.
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Affiliation(s)
| | - Dietlind L. Gerloff
- Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (FK); (DLG)
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Söker T, Dalke C, Puk O, Floss T, Becker L, Bolle I, Favor J, Hans W, Hölter SM, Horsch M, Kallnik M, Kling E, Moerth C, Schrewe A, Stigloher C, Topp S, Gailus-Durner V, Naton B, Beckers J, Fuchs H, Ivandic B, Klopstock T, Schulz H, Wolf E, Wurst W, Bally-Cuif L, de Angelis MH, Graw J. Pleiotropic effects in Eya3 knockout mice. BMC DEVELOPMENTAL BIOLOGY 2008; 8:118. [PMID: 19102749 PMCID: PMC2653502 DOI: 10.1186/1471-213x-8-118] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 12/22/2008] [Indexed: 01/29/2023]
Abstract
BACKGROUND In Drosophila, mutations in the gene eyes absent (eya) lead to severe defects in eye development. The functions of its mammalian orthologs Eya1-4 are only partially understood and no mouse model exists for Eya3. Therefore, we characterized the phenotype of a new Eya3 knockout mouse mutant. RESULTS Expression analysis of Eya3 by in-situ hybridizations and beta-Gal-staining of Eya3 mutant mice revealed abundant expression of the gene throughout development, e.g. in brain, eyes, heart, somites and limbs suggesting pleiotropic effects of the mutated gene. A similar complex expression pattern was observed also in zebrafish embryos. The phenotype of young adult Eya3 mouse mutants was systematically analyzed within the German Mouse Clinic. There was no obvious defect in the eyes, ears and kidneys of Eya3 mutant mice. Homozygous mutants displayed decreased bone mineral content and shorter body length. In the lung, the tidal volume at rest was decreased, and electrocardiography showed increased JT- and PQ intervals as well as decreased QRS amplitude. Behavioral analysis of the mutants demonstrated a mild increase in exploratory behavior, but decreased locomotor activity and reduced muscle strength. Analysis of differential gene expression revealed 110 regulated genes in heart and brain. Using real-time PCR, we confirmed Nup155 being down regulated in both organs. CONCLUSION The loss of Eya3 in the mouse has no apparent effect on eye development. The wide-spread expression of Eya3 in mouse and zebrafish embryos is in contrast to the restricted expression pattern in Xenopus embryos. The loss of Eya3 in mice leads to a broad spectrum of minor physiological changes. Among them, the mutant mice move less than the wild-type mice and, together with the effects on respiratory, muscle and heart function, the mutation might lead to more severe effects when the mice become older. Therefore, future investigations of Eya3 function should focus on aging mice.
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Affiliation(s)
- Torben Söker
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany.
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Usdin K. The biological effects of simple tandem repeats: lessons from the repeat expansion diseases. Genome Res 2008; 18:1011-9. [PMID: 18593815 DOI: 10.1101/gr.070409.107] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tandem repeats are common features of both prokaryote and eukaryote genomes, where they can be found not only in intergenic regions but also in both the noncoding and coding regions of a variety of different genes. The repeat expansion diseases are a group of human genetic disorders caused by long and highly polymorphic tandem repeats. These disorders provide many examples of the effects that such repeats can have on many biological processes. While repeats in the coding sequence can result in the generation of toxic or malfunctioning proteins, noncoding repeats can also have significant effects including the generation of chromosome fragility, the silencing of the genes in which they are located, the modulation of transcription and translation, and the sequestering of proteins involved in processes such as splicing and cell architecture.
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Affiliation(s)
- Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA.
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Matsuura T. [Molecular and genetic analysis of spinocerebellar ataxia type 10 (SCA10)]. Rinsho Shinkeigaku 2008; 48:1-10. [PMID: 18386626 DOI: 10.5692/clinicalneurol.48.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is a dominantly inherited neurodegenerative disease caused by expansion of the ATTCT pentanucleotide repeat in intron 9 of a novel gene, ATXN10, on chromosome 22q13.3. It is clinically characterized by progressive ataxia, seizures, and anticipation, which can vary within and between families. The length of the expanded ATTCT repeats is highly unstable on paternal transmission and shows a variable degree of somatic and germline instabilty, revealing complex SCA10 genetic mechanisms. Moreover, the purity of the expanded repeat element may be a disease modifier. ATTCT repeats have been recently shown to form unpaired DNA structure and may serve as an aberrant DNA replication origin, potentially contributing to repeat instability and cell death. How this untranslated ATTCT expansion leads to neurodegeneration has been still controversial. We discuss several possible pathogenic mechanisms for SCA10, and growing number of evidence indicates a gain-of-function RNA mechanism, similar to the myotonic dystrophies caused by non-coding CTG or CCTG repeat expansions.
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Affiliation(s)
- Tohru Matsuura
- Division of Neurogenetics and Bioinformatics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine
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Liu G, Bissler JJ, Sinden RR, Leffak M. Unstable spinocerebellar ataxia type 10 (ATTCT*(AGAAT) repeats are associated with aberrant replication at the ATX10 locus and replication origin-dependent expansion at an ectopic site in human cells. Mol Cell Biol 2007; 27:7828-38. [PMID: 17846122 PMCID: PMC2169150 DOI: 10.1128/mcb.01276-07] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is associated with expansion of (ATTCT)n repeats (where n is the number of repeats) within the ataxin 10 (ATX10/E46L) gene. The demonstration that (ATTCT)n tracts can act as DNA unwinding elements (DUEs) in vitro has suggested that aberrant replication origin activity occurs at expanded (ATTCT)n tracts and may lead to their instability. Here, we confirm these predictions. The wild-type ATX10 locus displays inefficient origin activity, but origin activity is elevated at the expanded ATX10 loci in patient-derived cells. To test whether (ATTCT)n tracts can potentiate origin activity, cell lines were constructed that contain ectopic copies of the c-myc replicator in which the essential DUE was replaced by ATX10 DUEs with (ATTCT)n. ATX10 DUEs containing (ATTCT)27 or (ATTCT)48, but not (ATTCT)8 or (ATTCT)13, could substitute functionally for the c-myc DUE, but (ATTCT)48 could not act as an autonomous replicator. Significantly, chimeric c-myc replicators containing ATX10 DUEs displayed length-dependent (ATTCT)n instability. By 250 population doublings, dramatic two- and fourfold length expansions were observed for (ATTCT)27 and (ATTCT)48 but not for (ATTCT)8 or (ATTCT)13. These results implicate replication origin activity as one molecular mechanism associated with the instability of (ATTCT)n tracts that are longer than normal length.
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Affiliation(s)
- Guoqi Liu
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA
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Stangegaard M, Petronis S, Jørgensen AM, Christensen CBV, Dufva M. A biocompatible micro cell culture chamber (microCCC) for the culturing and on-line monitoring of eukaryote cells. LAB ON A CHIP 2006; 6:1045-51. [PMID: 16874376 DOI: 10.1039/b603379b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We have previously shown that a polymeric (PMMA) chip with medium perfusion and integrated heat regulation provides sufficiently precise heat regulation, pH-control and medium exchange to support cell growth for weeks. However, it was unclear how closely the cells cultured in the chip resembled cells cultured in the culture flask. In the current study, gene expression profiles of cells cultured in the chip were compared with gene expression profiles of cells cultured in culture flasks. The results showed that there were only two genes that were differently expressed in cells grown in the cell culture chip compared to cell culture flasks. The cell culture chip could without further modification support cell growth of two other cell lines. Light coming from the microscope lamp during optical recordings of the cells was the only external factor identified, that could have a negative effect on cell survival. Low grade light exposure was however compatible with optical recordings as well as cell viability. These results strongly indicate that a cell culture chip could be constructed that allowed for on-line optical recording of cellular events without affecting the cell culturing condition compared to cell cultured in culture flasks incubated in a dark and CO2 conditioned incubator.
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Affiliation(s)
- Michael Stangegaard
- Department of Micro and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345 east, DK-2800 Kgs. Lyngby, Denmark
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Waragai M, Nagamitsu S, Xu W, Li YJ, Lin X, Ashizawa T. Ataxin 10 induces neuritogenesis via interaction with G-protein beta2 subunit. J Neurosci Res 2006; 83:1170-8. [PMID: 16498633 DOI: 10.1002/jnr.20807] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is a dominantly inherited disorder caused by an intronic ATTCT pentanucleotide repeat expansion. The ATXN10 gene encodes a novel protein, ataxin 10, known previously as E46L, which is widely expressed in the brain. Ataxin 10 deficiency has been shown recently to cause increased apoptosis in primary cerebellar cultures, thus implicated in SCA10 pathogenesis. The biologic functions of ataxin 10 remain largely unknown. By using yeast-two-hybrid screening of a human brain cDNA library, we identified the G-protein beta2 subunit (Gbeta2) as an ataxin 10 binding partner, and the interaction was confirmed by coimmunoprecipitation and colocalization in mammalian cells in culture. Overexpression of ataxin 10 in PC12 cells induced neurite extension and enhanced neuronal differentiation induced by nerve growth factor (NGF). Moreover, coexpression of ataxin 10 and Gbeta2 potently activated the Ras-MAP kinase-Elk-1 cascade. Dominant negative Ras or inhibitor of MEK-1/2 (U0126) aborted this activation, and blocked morphologic changes, whereas inhibition of TrkA receptor by K252a had no effects. Our data suggest that the ataxin 10-Gbeta2 interaction represents a novel mechanism for inducing neuritogenesis in PC12 cells by activating the Ras-MAP kinase-Elk-1 cascade.
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Affiliation(s)
- Masaaki Waragai
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas 77555-0539, USA
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Abstract
Myotonic dystrophy type 1 (DM1) is caused by a CTG expansion mutation located in the 3' untranslated portion of the dystrophica myotonin protein kinase gene. The identification and characterization of RNA-binding proteins that interact with expanded CUG repeats and the discovery that a similar transcribed but untranslated CCTG expansion in an intron causes myotonic dystrophy type 2 (DM2) have uncovered a new type of mechanism in which microsatellite expansion mutations cause disease through an RNA gain-of-function mechanism. This review discusses RNA pathogenesis in DM1 and DM2 and evidence that similar mechanisms may play a role in a growing number of dominant noncoding expansion disorders, including fragile X tremor ataxia syndrome (FXTAS), spinocerebellar ataxia type 8 (SCA8), SCA10, SCA12, and Huntington's disease-like 2 (HDL2).
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Affiliation(s)
- Laura P W Ranum
- Institute of Human Genetics and Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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März P, Stetefeld J, Bendfeldt K, Nitsch C, Reinstein J, Shoeman RL, Dimitriades-Schmutz B, Schwager M, Leiser D, Ozcan S, Otten U, Ozbek S. Ataxin-10 interacts with O-linked beta-N-acetylglucosamine transferase in the brain. J Biol Chem 2006; 281:20263-70. [PMID: 16714295 DOI: 10.1074/jbc.m601563200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Modification by O-GlcNAc involves a growing number of eucaryotic nuclear and cytosolic proteins. Glycosylation of intracellular proteins is a dynamic process that in several cases competes with and acts as a reciprocal modification system to phosphorylation. O-Linked beta-N-acetylglucosamine transferase (OGT) levels are highest in the brain, and neurodegenerative disorders such as Alzheimer disease have been shown to involve abnormally phosphorylated key proteins, probably as a result of hypoglycosylation. Here, we show that the neurodegenerative disease protein ataxin-10 (Atx-10) is associated with cytoplasmic OGT p110 in the brain. In PC12 cells and pancreas, this association is competed by the shorter OGT p78 splice form, which is down-regulated in brain. Overexpression of Atx-10 in PC12 cells resulted in the reconstitution of the Atx-10-OGT p110 complex and enhanced intracellular glycosylation activity. Moreover, in an in vitro enzyme assay using PC12 cell extracts, Atx-10 increased OGT activity 2-fold. These data indicate that Atx-10 might be essential for the maintenance of a critical intracellular glycosylation level and homeostasis in the brain.
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Affiliation(s)
- Pia März
- Institute of Physiology, Pestalozzistr. 20, University of Basel, CH-4056 Basel, Switzerland
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Andrali SS, März P, Ozcan S. Ataxin-10 interacts with O-GlcNAc transferase OGT in pancreatic β cells. Biochem Biophys Res Commun 2005; 337:149-53. [PMID: 16182253 DOI: 10.1016/j.bbrc.2005.09.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Accepted: 09/06/2005] [Indexed: 11/22/2022]
Abstract
Several nuclear and cytoplasmic proteins in metazoans are modified by O-linked N-acetylglucosamine (O-GlcNAc). This modification is dynamic and reversible similar to phosphorylation and is catalyzed by the O-linked GlcNAc transferase (OGT). Hyperglycemia has been shown to increase O-GlcNAc levels in pancreatic beta cells, which appears to interfere with beta-cell function. To obtain a better understanding of the role of O-linked GlcNAc modification in beta cells, we have isolated OGT interacting proteins from a cDNA library made from the mouse insulinoma MIN6 cell line. We describe here the identification of Ataxin-10, encoded by the SCA10 (spinocerebellar ataxia type 10) gene as an OGT interacting protein. Mutations in the SCA10 gene cause progressive cerebellar ataxias and seizures. We demonstrate that SCA10 interacts with OGT in vivo and is modified by O-linked glycosylation in MIN6 cells, suggesting a novel role for the Ataxin-10 protein in pancreatic beta cells.
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Affiliation(s)
- Sreenath S Andrali
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, 741 South Limestone Street, Lexington, KY 40536, USA
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Abstract
Spinocerebellar ataxia type 10 (SCA10) is a dominantly inherited ataxia caused by expansion of ATTCT pentanucleotide repeat in intron 9 of a novel gene, E46L, on chromosome 22q13.3. SCA10 is a complex neurodegenerative condition. Initial studies characterized SCA10 as pure cerebellar ataxia associated with seizures. Recent identification of new SCA10 families revealed more diverse phenotypes, including polyneuropathy, pyramidal signs, cognitive and neuropsychiatric impairment. Moreover, several families manifest with ataxia without seizures. Thus a complete clinical spectrum is emerging. Progress has also been made in understanding the molecular and genetic mechanisms of pathogenesis. The length of expanded ATTCT repeats is variable in different tissues and highly unstable during paternal transmission, revealing complex genetic and pathogenetic processes. Under torsional stress, ATTCT repeats form unpaired DNA structure and may serve as an erroneous DNA replication origin, potentially contributing to repeat instability and aberrant cell cycle entry. E46L is a cytoplasmic protein with unknown function. Reduced expression of E46L in primary neuronal cultures from cerebellum and cortex by small interfering RNAs (siRNAs) caused increased apoptosis, raising the possibility that reduced expression of E46L might also play an important role in SCA10 pathogenesis.
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Affiliation(s)
- Xi Lin
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas 77555, USA
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Jeffries AR, Curran S, Elmslie F, Sharma A, Wenger S, Hummel M, Powell J. Molecular and phenotypic characterization of ring chromosome 22. Am J Med Genet A 2005; 137:139-47. [PMID: 16059935 DOI: 10.1002/ajmg.a.30780] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We performed a phenotype study of 35 individuals (19 males, 16 females) with ring chromosome 22 or r(22) with a mean age of 10 years. In common with other studies, a phenotype of moderate-to-profound learning difficulties and delay or absence of speech affected all individuals with the exception of the case with the smallest deletion. Autistic traits were significantly associated with r(22), as shown by an autism screening questionnaire. Mild and variable dysmorphic features, predominantly craniofacial and distal limb, were observed. Internal organ involvement was uncommon. Even though ring chromosomes are reportedly associated with growth abnormalities, only 2 out of 24 individuals showed evidence of growth failure, while 2 showed accelerated growth. Chromosome 22 long arm deletions, as determined by hemizygosity for informative microsatellite markers, varied from <67 kb to 10.2 Mb in size (or <0.15 to 21% of total chromosome length), with no significant differences in the parental origin of the ring chromosome. Few phenotypic features correlated with deletion size suggesting a critical gene, or genes, of major effect lies close to the telomere. Loss of the SHANK3/PROSAP2 gene has been proposed to be responsible for the main neurological developmental deficits observed in 22q13 monosomies. This study supports this candidate gene by identifying a phenotypically normal r(22) individual whose ring chromosome does not disrupt SHANK3. All other r(22) individuals were hemizygous for SHANK3, and we propose it to be a candidate gene for autism or abnormal brain development.
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Affiliation(s)
- Aaron R Jeffries
- Department of Neuroscience, Institute of Psychiatry, Denmark Hill, London SE5 8AF, United Kingdom
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