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Adesanya O, Das D, Kalsotra A. Emerging roles of RNA-binding proteins in fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1840. [PMID: 38613185 PMCID: PMC11018357 DOI: 10.1002/wrna.1840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
A rampant and urgent global health issue of the 21st century is the emergence and progression of fatty liver disease (FLD), including alcoholic fatty liver disease and the more heterogenous metabolism-associated (or non-alcoholic) fatty liver disease (MAFLD/NAFLD) phenotypes. These conditions manifest as disease spectra, progressing from benign hepatic steatosis to symptomatic steatohepatitis, cirrhosis, and, ultimately, hepatocellular carcinoma. With numerous intricately regulated molecular pathways implicated in its pathophysiology, recent data have emphasized the critical roles of RNA-binding proteins (RBPs) in the onset and development of FLD. They regulate gene transcription and post-transcriptional processes, including pre-mRNA splicing, capping, and polyadenylation, as well as mature mRNA transport, stability, and translation. RBP dysfunction at every point along the mRNA life cycle has been associated with altered lipid metabolism and cellular stress response, resulting in hepatic inflammation and fibrosis. Here, we discuss the current understanding of the role of RBPs in the post-transcriptional processes associated with FLD and highlight the possible and emerging therapeutic strategies leveraging RBP function for FLD treatment. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
| | - Diptatanu Das
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
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Shkreta L, Delannoy A, Salvetti A, Chabot B. SRSF10: an atypical splicing regulator with critical roles in stress response, organ development, and viral replication. RNA (NEW YORK, N.Y.) 2021; 27:1302-1317. [PMID: 34315816 PMCID: PMC8522700 DOI: 10.1261/rna.078879.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Serine/arginine splicing factor 10 (SRSF10) is a member of the family of mammalian splicing regulators known as SR proteins. Like several of its SR siblings, the SRSF10 protein is composed of an RNA binding domain (RRM) and of arginine and serine-rich auxiliary domains (RS) that guide interactions with other proteins. The phosphorylation status of SRSF10 is of paramount importance for its activity and is subjected to changes during mitosis, heat-shock, and DNA damage. SRSF10 overexpression has functional consequences in a growing list of cancers. By controlling the alternative splicing of specific transcripts, SRSF10 has also been implicated in glucose, fat, and cholesterol metabolism, in the development of the embryonic heart, and in neurological processes. SRSF10 is also important for the proper expression and processing of HIV-1 and other viral transcripts. We discuss how SRSF10 could become a potentially appealing therapeutic target to combat cancer and viral infections.
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Affiliation(s)
- Lulzim Shkreta
- RNA group, Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8
| | - Aurélie Delannoy
- RNA group, Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8
| | - Anna Salvetti
- INSERM, U1111, Centre International de Recherche en Infectiologie de Lyon (CIRI), CNRS UMR 5308, Lyon, France
| | - Benoit Chabot
- RNA group, Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1E 4K8
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Du B, Zhang Y, Liang M, Du Z, Li H, Fan C, Zhang H, Jiang Y, Bi X. N6-methyladenosine (m6A) modification and its clinical relevance in cognitive dysfunctions. Aging (Albany NY) 2021; 13:20716-20737. [PMID: 34461609 PMCID: PMC8436914 DOI: 10.18632/aging.203457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND N6 adenosine methylation (m6A) is the most abundant internal RNA modification in eukaryotic cells. Dysregulation of m6A has been associated with the perturbations of cell proliferation and cell death in different diseases. However, the roles of m6A in the neurodegenerative process and cognitive dysfunction are unclear. METHODS We systematically investigated the molecular alterations of m6A regulators and their clinical relevance with cognitive dysfunctions using published datasets of Alzheimer's Disease (AD), vascular dementia, and mild cognitive impairment (MCI). FINDINGS The expressions of m6A regulators vary in different tissues and closely correlate with neurodegenerative pathways. We identified co-expressive m6A regulators SNRPG and SNRPD2 as potential biomarkers to predict transformation from MCI to AD. Moreover, we explored correlations between Apolipoprotein E4 and m6A methylations. INTERPRETATION Collectively, these findings suggest that m6A methylations as potential biomarkers and therapeutic targets for cognitive dysfunction. FUNDING This work was supported by the National Natural Science Foundation of China (81871040) and the Shanghai Health System Talent Training Program (2018BR29).
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Affiliation(s)
- Bingying Du
- Department of Neurology, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, PR China
| | - Yanbo Zhang
- Department of Psychiatry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Meng Liang
- Department of Neurology, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, PR China
| | - Zengkan Du
- Faculty of Basic Medical Sciences, The Second Military Medical University, Shanghai, PR China
| | - Haibo Li
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Cunxiu Fan
- Department of Neurology, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, PR China
| | - Hailing Zhang
- Department of Neurology, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, PR China
| | - Yan Jiang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Xiaoying Bi
- Department of Neurology, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, PR China
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Frederiksen SB, Holm LL, Larsen MR, Doktor TK, Andersen HS, Hastings ML, Hua Y, Krainer AR, Andresen BS. Identification of SRSF10 as a regulator of SMN2 ISS-N1. Hum Mutat 2020; 42:246-260. [PMID: 33300159 DOI: 10.1002/humu.24149] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 10/22/2020] [Accepted: 12/06/2020] [Indexed: 01/02/2023]
Abstract
Understanding the splicing code can be challenging as several splicing factors bind to many splicing-regulatory elements. The SMN1 and SMN2 silencer element ISS-N1 is the target of the antisense oligonucleotide drug, Spinraza, which is the treatment against spinal muscular atrophy. However, limited knowledge about the nature of the splicing factors that bind to ISS-N1 and inhibit splicing exists. It is likely that the effect of Spinraza comes from blocking binding of these factors, but so far, an unbiased characterization has not been performed and only members of the hnRNP A1/A2 family have been identified by Western blot analysis and nuclear magnetic resonance to bind to this silencer. Employing an MS/MS-based approach and surface plasmon resonance imaging, we show for the first time that splicing factor SRSF10 binds to ISS-N1. Furthermore, using splice-switching oligonucleotides we modulated the splicing of the SRSF10 isoforms generating either the long or the short protein isoform of SRSF10 to regulate endogenous SMN2 exon 7 inclusion. We demonstrate that the isoforms of SRSF10 regulate SMN1 and SMN2 splicing with different strength correlating with the length of their RS domain. Our results suggest that the ratio between the SRSF10 isoforms is important for splicing regulation.
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Affiliation(s)
- Sabrina B Frederiksen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Lise L Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Henriette S Andersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Michelle L Hastings
- Department of Cell Biology and Anatomy, Center for Genetic Diseases, Chicago Medical School and School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, USA
| | - Yimin Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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5
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Yan T, Ding F, Zhao Y. Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses. Hereditas 2019; 156:25. [PMID: 31346329 PMCID: PMC6636172 DOI: 10.1186/s41065-019-0101-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/09/2019] [Indexed: 12/23/2022] Open
Abstract
Background Alzheimer's disease (AD) is known to be caused by multiple factors, meanwhile the pathogenic mechanism and development of AD associate closely with genetic factors. Existing understanding of the molecular mechanisms underlying AD remains incomplete. Methods Gene expression data (GSE48350) derived from post-modern brain was extracted from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were derived from hippocampus and entorhinal cortex regions between AD patients and healthy controls and detected via Morpheus. Functional enrichment analyses, including Gene Ontology (GO) and pathway analyses of DEGs, were performed via Cytoscape and followed by the construction of protein-protein interaction (PPI) network. Hub proteins were screened using the criteria: nodes degree≥10 (for hippocampus tissues) and ≥ 8 (for entorhinal cortex tissues). Molecular Complex Detection (MCODE) was used to filtrate the important clusters. University of California Santa Cruz (UCSC) and the database of RNA-binding protein specificities (RBPDB) were employed to identify the RNA-binding proteins of the long non-coding RNA (lncRNA). Results 251 & 74 genes were identified as DEGs, which consisted of 56 & 16 up-regulated genes and 195 & 58 down-regulated genes in hippocampus and entorhinal cortex, respectively. Biological analyses demonstrated that the biological processes and pathways related to memory, transmembrane transport, synaptic transmission, neuron survival, drug metabolism, ion homeostasis and signal transduction were enriched in these genes. 11 genes were identified as hub genes in hippocampus and entorhinal cortex, and 3 hub genes were identified as the novel candidates involved in the pathology of AD. Furthermore, 3 lncRNAs were filtrated, whose binding proteins were closely associated with AD. Conclusions Through GO enrichment analyses, pathway analyses and PPI analyses, we showed a comprehensive interpretation of the pathogenesis of AD at a systematic biology level, and 3 novel candidate genes and 3 lncRNAs were identified as novel and potential candidates participating in the pathology of AD. The results of this study could supply integrated insights for understanding the pathogenic mechanism underlying AD and potential novel therapeutic targets.
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Affiliation(s)
- Tingting Yan
- Department of Bioengineering, Harbin Institute of Technology, Weihai, 264209 Shandong China
| | - Feng Ding
- Department of Bioengineering, Harbin Institute of Technology, Weihai, 264209 Shandong China
| | - Yan Zhao
- Department of Bioengineering, Harbin Institute of Technology, Weihai, 264209 Shandong China
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Vasquez JB, Simpson JF, Harpole R, Estus S. Alzheimer's Disease Genetics and ABCA7 Splicing. J Alzheimers Dis 2018; 59:633-641. [PMID: 28655137 DOI: 10.3233/jad-170872] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Both common and rare polymorphisms within ABCA7 have been associated with Alzheimer's disease (AD). In particular, the rare AD associated polymorphism rs200538373 was associated with altered ABCA7 exon 41 splicing and an AD risk odds ratio of ∼1.9. To probe the role of this polymorphism in ABCA7 splicing, we used minigene studies and qPCR of human brain RNA. We report aberrant ABCA7 exon 41 splicing in the brain of a carrier of the rs200538373 minor C allele. Moreover, minigene studies show that rs200538373 acts as a robust functional variant in vitro. Lastly, although the ABCA7 isoform with an extended exon 41 is predicted to undergo nonsense mediated RNA decay, this was not supported by qPCR analyses, which showed relatively normal ABCA7 mRNA levels in the carrier of the rs200538373 minor C allele. In summary, rs200538373 is a functional polymorphism that alters ABCA7 exon 41 splicing without grossly altering the level of ABCA7 mRNA.
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Affiliation(s)
- Jared B Vasquez
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - James F Simpson
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Ryan Harpole
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Steven Estus
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
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De Rossi P, Buggia-Prévot V, Clayton BLL, Vasquez JB, van Sanford C, Andrew RJ, Lesnick R, Botté A, Deyts C, Salem S, Rao E, Rice RC, Parent A, Kar S, Popko B, Pytel P, Estus S, Thinakaran G. Predominant expression of Alzheimer's disease-associated BIN1 in mature oligodendrocytes and localization to white matter tracts. Mol Neurodegener 2016; 11:59. [PMID: 27488240 PMCID: PMC4973113 DOI: 10.1186/s13024-016-0124-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 07/27/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified BIN1 within the second most significant susceptibility locus in late-onset Alzheimer's disease (AD). BIN1 undergoes complex alternative splicing to generate multiple isoforms with diverse functions in multiple cellular processes including endocytosis and membrane remodeling. An increase in BIN1 expression in AD and an interaction between BIN1 and Tau have been reported. However, disparate descriptions of BIN1 expression and localization in the brain previously reported in the literature and the lack of clarity on brain BIN1 isoforms present formidable challenges to our understanding of how genetic variants in BIN1 increase the risk for AD. METHODS In this study, we analyzed BIN1 mRNA and protein levels in human brain samples from individuals with or without AD. In addition, we characterized the BIN1 expression and isoform diversity in human and rodent tissue by immunohistochemistry and immunoblotting using a panel of BIN1 antibodies. RESULTS Here, we report on BIN1 isoform diversity in the human brain and document alterations in the levels of select BIN1 isoforms in individuals with AD. In addition, we report striking BIN1 localization to white matter tracts in rodent and the human brain, and document that the large majority of BIN1 is expressed in mature oligodendrocytes whereas neuronal BIN1 represents a minor fraction. This predominant non-neuronal BIN1 localization contrasts with the strict neuronal expression and presynaptic localization of the BIN1 paralog, Amphiphysin 1. We also observe upregulation of BIN1 at the onset of postnatal myelination in the brain and during differentiation of cultured oligodendrocytes. Finally, we document that the loss of BIN1 significantly correlates with the extent of demyelination in multiple sclerosis lesions. CONCLUSION Our study provides new insights into the brain distribution and cellular expression of an important risk factor associated with late-onset AD. We propose that efforts to define how genetic variants in BIN1 elevate the risk for AD would behoove to consider BIN1 function in the context of its main expression in mature oligodendrocytes and the potential for a role of BIN1 in the membrane remodeling that accompanies the process of myelination.
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Affiliation(s)
- Pierre De Rossi
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Virginie Buggia-Prévot
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | | | - Jared B. Vasquez
- Sanders-Brown Center on Aging and Department of Physiology, University of Kentucky, Lexington, KY 40536 USA
| | - Carson van Sanford
- Sanders-Brown Center on Aging and Department of Physiology, University of Kentucky, Lexington, KY 40536 USA
| | - Robert J. Andrew
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Ruben Lesnick
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Alexandra Botté
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Carole Deyts
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Someya Salem
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Eshaan Rao
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Richard C. Rice
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Angèle Parent
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
| | - Satyabrata Kar
- Centre for prions and protein folding diseases, University of Alberta, Edmonton, AB T6G 2B7 Canada
| | - Brian Popko
- Department of Neurology, The University of Chicago, Chicago, IL 60637 USA
| | - Peter Pytel
- Department of Pathology, The University of Chicago, Chicago, IL 60637 USA
| | - Steven Estus
- Sanders-Brown Center on Aging and Department of Physiology, University of Kentucky, Lexington, KY 40536 USA
| | - Gopal Thinakaran
- Department of Neurobiology, The University of Chicago, JFK R212, 924 East 57th Street, Chicago, IL 60637 USA
- Department of Neurology, The University of Chicago, Chicago, IL 60637 USA
- Department of Pathology, The University of Chicago, Chicago, IL 60637 USA
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Yip L, Fuhlbrigge R, Taylor C, Creusot RJ, Nishikawa-Matsumura T, Whiting CC, Schartner JM, Akter R, von Herrath M, Fathman CG. Inflammation and hyperglycemia mediate Deaf1 splicing in the pancreatic lymph nodes via distinct pathways during type 1 diabetes. Diabetes 2015; 64:604-17. [PMID: 25187368 PMCID: PMC4303971 DOI: 10.2337/db14-0803] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Peripheral tolerance is partially controlled by the expression of peripheral tissue antigens (PTAs) in lymph node stromal cells (LNSCs). We previously identified a transcriptional regulator, deformed epidermal autoregulatory factor 1 (Deaf1), that can regulate PTA expression in LNSCs of the pancreatic lymph nodes (PLNs). During the pathogenesis of type 1 diabetes (T1D), Deaf1 is spliced to form the dominant-negative isoform Deaf1-Var1. Here we show that Deaf1-Var1 expression correlates with the severity of disease in NOD mice and is reduced in the PLNs of mice that do not develop hyperglycemia. Inflammation and hyperglycemia independently drive Deaf1 splicing through activation of the splicing factors Srsf10 and Ptbp2, respectively. Inflammation induced by injection of activated splenocytes increased Deaf1-Var1 and Srsf10, but not Ptbp2, in the PLNs of NOD.SCID mice. Hyperglycemia induced by treatment with the insulin receptor agonist S961 increased Deaf1-Var1 and Ptbp2, but not Srsf10, in the PLNs of NOD.B10 and NOD mice. Overexpression of PTBP2 and/or SRSF10 also increased human DEAF1-VAR1 and reduced PTA expression in HEK293T cells. These data suggest that during the progression of T1D, inflammation and hyperglycemia mediate the splicing of DEAF1 and loss of PTA expression in LNSCs by regulating the expression of SRSF10 and PTBP2.
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Affiliation(s)
- Linda Yip
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA
| | - Rebecca Fuhlbrigge
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA
| | - Cariel Taylor
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA
| | - Remi J Creusot
- Department of Medicine, Columbia Center for Translational Immunology and Naomi Berrie Diabetes Center, Columbia University Medical Center, New York, NY
| | | | - Chan C Whiting
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA
| | - Jill M Schartner
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA
| | - Rahima Akter
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA
| | - Matthias von Herrath
- Type 1 Diabetes Center, The La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - C Garrison Fathman
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA
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Kampschulte M, Stöckl C, Langheinrich AC, Althöhn U, Bohle RM, Krombach GA, Stieger P, Churin Y, Kremer S, Dierkes C, Rath T, Roeb E, Roderfeld M. Western diet in ApoE-LDLR double-deficient mouse model of atherosclerosis leads to hepatic steatosis, fibrosis, and tumorigenesis. J Transl Med 2014; 94:1273-82. [PMID: 25199052 DOI: 10.1038/labinvest.2014.112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/17/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic fatty liver disease has been linked to cardiovascular diseases and atherosclerosis. The aim of the current study was to characterize the hepatic pathology leading to fibrosis and tumors in a murine model of atherosclerosis. Male apolipoprotein E/low-density lipoprotein receptor double-knockout mice (AL) mice were fed with a high fat and high cholesterol western diet for 35 weeks (AL mice on WD). Protein and mRNA analysis as well as micro-computed tomography (micro-CT) were performed to assess oxidative stress, liver damage, inflammation, fibrosis, signaling pathways, vascularization, and tumorigenesis. Controls were chosen to distinguish between genetically and dietary effects in steatohepatitis and associated tumorigenesis. Hepatic inflammation and dyslipidemia were increased in AL mice on WD compared with wild-type mice on WD. Uniquely, AL mice on WD showed a spontaneous development of tumors (30% of cases) and thickening of intrahepatic vessel walls. Functionally relevant underlying signaling pathways such as NF-κB, Stat3, JNK, and AKT were differentially regulated between AL and wild-type mice on WD. Micro-CT was capable of visualizing and quantitatively distinguishing tumor neovascularization from vascularization in non-neoplastic liver tissue. AL mice on WD diet represent a novel model combining atherosclerosis and nonalcoholic fatty liver disease. Signaling pathways of liver cell damage and compensatory liver regeneration in combination with enhanced inflammation appear to be crucial for the spontaneous development of tumors in AL mice on WD. Micro-CT represents a new and powerful technique for the ultrastructural and three-dimensional assessment of the vascular architecture of liver tumors.
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Affiliation(s)
- Marian Kampschulte
- Department of Radiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Christiane Stöckl
- Department of Radiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Alexander C Langheinrich
- Department of Diagnostic and Interventional Radiology, BG Trauma Hospital, Frankfurt/Main, Germany
| | - Ulrike Althöhn
- Department of Radiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Rainer M Bohle
- Department of Pathology, Saarland University, Homburg, Germany
| | | | - Philipp Stieger
- Department of Cardiology, Angiology and Pneumology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yuri Churin
- Department of Gastroenterology, Justus-Liebig University Giessen, Giessen, Germany
| | - Sandra Kremer
- Department of Gastroenterology, Justus-Liebig University Giessen, Giessen, Germany
| | | | - Timo Rath
- 1] Department of Gastroenterology, Justus-Liebig University Giessen, Giessen, Germany [2] Department of Medicine 1, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Elke Roeb
- Department of Gastroenterology, Justus-Liebig University Giessen, Giessen, Germany
| | - Martin Roderfeld
- Department of Gastroenterology, Justus-Liebig University Giessen, Giessen, Germany
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10
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Howard JM, Sanford JR. The RNAissance family: SR proteins as multifaceted regulators of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:93-110. [PMID: 25155147 DOI: 10.1002/wrna.1260] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Abstract
Serine and arginine-rich (SR) proteins play multiple roles in the eukaryotic gene expression pathway. Initially described as constitutive and alternative splicing factors, now it is clear that SR proteins are key determinants of exon identity and function as molecular adaptors, linking the pre-messenger RNA (pre-mRNA) to the splicing machinery. In addition, now SR proteins are implicated in many aspects of mRNA and noncoding RNA (ncRNA) processing well beyond splicing. These unexpected roles, including RNA transcription, export, translation, and decay, may prove to be the rule rather than the exception. To simply define, this family of RNA-binding proteins as splicing factors belies the broader roles of SR proteins in post-transcriptional gene expression.
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Affiliation(s)
- Jonathan M Howard
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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11
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Vasquez JB, Fardo DW, Estus S. ABCA7 expression is associated with Alzheimer's disease polymorphism and disease status. Neurosci Lett 2013; 556:58-62. [PMID: 24141082 DOI: 10.1016/j.neulet.2013.09.058] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have implicated a series of single nucleotide polymorphisms (SNPs) in Alzheimer's disease (AD) risk. Elucidating the function of these SNPs is critical to identify the underlying pathways and, potentially, novel therapeutic agents. SNPs within the gene ATP binding cassette A7 (ABCA7) reached significance in these studies, warranting investigation into their actions. Here, we analyzed ABCA7 expression in a set of human brain samples as a function of AD-associated SNPs and AD status. We report that the rs3764650T allele that decreases AD risk is associated with increased ABCA7 expression. However, ABCA7 expression is increased in AD individuals. We interpret our findings as suggesting a model wherein increased ABCA7 expression reduces AD risk and that the increased ABCA7 observed in AD reflects an inadequate compensatory change.
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Affiliation(s)
- Jared B Vasquez
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, United States
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Liu B, Anderson SL, Qiu J, Rubin BY. Cardiac glycosides correct aberrant splicing of IKBKAP-encoded mRNA in familial dysautonomia derived cells by suppressing expression of SRSF3. FEBS J 2013; 280:3632-46. [PMID: 23711097 DOI: 10.1111/febs.12355] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/30/2013] [Accepted: 05/21/2013] [Indexed: 12/11/2022]
Abstract
The ability to modulate the production of the wild-type transcript in cells bearing the splice-altering familial dysautonomia (FD) causing mutation in the IKBKAP gene prompted a study of the impact of a panel of pharmaceuticals on the splicing of this transcript, which revealed the ability of the cardiac glycoside digoxin to increase the production of the wild-type, exon-20-containing, IKBKAP-encoded transcript and the full-length IκB-kinase-complex-associated protein in FD-derived cells. Characterization of the cis elements and trans factors involved in the digoxin-mediated effect on splicing reveals that this response is dependent on an SRSF3 binding site(s) located in the intron 5' of the alternatively spliced exon and that digoxin mediates its effect by suppressing the level of the SRSF3 protein. Characterization of the digoxin-mediated effect on the RNA splicing process was facilitated by the identification of several RNA splicing events in which digoxin treatment mediates the enhanced inclusion of exonic sequence. Moreover, we demonstrate the ability of digoxin to impact the splicing process in neuronal cells, a cell type profoundly impacted by FD. This study represents the first demonstration that digoxin possesses splice-altering capabilities that are capable of reversing the impact of the FD-causing mutation. These findings support the clinical evaluation of the impact of digoxin on the FD patient population.
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Affiliation(s)
- Bo Liu
- Laboratory for Familial Dysautonomia Research, Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
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Filali H, Martin-Burriel I, Harders F, Varona L, Serrano C, Acín C, Badiola JJ, Bossers A, Bolea R. Medulla oblongata transcriptome changes during presymptomatic natural scrapie and their association with prion-related lesions. BMC Genomics 2012; 13:399. [PMID: 22897917 PMCID: PMC3495657 DOI: 10.1186/1471-2164-13-399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 08/06/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pathogenesis of natural scrapie and other prion diseases is still poorly understood. Determining the variations in the transcriptome in the early phases of the disease might clarify some of the molecular mechanisms of the prion-induced pathology and allow for the development of new biomarkers for diagnosis and therapy. This study is the first to focus on the identification of genes regulated during the preclinical phases of natural scrapie in the ovine medulla oblongata (MO) and the association of these genes with prion deposition, astrocytosis and spongiosis. RESULTS A custom microarray platform revealed that 86 significant probes had expression changes greater than 2-fold. From these probes, we identified 32 genes with known function; the highest number of regulated genes was included in the phosphoprotein-encoding group. Genes encoding extracellular marker proteins and those involved in the immune response and apoptosis were also differentially expressed. In addition, we investigated the relationship between the gene expression profiles and the appearance of the main scrapie-associated brain lesions. Quantitative Real-time PCR was used to validate the expression of some of the regulated genes, thus showing the reliability of the microarray hybridization technology. CONCLUSIONS Genes involved in protein and metal binding and oxidoreductase activity were associated with prion deposition. The expression of glial fibrillary acidic protein (GFAP) was associated with changes in the expression of genes encoding proteins with oxidoreductase and phosphatase activity, and the expression of spongiosis was related to genes encoding extracellular matrix components or transmembrane transporters. This is the first genome-wide expression study performed in naturally infected sheep with preclinical scrapie. As in previous studies, our findings confirm the close relationship between scrapie and other neurodegenerative diseases.
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Affiliation(s)
- Hicham Filali
- Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
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14
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Ling IF, Bhongsatiern J, Simpson JF, Fardo DW, Estus S. Genetics of clusterin isoform expression and Alzheimer's disease risk. PLoS One 2012; 7:e33923. [PMID: 22506010 PMCID: PMC3323613 DOI: 10.1371/journal.pone.0033923] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 02/21/2012] [Indexed: 01/13/2023] Open
Abstract
The minor allele of rs11136000 within CLU is strongly associated with reduced Alzheimer's disease (AD) risk. The mechanism underlying this association is unclear. Here, we report that CLU1 and CLU2 are the two primary CLU isoforms in human brain; CLU1 and CLU2 share exons 2-9 but differ in exon 1 and proximal promoters. The expression of both CLU1 and CLU2 was increased in individuals with significant AD neuropathology. However, only CLU1 was associated with the rs11136000 genotype, with the minor "protective" rs11136000T allele being associated with increased CLU1 expression. Since CLU1 and CLU2 are predicted to encode intracellular and secreted proteins, respectively, we compared their expression; for both CLU1 and CLU2 transfected cells, clusterin is present in the secretory pathway, accumulates in the extracellular media, and is similar in size to clusterin in human brain. Overall, we interpret these results as indicating that the AD-protective minor rs11136000T allele is associated with increased CLU1 expression. Since CLU1 and CLU2 appear to produce similar proteins and are increased in AD, the AD-protection afforded by the rs11136000T allele may reflect increased soluble clusterin throughout life.
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Affiliation(s)
- I-Fang Ling
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jiraganya Bhongsatiern
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - James F. Simpson
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - David W. Fardo
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Steven Estus
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
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Holler CJ, Webb RL, Laux AL, Beckett TL, Niedowicz DM, Ahmed RR, Liu Y, Simmons CR, Dowling ALS, Spinelli A, Khurgel M, Estus S, Head E, Hersh LB, Murphy MP. BACE2 expression increases in human neurodegenerative disease. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 180:337-50. [PMID: 22074738 DOI: 10.1016/j.ajpath.2011.09.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 08/02/2011] [Accepted: 09/20/2011] [Indexed: 11/25/2022]
Abstract
β-Secretase, the rate-limiting enzymatic activity in the production of the amyloid-β (Aβ) peptide, is a major target of Alzheimer's disease (AD) therapeutics. There are two forms of the enzyme: β-site Aβ precursor protein cleaving enzyme (BACE) 1 and BACE2. Although BACE1 increases in late-stage AD, little is known about BACE2. We conducted a detailed examination of BACE2 in patients with preclinical to late-stage AD, including amnestic mild cognitive impairment, and age-matched controls, cases of frontotemporal dementia, and Down's syndrome. BACE2 protein and enzymatic activity increased as early as preclinical AD and were found in neurons and astrocytes. Although the levels of total BACE2 mRNA were unchanged, the mRNA for BACE2 splice form C (missing exon 7) increased in parallel with BACE2 protein and activity. BACE1 and BACE2 were strongly correlated with each other at all levels, suggesting that their regulatory mechanisms may be largely shared. BACE2 was also elevated in frontotemporal dementia but not in Down's syndrome, even in patients with substantial Aβ deposition. Thus, expression of both forms of β-secretase are linked and may play a combined role in human neurologic disease. A better understanding of the normal functions of BACE1 and BACE2, and how these change in different disease states, is essential for the future development of AD therapeutics.
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Affiliation(s)
- Christopher J Holler
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0230, USA
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16
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Xiao PJ, Peng ZY, Huang L, Li Y, Chen XH. Dephosphorylated NSSR1 is induced by androgen in mouse epididymis and phosphorylated NSSR1 is increased during sperm maturation. PLoS One 2011; 6:e25667. [PMID: 21980524 PMCID: PMC3183062 DOI: 10.1371/journal.pone.0025667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 09/09/2011] [Indexed: 12/15/2022] Open
Abstract
NSSR1 (Neural salient serine/arginine rich protein 1, alternatively SRp38) is a newly identified RNA splicing factor and predominantly expressed in neural tissues. Here, by Western blot analysis and immunofluorescent staining, we showed that the expression of dephosphorylated NSSR1 increased significantly during development of the caput epididymis. In adult mice, phosphorylated NSSR1 was mainly expressed in the apical side of epithelial cells, and dephosphorylated NSSR1 in caput epididymis was upregulated in a testosterone dependent manner. In addition, subcellular immunoreactive distribution of NSSR1 varied in different regions of the epididymis. With respect to the sperm, phosphorylated NSSR1 was detected in the mid-piece of the tail as well as the acrosome. Furthermore, NSSR1 was released from the sperm head during the capacitation and acrosome reaction. These findings for the first time provide the evidence for the potential roles of NSSR1 in sperm maturation and fertilization.
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Affiliation(s)
- Ping-Jie Xiao
- Laboratory of Genomic Physiology and State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Zheng-Yu Peng
- Laboratory of Genomic Physiology and State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lu Huang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Ya Li
- Laboratory of Genomic Physiology and State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xian-Hua Chen
- Laboratory of Genomic Physiology and State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
- * E-mail:
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Simmons CR, Zou F, Younkin SG, Estus S. Evaluation of the global association between cholesterol-associated polymorphisms and Alzheimer's disease suggests a role for rs3846662 and HMGCR splicing in disease risk. Mol Neurodegener 2011; 6:62. [PMID: 21867541 PMCID: PMC3180274 DOI: 10.1186/1750-1326-6-62] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 08/25/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Recent genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNP)s that are essentially unequivocally associated with peripheral cholesterol. Since the alleles of the APOE gene, which modulate peripheral cholesterol metabolism, and midlife plasma cholesterol are both associated with Alzheimer's disease (AD) risk, we have evaluated the hypothesis that SNPs associated with plasma cholesterol are also associated with AD. RESULTS Seventeen non-APOE SNPs reproducibly associated with cholesterol per GWAS were tested for association with AD in ~2,000 AD and ~4,000 non-AD subjects. As a group, these SNPs are associated with AD. Two SNPs in particular, rs3846662 and rs1532085, are associated with AD risk and age-of-onset. Additionally, rs3846662 was associated with HMGCR exon 13 splicing in human liver but not brain, possibly obscured by CNS cell-type heterogeneity. However, rs3846662 was associated with HMGCR exon 13 splicing in liver- and brain-derived cell lines. CONCLUSIONS Cholesterol-associated SNPs outside of APOE confer a global risk for AD. Rs3846662 and rs1532085 are associated with both AD risk and age-of-onset. Rs3846662 is associated with HMGCR exon 13 inclusion. Since rs3846662 affects AD risk and age-of-onset as well as statin responsiveness, this SNP may confound clinical trials evaluating the protective effects of statins on AD.
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Affiliation(s)
- Christopher R Simmons
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
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Burchett ME, Ling IF, Estus S. FBN1 isoform expression varies in a tissue and development-specific fashion. Biochem Biophys Res Commun 2011; 411:323-8. [PMID: 21726527 DOI: 10.1016/j.bbrc.2011.06.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 06/18/2011] [Indexed: 12/17/2022]
Abstract
Mutations in FBN1 cause Marfan syndrome, a heritable disorder of connective tissue. FBN1 encodes the extracellular matrix protein, fibrillin. Our objective was to elucidate the extent that variation in RNA splicing contributes to FBN1 isoforms. To identify FBN1 splice variants, we scanned each of its 64 internal exons in a set of pooled human brain cDNA samples. FBN1 splicing is generally efficient as we identified only two variants. Neither variant has previously been reported in the literature and include (i) an isoform which contains a cryptic 105 basepair exon between exons 54 and 55 (54A-FBN1) and (ii) an isoform which contains a cryptic 62 basepair exon between exons 57 and 58 (57A-FBN1). We compared 57A-FBN1 and FBN1 expression in multiple human tissues, including adult skeletal muscle and brain, as well as fetal skeletal muscle, brain, liver, aorta, lung, skin, and heart. 57A-FBN1 represents 8-44% of FBN1 mRNA and varies in a tissue- and development-specific fashion. In adult brain, 57A-FBN1 represented 39±3 (%, mean±SD) of total FBN1 expression. In contrast, 57A-FBN1 represented 19±2 (%, mean±SD) of FBN1 expression in skeletal muscle. In fetal tissue, the 57A-FBN1 proportion was highest in brain (27%) and low elsewhere, e.g., skin, aorta and lung (9-13%). In summary, a significant proportion of FBN1 is expressed as 57A-FBN1 and this proportion varies in a tissue- and development-specific fashion. Since the 57A insertion creates a premature stop codon that mimics Marfan-associated mutations, the protein encoded by 57A-FBN1 is likely to not be functional. These results suggest that altered splicing may modulate disease severity, regulate FBN1 expression, and potentially represent a therapeutic target.
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Affiliation(s)
- Mary E Burchett
- University of Kentucky College of Medicine, University of Kentucky, Lexington, KY, USA.
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Simmons CR, Zou F, Younkin SG, Estus S. Rheumatoid arthritis-associated polymorphisms are not protective against Alzheimer's disease. Mol Neurodegener 2011; 6:33. [PMID: 21595938 PMCID: PMC3120711 DOI: 10.1186/1750-1326-6-33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/19/2011] [Indexed: 01/29/2023] Open
Abstract
Background Rheumatoid arthritis (RA) and Alzheimer's disease (AD) are inversely associated. To test the hypothesis that genetic elements associated with increased RA risk are associated with decreased AD risk, we evaluated RA genetic risk factors recently identified in genome-wide association studies (GWAS) for their association with AD in a two-stage, case-control analysis. Results In our Stage 1 analysis of ~800 AD and ~1,200 non-AD individuals, three of seventeen RA-associated SNPs were nominally associated with AD (p < 0.05) with one SNP, rs2837960, retaining significance after correction for multiple testing (p = 0.03). The rs2837960_G (minor) allele, which is associated with increased RA risk, was associated with increased AD risk. Analysis of these three SNPs in a Stage 2 population, consisting of ~1,100 AD and ~2,600 non-AD individuals, did not confirm their association with AD. Analysis of Stage 1 and 2 combined suggested that rs2837960 shows a trend for association with AD. When the Stage 2 population was age-matched for the Stage 1 population, rs2837960 exhibited a non-significant trend with AD. Combined analysis of Stage 1 and the age-matched Stage 2 subset showed a significant association of rs2837960 with AD (p = 0.002, OR 1.24) that retained significance following correction for age, sex and APOE (p = 0.02, OR = 1.20). Rs2837960 is near BACE2, which encodes an aspartic protease capable of processing the AD-associated amyloid precursor protein. Testing for an association between rs2837960 and the expression of BACE2 isoforms in human brain, we observed a trend between rs2837960 and the total expression of BACE2 and the expression of a BACE2 transcript lacking exon 7 (p = 0.07 and 0.10, respectively). Conclusions RA-associated SNPs are generally not associated with AD. Moreover, rs2837960_G is associated with increased risk of both RA and, in individuals less than 80 years of age, with AD. Overall, these results contest the hypothesis that genetic variants associated with RA confer protection against AD. Further investigation of rs2837960 is necessary to elucidate the mechanism by which rs2837960 contributes to both AD and RA risk, likely via modulation of BACE2 expression.
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Affiliation(s)
- Christopher R Simmons
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
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Ling IF, Gopalraj RK, Simpson JF, Estus S. Expression and regulation of a low-density lipoprotein receptor exon 12 splice variant. J Neurochem 2010; 115:614-24. [PMID: 20807319 DOI: 10.1111/j.1471-4159.2010.06972.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
As low-density lipoprotein receptor (LDLR) contributes to cholesterol and amyloid beta homeostasis, insights into LDLR regulation may facilitate our understanding of cardiovascular disease and Alzheimer's disease. Previously, we identified LDLR isoforms that lacked exon 12 or exons 11-12 and that are predicted to encode soluble, dominant negative, LDLR. Moreover, these isoforms were associated with rs688, an exon 12 polymorphism that was associated with LDL-cholesterol and Alzheimer's disease risk. In this study, we present evidence that although the truncated LDLR isoforms are translated in vitro, they represent < 0.1% of CSF proteins. As these LDLR isoforms likely represent a loss of mRNA-encoding functional LDLR, we then focused upon identifying intron-exon boundary and exonic splicing enhancer elements critical to splicing. Exon 12 inclusion is enhanced by altering the 5' splice site in intron 12 towards a consensus splice donor sequence, consistent with its being a weak 5' splice site. Additionally, of the nine evolutionarily conserved putative splicing enhancer regions within exon 12, two regions that flank rs688 were critical to exon 12 inclusion. Overall, these results suggest that LDLR splice variants represent a loss of mRNA encoding functional LDLR and provide insights into the regulatory elements critical for LDLR exon 12 splicing.
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Affiliation(s)
- I-Fang Ling
- Department of Physiology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky 40536-0230, USA
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Polymorphisms at LDLR locus may be associated with coronary artery disease through modulation of coagulation factor VIII activity and independently from lipid profile. Blood 2010; 116:5688-97. [PMID: 20810930 DOI: 10.1182/blood-2010-03-277079] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High levels of coagulation factor VIII (FVIII) have been associated with cardiovascular disease. Low-density lipoprotein receptor (LDLR) has been recently demonstrated to contribute to FVIII clearance from plasma. The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (rs1122608, rs2228671, and rs688) and FVIII coagulant activity (FVIII:c) in subjects with (n = 692) or without (n = 291) angiographically confirmed coronary artery disease (CAD). High FVIII:c levels were an independent risk factor for CAD. The rs688 and rs2228671 genotypes were predictors of FVIII:c with T alleles associated with higher FVIII:c levels. The rs2228671T allele was associated also with reduced total and LDL-cholesterol levels. With respect to the risk of CAD, no association was found for rs2228671. Consistently with higher FVIII:c levels, the rs688T allele was associated with CAD, whereas, consistently with a favorable lipid profile, the rs1122608T allele was associated with a decreased CAD prevalence. After adjustment for classic cardiovascular risk factors, including plasma lipids, rs688 remained associated with CAD (OR for T carriers: 1.67 with 95% confidence interval, 1.10-2.54). Haplotype analysis confirmed such results. Our data suggest that polymorphisms at LDLR locus modulate FVIII:c levels and may be associated with CAD risk independently from plasma lipids.
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