DOCSLIB.ORG

A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. In parallel, we generated an RNA-sequencing dataset from human islets treated with brefeldin A (BFA), a known GA stress inducer. Overlapping the T1D and T2D groups with the BFA dataset, we identified 120 and 204 differentially expressed genes, respectively. In both the T1D and T2D models, pathway analyses revealed that the top pathways were associated with GA integrity, organization, and trafficking. Quantitative RT-PCR was used to validate a common signature of GA stress that included ATF3, ARF4, CREB3, and COG6. Taken together, these data indicate that GA-associated genes are dysregulated in diabetes and identify putative markers of β-cell GA stress. 2 Page 3 of 781 Diabetes INTRODUCTION Diabetes mellitus impacts over 425 million individuals worldwide, and this number is expected to approach 629 million by the year 2045 (1). Type 1 diabetes (T1D) accounts for 5- 10% of all diabetes cases and results from autoimmune destruction of pancreatic β cells, whereas type 2 diabetes (T2D) accounts for 90-95% of cases and results from a combination of peripheral insulin resistance and β-cell dysfunction (2). While the origins of T1D and T2D have been viewed classically as distinct, inadequate insulin secretion plays a central role in the pathophysiology of both forms of diabetes. Accumulating data suggest that common β-cell stress pathways underlie the diminished insulin secretory capacity and reduced β-cell survival observed during T1D and T2D progression. The primary function of the β cell is to rapidly sense elevations in blood glucose and respond with carefully titrated levels of insulin secretion (3). To meet the heavy biosynthetic burden of insulin production, β cells possess a highly developed secretory pathway in which insulin is sequentially folded, processed, and packaged into vesicles for exocytosis. Insulin production begins within the lumen of the endoplasmic reticulum (ER) with conversion of preproinsulin to proinsulin following cleavage of the preproinsulin signal peptide by signal peptidase (3). Proinsulin exits the ER and enters the Golgi apparatus (GA), where it undergoes packaging into early secretory vesicles, and these immature vesicles undergo a series of maturation steps (3). Cleavage of proinsulin by prohormone convertases to produce mature insulin begins within the trans-GA sub-compartment, and this process is completed within the mature secretory vesicles (3). The mild acidity of the GA aids the maturation of the prohormone convertases needed for insulin maturation (3), and this process continues and accelerates in the more acidic secretory vesicles to form mature insulin granules. The vesicles are then stored near 3 Diabetes Page 4 of 781 the plasma membrane as a readily releasable pool that is rapidly mobilized during glucose- stimulated insulin secretion (3). As insulin accounts for nearly half of the total protein produced in β cells (4), disruptions in the fidelity of proinsulin processing and alterations in secretory organelle function can significantly affect β-cell function and health (5; 6). In this regard, ER stress has been well documented as playing a role in the pathogenesis of both T1D and T2D (7-10), and the tripartite ER stress response has been studied extensively, resulting in multiple well-validated protein and transcriptional markers of ER stress. The concept of GA stress has been proposed primarily in the context of neurologic disorders (11; 12) but has also been suggested to occur in other secretory cells, such as monocytes (13) and Brunner’s gland cells (14). Several candidate GA stress markers were recently identified in other cell types and linked with GA morphologic changes observed by electron microscopy (15). In contrast with ER stress, the pathways underlying GA stress are incompletely described and may be much more diverse in nature (14). Despite the importance of the GA in insulin processing and maturation, whether GA stress plays a role in β cells or if it exists in either T1D or T2D remain unclear. To this end, we identified publicly available human islet datasets from T1D and T2D models, including a combination of datasets from donors with diabetes and datasets where diabetes pathophysiology was modeled ex vivo, and we analyzed these datasets for changes in the expression of GA-associated genes. In parallel, we treated human islets with the known GA stress inducer brefeldin A (BFA) and used a computational approach to identify overlap between the T1D, T2D, and BFA datasets. From this analysis, we identified a set of genes and pathways associated with β-cell GA stress in diabetes. 4 Page 5 of 781 Diabetes RESEARCH DESIGN AND METHODS Selection and Classification of Datasets Studies of interest were identified by searching specific terms in the NCBI Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/gds). Search terms included: “islet & cytokine,” “islet & palmitate,” “islet & type 2 diabetes,” and “islet & type 1 diabetes.” Some datasets were found in more than one search query, but these were weighted equally with datasets appearing in only one query. Datasets were excluded if the primary tissue was not human islets or if there was no non-diabetic control or control condition available for comparison. The experimental procedures of all the publicly available microarray and RNA- sequencing human pancreatic islets samples used in this paper have been fully described elsewhere (16-24). T1D datasets included cadaveric human islets treated with or without pro-inflammatory cytokines analogous to autoimmune mediated β-cell insult in T1D (datasets 1 (18) and 3 [data under review; islets treated with or without 50 U/mL IL-1β and 1000 U/mL IFNγ for 24 h] and from organ donors with T1D [dataset 2]) (25). T2D datasets included cadaveric human islets from donors diagnosed with T2D (datasets 4 & 5) (17; 24) and cadaveric human islets treated with palmitate as a model of T2D (dataset 6) (16). The BFA dataset (dataset 7) included cadaveric human islets treated with BFA or DMSO as a control. Further information on the dataset characteristics, including GEO accession numbers, number of samples, profiling technology, and number of probe sets or genes, is shown in Table 1. Human islet donor characteristics are shown in Table 2. 5 Diabetes Page 6 of 781 Generation of BFA-treated Human Islet Datasets For the generation of the BFA dataset, human cadaveric donor islets were obtained from the Integrated Islet Distribution Program (26). Upon receipt, islets were allowed to recover overnight in phenol red–free DMEM containing 10% FBS, 10 mM HEPES, 2 mM L-glutamate, and 100 U/0.1 mg/L penicillin/streptomycin. Islets were handpicked (250 per condition) and then treated for 24 h with DMSO or 0.1 µg/mL BFA. Islets were collected, washed in PBS, and lysed in TRIzol (Thermo Fisher Scientific, Waltham, MA). Total RNA was isolated using a miRNeasy kit (Qiagen, Hilden, Germany) for RNA-sequencing and RNeasy Micro kit for qRT- PCR. Raw data were deposited in the GEO database (GSE152615). RNA-Seq Library Preparation and Sequencing of BFA-treated Islets The concentration and quality of total RNA samples were first assessed using an Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) ≥5 was required to pass quality control (RIN 8.063 ± 0.4031). Then, 100 ng of RNA per sample were used to prepare single-indexed strand- specific cDNA libraries using a KAPA mRNA Hyperprep kit (Roche Sequencing & Life Science, Indianapolis, IN). The resulting libraries were assessed for quantity and size distribution using Qubit and an Agilent 2100 Bioanalyzer. Pooled libraries (300 pM) were sequenced with a 2×100 bp paired-end configuration on a NovaSeq6000 (Illumina, San Diego, CA). A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy). Data Preprocessing and Normalization 6 Page 7 of 781 Diabetes For microarray datasets, transcriptomic data were background adjusted, summarized, and normalized to probe sets using Robust Multi-Array Average methods from the Bioconductor package Affy in R (27) for datasets 4 and 5. Batch correction of dataset 5 was performed using the ComBat function from the R/Bioconductor package sva (28).
Load more

Recommended publications
  • Small Cell Ovarian Carcinoma: Genomic Stability and Responsiveness to Therapeutics
    Gamwell et al. Orphanet Journal of Rare Diseases 2013, 8:33 http://www.ojrd.com/content/8/1/33 RESEARCH Open Access Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics Lisa F Gamwell1,2, Karen Gambaro3, Maria Merziotis2, Colleen Crane2, Suzanna L Arcand4, Valerie Bourada1,2, Christopher Davis2, Jeremy A Squire6, David G Huntsman7,8, Patricia N Tonin3,4,5 and Barbara C Vanderhyden1,2* Abstract Background: The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Method: The tumourigenic potential of BIN-67 cells was determined and the tumours formed in a xenograft model was compared to human SCCOHT. DNA sequencing, spectral karyotyping and high density SNP array analysis was performed. The sensitivity of the BIN-67 cells to standard chemotherapeutic agents and to vesicular stomatitis virus (VSV) and the JX-594 vaccinia virus was tested. Results: BIN-67 cells were capable of forming spheroids in hanging drop cultures. When xenografted into immunodeficient mice, BIN-67 cells developed into tumours that reflected the hypercalcemia and histology of human SCCOHT, notably intense expression of WT-1 and vimentin, and lack of expression of inhibin. Somatic mutations in TP53 and the most common activating mutations in KRAS and BRAF were not found in BIN-67 cells by DNA sequencing.
    [Show full text]
  • Cell Death Via Lipid Peroxidation and Protein Aggregation Diseases
    biology Review Cell Death via Lipid Peroxidation and Protein Aggregation Diseases Katsuya Iuchi * , Tomoka Takai and Hisashi Hisatomi Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijojikitamachi, Musashino-shi, Tokyo 180-8633, Japan; [email protected] (T.T.); [email protected] (H.H.) * Correspondence: [email protected] or [email protected]; Tel.: +81-422-37-3523 Simple Summary: It is essential for cellular homeostasis that biomolecules, such as DNA, proteins, and lipids, function properly. Disturbance of redox homeostasis produces aberrant biomolecules, including oxidized lipids and misfolded proteins, which increase in cells. Aberrant biomolecules are removed by excellent cellular clearance systems. However, when excess aberrant biomolecules remain in the cell, they disrupt organelle and cellular functions, leading to cell death. These aberrant molecules aggregate and cause apoptotic and non-apoptotic cell death, leading to various protein aggregation diseases. Thus, we investigated the cell-death cross-linking between lipid peroxidation and protein aggregation. Abstract: Lipid peroxidation of cellular membranes is a complicated cellular event, and it is both the cause and result of various diseases, such as ischemia-reperfusion injury, neurodegenerative diseases, and atherosclerosis. Lipid peroxidation causes non-apoptotic cell death, which is associated with cell fate determination: survival or cell death. During the radical chain reaction of lipid peroxidation, Citation: Iuchi, K.; Takai, T.; various oxidized lipid products accumulate in cells, followed by organelle dysfunction and the Hisatomi, H. Cell Death via Lipid induction of non-apoptotic cell death. Highly reactive oxidized products from unsaturated fatty acids Peroxidation and Protein are detected under pathological conditions.
    [Show full text]
  • Implications in Parkinson's Disease
    Journal of Clinical Medicine Review Lysosomal Ceramide Metabolism Disorders: Implications in Parkinson’s Disease Silvia Paciotti 1,2 , Elisabetta Albi 3 , Lucilla Parnetti 1 and Tommaso Beccari 3,* 1 Laboratory of Clinical Neurochemistry, Department of Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy; [email protected] (S.P.); [email protected] (L.P.) 2 Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy 3 Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti, 06123 Perugia, Italy; [email protected] * Correspondence: [email protected] Received: 29 January 2020; Accepted: 20 February 2020; Published: 21 February 2020 Abstract: Ceramides are a family of bioactive lipids belonging to the class of sphingolipids. Sphingolipidoses are a group of inherited genetic diseases characterized by the unmetabolized sphingolipids and the consequent reduction of ceramide pool in lysosomes. Sphingolipidoses include several disorders as Sandhoff disease, Fabry disease, Gaucher disease, metachromatic leukodystrophy, Krabbe disease, Niemann Pick disease, Farber disease, and GM2 gangliosidosis. In sphingolipidosis, lysosomal lipid storage occurs in both the central nervous system and visceral tissues, and central nervous system pathology is a common hallmark for all of them. Parkinson’s disease, the most common neurodegenerative movement disorder, is characterized by the accumulation and aggregation of misfolded α-synuclein that seem associated to some lysosomal disorders, in particular Gaucher disease. This review provides evidence into the role of ceramide metabolism in the pathophysiology of lysosomes, highlighting the more recent findings on its involvement in Parkinson’s disease. Keywords: ceramide metabolism; Parkinson’s disease; α-synuclein; GBA; GLA; HEX A-B; GALC; ASAH1; SMPD1; ARSA * Correspondence [email protected] 1.
    [Show full text]
  • PRODUCT SPECIFICATION Prest Antigen ACRV1 Product
    PrEST Antigen ACRV1 Product Datasheet PrEST Antigen PRODUCT SPECIFICATION Product Name PrEST Antigen ACRV1 Product Number APrEST80590 Gene Description acrosomal vesicle protein 1 Alternative Gene D11S4365, SP-10, SPACA2 Names Corresponding Anti-ACRV1 (HPA038718) Antibodies Description Recombinant protein fragment of Human ACRV1 Amino Acid Sequence Recombinant Protein Epitope Signature Tag (PrEST) antigen sequence: TSSQPNELSGSIDHQTSVQQLPGEFFSLENPSDAEALYETSSGLNTLSEH GSSEHGSSKHTVAEHTSGEHAE Fusion Tag N-terminal His6ABP (ABP = Albumin Binding Protein derived from Streptococcal Protein G) Expression Host E. coli Purification IMAC purification Predicted MW 25 kDa including tags Usage Suitable as control in WB and preadsorption assays using indicated corresponding antibodies. Purity >80% by SDS-PAGE and Coomassie blue staining Buffer PBS and 1M Urea, pH 7.4. Unit Size 100 µl Concentration Lot dependent Storage Upon delivery store at -20°C. Avoid repeated freeze/thaw cycles. Notes Gently mix before use. Optimal concentrations and conditions for each application should be determined by the user. Product of Sweden. For research use only. Not intended for pharmaceutical development, diagnostic, therapeutic or any in vivo use. No products from Atlas Antibodies may be resold, modified for resale or used to manufacture commercial products without prior written approval from Atlas Antibodies AB. Warranty: The products supplied by Atlas Antibodies are warranted to meet stated product specifications and to conform to label descriptions when used and stored properly. Unless otherwise stated, this warranty is limited to one year from date of sales for products used, handled and stored according to Atlas Antibodies AB's instructions. Atlas Antibodies AB's sole liability is limited to replacement of the product or refund of the purchase price.
    [Show full text]
  • Constitutive Activation of RAS/MAPK Pathway Cooperates with Trisomy 21 and Is Therapeutically Exploitable in Down Syndrome B-Cell Leukemia
    Author Manuscript Published OnlineFirst on March 27, 2020; DOI: 10.1158/1078-0432.CCR-19-3519 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Constitutive activation of RAS/MAPK pathway cooperates with trisomy 21 and is therapeutically exploitable in Down syndrome B-cell Leukemia Anouchka P. Laurent1,2, Aurélie Siret1, Cathy Ignacimouttou1, Kunjal Panchal3, M’Boyba K. Diop4, Silvia Jenny5, Yi-Chien Tsai5, Damien Ross-Weil1, Zakia Aid1, Naïs Prade6, Stéphanie Lagarde6, Damien Plassard7, Gaelle Pierron8, Estelle Daudigeos-Dubus4, Yann Lecluse4, Nathalie Droin1, Beat Bornhauser5, Laurence C. Cheung3,9, John D. Crispino10, Muriel Gaudry1, Olivier A. Bernard1, Elizabeth Macintyre11, Carole Barin Bonnigal12, Rishi S. Kotecha3,9,13, Birgit Geoerger4, Paola Ballerini14, Jean-Pierre Bourquin5, Eric Delabesse6, Thomas Mercher1,15 and Sébastien Malinge1,3 1INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France 2Université Paris Diderot, Paris, France 3Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia 4Gustave Roussy Institute Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Université Paris-Saclay, Villejuif, France 5Department of Pediatric Oncology, Children’s Research Centre, University Children’s Hospital Zurich, Zurich, Switzerland 6Centre of Research on Cancer of Toulouse (CRCT), CHU Toulouse, Université Toulouse III, Toulouse, France 7IGBMC, Plateforme GenomEast, UMR7104 CNRS, Ilkirch, France 8Service de Génétique, Institut Curie, Paris, France 9School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia 10Division of Hematology/Oncology, Northwestern University, Chicago, USA 11Hematology, Université de Paris, Institut Necker-Enfants Malades and Assistance Publique – Hopitaux de Paris, Paris, France 12Centre Hospitalier Universitaire de Tours, Tours, France 1 Downloaded from clincancerres.aacrjournals.org on September 30, 2021.
    [Show full text]
  • TCTE1 Is a Conserved Component of the Dynein Regulatory Complex and Is Required for Motility and Metabolism in Mouse Spermatozoa
    TCTE1 is a conserved component of the dynein regulatory complex and is required for motility and metabolism in mouse spermatozoa Julio M. Castanedaa,b,1, Rong Huac,d,1, Haruhiko Miyatab, Asami Ojib,e, Yueshuai Guoc,d, Yiwei Chengc,d, Tao Zhouc,d, Xuejiang Guoc,d, Yiqiang Cuic,d, Bin Shenc, Zibin Wangc, Zhibin Huc,f, Zuomin Zhouc,d, Jiahao Shac,d, Renata Prunskaite-Hyyrylainena,g,h, Zhifeng Yua,i, Ramiro Ramirez-Solisj, Masahito Ikawab,e,k,2, Martin M. Matzuka,g,i,l,m,n,2, and Mingxi Liuc,d,2 aDepartment of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030; bResearch Institute for Microbial Diseases, Osaka University, Suita, Osaka 5650871, Japan; cState Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, People’s Republic of China; dDepartment of Histology and Embryology, Nanjing Medical University, Nanjing 210029, People’s Republic of China; eGraduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 5650871, Japan; fAnimal Core Facility of Nanjing Medical University, Nanjing 210029, People’s Republic of China; gCenter for Reproductive Medicine, Baylor College of Medicine, Houston, TX 77030; hFaculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland; iCenter for Drug Discovery, Baylor College of Medicine, Houston, TX 77030; jWellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom; kThe Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; lDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; mDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; and nDepartment of Pharmacology, Baylor College of Medicine, Houston, TX 77030 Contributed by Martin M.
    [Show full text]
  • ACRV1 (NM 020069) Human Tagged ORF Clone Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC214263 ACRV1 (NM_020069) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: ACRV1 (NM_020069) Human Tagged ORF Clone Tag: Myc-DDK Symbol: ACRV1 Synonyms: D11S4365; SP-10; SPACA2 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RC214263 representing NM_020069 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGAACAGGTTTCTCTTGCTAATGAGTCTTTATCTGCTTGGATCTGCCAGAGGAACATCAAGTCAGCCTA ATGAGCTTTCTGGCTCCATAGATCATCAAACTTCAGTTCAGCAACTTCCAGGTGAGTTCTTTTCACTTGA AAACCCTTCTGATGCTGAGGCTTTATATGAGACTTCTTCAGGCCTGAACACTTTAAGTGAGCATGGTTCC AGTGAGCATGGTTCAAGCAAGCACACTGTGGCCGAGCACACTTCTGGAGAACATGCTGAGAGTGAGCATG CTTCAGGTGAGCCCGCTGCGACTGAACATGCTGAAGGTGAGCATACTGTAGGTGAGCAGCCTTCAGGAGA ACAGCCTTCAGGTGAACACCTCTCCGGAGAACAGCCTTTGAGTGAGCTTGAGTCAGGTGAACAGCCTTCA GATGAACAGCCTTCAGGTGAACATGGCTCCGGTGAACAGCCTTCTGGTGAGCAGGCCTCGGGTGAACAGC CTTCAGGCACAATATTAAATTGCTACACATGTGCTTATATGAATGATCAAGGAAAATGTCTTCGTGGAGA GGGAACCTGCATCACTCAGAATTCCCAGCAGTGCATGTTAAAGAAGATCTTTGAAGGTGGAAAACTCCAA TTCATGGTTCAAGGGTGTGAGAACATGTGCCCATCTATGAACCTCTTCTCCCATGGAACGAGGATGCAAA TTATATGCTGTCGAAATCAATCTTTCTGCAATAAGATC ACGCGTACGCGGCCGCTCGAGCAGAAACTCATCTCAGAAGAGGATCTGGCAGCAAATGATATCCTGGATT ACAAGGATGACGACGATAAGGTTTAA This product is
    [Show full text]
  • Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
    Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human.
    [Show full text]
  • Actin Binding LIM 1 (Ablim1) Negatively Controls Osteoclastogenesis by Regulating Cell Migration and Fusion
    Received: 14 September 2017 | Accepted: 16 March 2018 DOI: 10.1002/jcp.26605 ORIGINAL RESEARCH ARTICLE Actin binding LIM 1 (abLIM1) negatively controls osteoclastogenesis by regulating cell migration and fusion Haruna Narahara1,2 | Eiko Sakai1 | Yu Yamaguchi1 | Shun Narahara1 | Mayumi Iwatake1,* | Kuniaki Okamoto1,† | Noriaki Yoshida2 | Takayuki Tsukuba1 1 Department of Dental Pharmacology, Graduate School of Biomedical Sciences, Actin binding LIM 1 (abLIM1) is a cytoskeletal actin-binding protein that has been Nagasaki University, Nagasaki, Japan implicated in interactions between actin filaments and cytoplasmic targets. Previous 2 Department of Orthodontics and Dentofacial Orthopedics, Graduate School of Biomedical biochemical and cytochemical studies have shown that abLIM1 interacts and co- Sciences, Nagasaki University, Nagasaki, Japan localizes with F-actin in the retina and muscle. However, whether abLIM1 regulates Correspondence osteoclast differentiation has not yet been elucidated. In this study, we examined the Takayuki Tsukuba, Department of Dental role of abLIM1 in osteoclast differentiation and function. We found that abLIM1 Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852- expression was upregulated during receptor activator of nuclear factor kappa-B ligand 8588, Japan. (RANKL)-induced osteoclast differentiation, and that a novel transcript of abLIM1 was Email: [email protected] exclusively expressed in osteoclasts. Overexpression of abLIM1 in the murine Funding information monocytic cell line, RAW-D suppressed osteoclast differentiation and decreased JSPS KAKENHI, Grant numbers: 15H05298, 16K15790, 17H04379 expression of several osteoclast-marker genes. By contrast, small interfering RNA-induced knockdown of abLIM1 enhanced the formation of multinucleated osteoclasts and markedly increased the expression of the osteoclast-marker genes. Mechanistically, abLIM1 regulated the localization of tubulin, migration, and fusion in osteoclasts.
    [Show full text]
  • Functional Significance of the Two ACOX1 Isoforms and Their
    Laboratory Investigation (2010) 90, 696–708 & 2010 USCAP, Inc All rights reserved 0023-6837/10 $32.00 Functional significance of the two ACOX1 isoforms and their crosstalks with PPARa and RXRa Aurore Vluggens1,2,3, Pierre Andreoletti1,2, Navin Viswakarma3, Yuzhi Jia3, Kojiro Matsumoto3, Wim Kulik4, Mushfiquddin Khan5, Jiansheng Huang3, Dongsheng Guo3, Sangtao Yu3, Joy Sarkar3, Inderjit Singh5, M Sambasiva Rao3, Ronald J Wanders4, Janardan K Reddy3 and Mustapha Cherkaoui-Malki1,2 Disruption of the peroxisomal acyl-CoA oxidase 1 (Acox1) gene in the mouse results in the development of severe microvesicular hepatic steatosis and sustained activation of peroxisome proliferator-activated receptor-a (PPARa). These mice manifest spontaneous massive peroxisome proliferation in regenerating hepatocytes and eventually develop hepatocellular carcinomas. Human ACOX1, the first and rate-limiting enzyme of the peroxisomal b-oxidation pathway, has two isoforms including ACOX1a and ACOX1b, transcribed from a single gene. As ACOX1a shows reduced activity toward palmitoyl-CoA as compared with ACOX1b, we used adenovirally driven ACOX1a and ACOX1b to investigate their efficacy in the reversal of hepatic phenotype in Acox1(À/À) mice. In this study, we show that human ACOX1b is markedly effective in reversing the ACOX1 null phenotype in the mouse. In addition, expression of human ACOX1b was found to restore the production of nervonic (24:1) acid and had a negative impact on the recruitment of coactivators to the PPARa-response unit, which suggests that nervonic acid might well be an endogenous PPARa antagonist, with nervonoyl-CoA probably being the active form of nervonic acid. In contrast, restoration of docosahexaenoic (22:6) acid level, a retinoid-X-receptor (RXRa) agonist, was dependent on the concomitant hepatic expression of both ACOX1a and ACOX1b isoforms.
    [Show full text]
  • Novel Alternative Splicing Variants of ACOX1 and Their Differential Expression Patterns in Goats
    Arch. Anim. Breed., 61, 59–70, 2018 https://doi.org/10.5194/aab-61-59-2018 Open Access © Author(s) 2018. This work is distributed under the Creative Commons Attribution 4.0 License. Archives Animal Breeding Novel alternative splicing variants of ACOX1 and their differential expression patterns in goats Xian-Feng Wu1,*, Yuan Liu1,*, Cheng-Fang Gao1, Xin-Zhu Chen1, Xiao-Pei Zhang1, and Wen-Yang Li1 1Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, PR China *These authors contributed equally to this work. Correspondence: Wen-Yang Li ([email protected]) Received: 6 August 2017 – Revised: 29 October 2017 – Accepted: 14 November 2017 – Published: 24 January 2018 Abstract. As the first and rate-limiting enzyme of the peroxisomal β-oxidation pathway, acyl-coenzyme A ox- idase 1 (ACOX1), which is regulated by peroxisome proliferator-activated alfa (PPARα), is vital for fatty acid oxidation and deposition, especially in the lipid metabolism of very long-chain fatty acids. Alternative splicing events of ACOX1 have been detected in rodents, Nile tilapia, zebra fish and humans but not in goats. Herein, we identified a novel splice variant of the ACOX1 gene, which was designated as ACOX1-SV1, in addition to the complete transcript, ACOX1, in goats. The length of the ACOX1-SV1 coding sequence was 1983 bp, which presented a novel exon 2 variation owing to alternative 50-splice site selection in exon 2 and partial in- tron 1, compared to that in ACOX1. The protein sequence analysis indicated that ACOX1-SV1 was conserved across different species.
    [Show full text]
  • The Expanded Endocannabinoid System/Endocannabinoidome As a Potential Target for Treating Diabetes Mellitus
    Current Diabetes Reports (2019) 19:117 https://doi.org/10.1007/s11892-019-1248-9 OBESITY (KM GADDE, SECTION EDITOR) The Expanded Endocannabinoid System/Endocannabinoidome as a Potential Target for Treating Diabetes Mellitus Alain Veilleux1,2,3 & Vincenzo Di Marzo1,2,3,4,5 & Cristoforo Silvestri3,4,5 # Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Purpose of Review The endocannabinoid (eCB) system, i.e. the receptors that respond to the psychoactive component of cannabis, their endogenous ligands and the ligand metabolic enzymes, is part of a larger family of lipid signals termed the endocannabinoidome (eCBome). We summarize recent discoveries of the roles that the eCBome plays within peripheral tissues in diabetes, and how it is being targeted, in an effort to develop novel therapeutics for the treatment of this increasingly prevalent disease. Recent Findings As with the eCB system, many eCBome members regulate several physiological processes, including energy intake and storage, glucose and lipid metabolism and pancreatic health, which contribute to the development of type 2 diabetes (T2D). Preclinical studies increasingly support the notion that targeting the eCBome may beneficially affect T2D. Summary The eCBome is implicated in T2D at several levels and in a variety of tissues, making this complex lipid signaling system a potential source of many potential therapeutics for the treatments for T2D. Keywords Endocannabinoidome . Bioactive lipids . Peripheral tissues . Glucose . Insulin Introduction: The Endocannabinoid System cannabis-derived natural product, Δ9-tetrahydrocannabinol and its Subsequent Expansion (THC), responsible for most of the psychotropic, euphoric to the “Endocannabinoidome” and appetite-stimulating actions (via CB1 receptors) and immune-modulatory effects (via CB2 receptors) of marijuana, The discovery of two G protein-coupled receptors, the canna- opened the way to the identification of the endocannabinoids binoid receptor type-1 (CB1) and − 2 (CB2) [1, 2], for the (eCBs).
    [Show full text]