SEC16A Is a RAB10 Effector Required for Insulin- Stimulated GLUT4 Trafficking in Adipocytes
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Disruption of Adipose Rab10-Dependent Insulin
Page 1 of 35 Diabetes Vazirani et al. Disruption of Adipose Rab10-Dependent Insulin Signaling Causes Hepatic Insulin Resistance Reema P. Vazirani1, Akanksha Verma2, L. Amanda Sadacca1, Melanie S. Buckman3, Belen Picatoste1, Muheeb Beg1, Christopher Torsitano1, Joanne H. Bruno1, Rajesh T. Patel1, Kotryna Simonyte4, Joao P. Camporez5, Gabriela Moreira5, Domenick J. Falcone6, Domenico Accili7, Olivier Elemento2, Gerald I. Shulman6,8, Barbara B. Kahn4 and Timothy E. McGraw1,3* 1Department of Biochemistry, Weill Cornell Medical College 2Department of Physiology and Biophysics, Weill Cornell Medical College 3Department of Cardiothoracic Surgery, Weill Cornell Medical College 4Beth Israel Deaconess Medical Center, Harvard Medical School 5Departments of Internal Medicine and Cellular & Molecular Physiology, Yale University 6Department of Pathology, Weill Cornell Medical College 7Department of Medicine and Berrie Diabetes Center, Columbia University 8Howard Hughes Medical Institute, Yale University *Contact: Timothy E. McGraw, PhD 1300 York Ave New York, NY 10065 212-746-4982 [email protected] The authors have declared that no conflict of interest exists. 1 Diabetes Publish Ahead of Print, published online March 25, 2016 Diabetes Page 2 of 35 Vazirani et al. Abstract Insulin controls glucose uptake into adipose and muscle cells by regulating the amount of the Glut4 glucose transporter in the plasma membrane. The effect of insulin is to promote translocation of intracellular Glut4 to the plasma membrane. The small Rab GTPase Rab10 is required for insulin-stimulated Glut4 translocation in cultured 3T3-L1 adipocytes. Here we demonstrate that both insulin-stimulated glucose uptake and Glut4 translocation to the plasma membrane are reduced by about half in adipocytes from adipose-specific Rab10 knockout mice. -
MBNL1 Regulates Essential Alternative RNA Splicing Patterns in MLL-Rearranged Leukemia
ARTICLE https://doi.org/10.1038/s41467-020-15733-8 OPEN MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia Svetlana S. Itskovich1,9, Arun Gurunathan 2,9, Jason Clark 1, Matthew Burwinkel1, Mark Wunderlich3, Mikaela R. Berger4, Aishwarya Kulkarni5,6, Kashish Chetal6, Meenakshi Venkatasubramanian5,6, ✉ Nathan Salomonis 6,7, Ashish R. Kumar 1,7 & Lynn H. Lee 7,8 Despite growing awareness of the biologic features underlying MLL-rearranged leukemia, 1234567890():,; targeted therapies for this leukemia have remained elusive and clinical outcomes remain dismal. MBNL1, a protein involved in alternative splicing, is consistently overexpressed in MLL-rearranged leukemias. We found that MBNL1 loss significantly impairs propagation of murine and human MLL-rearranged leukemia in vitro and in vivo. Through transcriptomic profiling of our experimental systems, we show that in leukemic cells, MBNL1 regulates alternative splicing (predominantly intron exclusion) of several genes including those essential for MLL-rearranged leukemogenesis, such as DOT1L and SETD1A.Wefinally show that selective leukemic cell death is achievable with a small molecule inhibitor of MBNL1. These findings provide the basis for a new therapeutic target in MLL-rearranged leukemia and act as further validation of a burgeoning paradigm in targeted therapy, namely the disruption of cancer-specific splicing programs through the targeting of selectively essential RNA binding proteins. 1 Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 2 Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 3 Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. -
Investigation Into the Effect of LRRK2-Rab10 Protein Interactions on the Proboscis Extension Response of the Fruit Fly Drosophila Melanogaster
Investigation into the effect of LRRK2-Rab10 protein interactions on the Proboscis Extension Response of the fruit fly Drosophila melanogaster Laura Covill Masters by Research University of York Biology December 2018 Abstract Parkinson’s Disease (PD) is a debilitating disease which affects 1% of the population worldwide and is characterised by stiffness, tremor and bradykinesia. PD is a complex disease with many suspected genetic and environmental causes, and it is critical to understand all the pathways involved in disease progression to develop effective therapies for PD, which currently has no cure. A kinase- coding gene, LRRK2 has emerged as a focal point for much PD research, particularly PD-associated SNP LRRK2-G2019S, which leads to LRRK2 overactivity. Rab proteins, a series of small GTPases, have been identified among the proteins phosphorylated by LRRK2. These interactions may be modelled in the fruit fly Drosophila melanogaster. Using optogenetics in the fly, this project investigates the relationship between the LRRK2-G2019S and Rab10 interaction, and the speed and degree of tremor of Proboscis Extension Response (PER) by triggering a PER in fly lines of different genotypes. Significant bradykinesia in Rab10 null flies which was not recreated in flies with dopaminergic neuron Rab10RNAi suggests that the bradykinesia PER phenotype is caused by off-target effect of Rab10-KO in another tissue of the fly than the dopaminergic neurons. Over-expression of Rab10 in dopaminergic neurons of flies also expressing LRRK2-G2019S produced -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
Genome-Wide Association and Gene Enrichment Analyses of Meat Sensory Traits in a Crossbred Brahman-Angus
Proceedings of the World Congress on Genetics Applied to Livestock Production, 11. 124 Genome-wide association and gene enrichment analyses of meat tenderness in an Angus-Brahman cattle population J.D. Leal-Gutíerrez1, M.A. Elzo1, D. Johnson1 & R.G. Mateescu1 1 University of Florida, Department of Animal Sciences, 2250 Shealy Dr, 32608 Gainesville, Florida, United States. [email protected] Summary The objective of this study was to identify genomic regions associated with meat tenderness related traits using a whole-genome scan approach followed by a gene enrichment analysis. Warner-Bratzler shear force (WBSF) was measured on 673 steaks, and tenderness and connective tissue were assessed by a sensory panel on 496 steaks. Animals belong to the multibreed Angus-Brahman herd from University of Florida and range from 100% Angus to 100% Brahman. All animals were genotyped with the Bovine GGP F250 array. Gene enrichment was identified in two pathways; the first pathway is involved in negative regulation of transcription from RNA polymerase II, and the second pathway groups several cellular component of the endoplasmic reticulum membrane. Keywords: tenderness, gene enrichment, regulation of transcription, cell growth, cell proliferation Introduction Identification of quantitative trait loci (QTL) for any complex trait, including meat tenderness, is the first most important step in the process of understanding the genetic architecture underlying the phenotype. Given a large enough population and a dense coverage of the genome, a genome-wide association study (GWAS) is usually successful in uncovering major genes and QTLs with large and medium effect on these type of traits. Several GWA studies on Bos indicus (Magalhães et al., 2016; Tizioto et al., 2013) or crossbred beef cattle breeds (Bolormaa et al., 2011b; Hulsman Hanna et al., 2014; Lu et al., 2013) were successful at identifying QTL for meat tenderness; and most of them include the traditional candidate genes µ-calpain and calpastatin. -
ADHD) Gene Networks in Children of Both African American and European American Ancestry
G C A T T A C G G C A T genes Article Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American Ancestry Yichuan Liu 1 , Xiao Chang 1, Hui-Qi Qu 1 , Lifeng Tian 1 , Joseph Glessner 1, Jingchun Qu 1, Dong Li 1, Haijun Qiu 1, Patrick Sleiman 1,2 and Hakon Hakonarson 1,2,3,* 1 Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; [email protected] (Y.L.); [email protected] (X.C.); [email protected] (H.-Q.Q.); [email protected] (L.T.); [email protected] (J.G.); [email protected] (J.Q.); [email protected] (D.L.); [email protected] (H.Q.); [email protected] (P.S.) 2 Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA 3 Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA * Correspondence: [email protected]; Tel.: +1-267-426-0088 Abstract: Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with poorly understood molecular mechanisms that results in significant impairment in children. In this study, we sought to assess the role of rare recurrent variants in non-European populations and outside of coding regions. We generated whole genome sequence (WGS) data on 875 individuals, Citation: Liu, Y.; Chang, X.; Qu, including 205 ADHD cases and 670 non-ADHD controls. The cases included 116 African Americans H.-Q.; Tian, L.; Glessner, J.; Qu, J.; Li, (AA) and 89 European Americans (EA), and the controls included 408 AA and 262 EA. -
Private Rare Deletions in SEC16A and MAMDC4 May Represent Novel
Basic and translational research Ann Rheum Dis: first published as 10.1136/annrheumdis-2014-206484 on 8 May 2015. Downloaded from EXTENDED REPORT Private rare deletions in SEC16A and MAMDC4 may represent novel pathogenic variants in familial axial spondyloarthritis Darren D O’Rielly,1 Mohammed Uddin,2 Dianne Codner,1 Michael Hayley,3 Jiayi Zhou,4 Lourdes Pena-Castillo,4 Ahmed A Mostafa,1 S M Mahmudul Hasan,1 William Liu,1 Nigil Haroon,5 Robert Inman,5 Proton Rahman1 Handling editor Tore K Kvien ABSTRACT This ‘missing heritability’ is attributed, at least in ▸ Additional material is Objective Axial spondyloarthritis (AxSpA) represents a part, to inherent limitations of GWAS studies, which published online only. To view group of inflammatory axial diseases that share common primarily assess one type of genetic variation please visit the journal online clinical and histopathological manifestations. Ankylosing (ie, single nucleotide polymorphisms) in a case– (http://dx.doi.org/10.1136/ annrheumdis-2014-206484). spondylitis (AS) is the best characterised subset of AxSpA, control approach, and consequently limits searches to and its genetic basis has been extensively investigated. common variants. Rare variants, which might also fi For numbered af liations see Given that genome-wide association studies account for contribute to SpA susceptibility, occur in approxi- end of article. only 25% of AS heritability, the objective of this study mately 1% of the population, and many are likely to 6 Correspondence to was to discover rare, highly penetrant genetic variants in be specific to ethnic groups, isolates or families. Dr Proton Rahman, Faculty of AxSpA pathogenesis using a well-characterised, That SpA clearly clusters within families, evident Medicine, Memorial University, multigenerational family. -
Linkage, Whole Genome Sequence, and Biological Data Implicate Variants in RAB10 in Alzheimer’S Disease Resilience Perry G
Ridge et al. Genome Medicine (2017) 9:100 DOI 10.1186/s13073-017-0486-1 RESEARCH Open Access Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience Perry G. Ridge1†, Celeste M. Karch2†, Simon Hsu2, Ivan Arano1, Craig C. Teerlink3, Mark T. W. Ebbert1,4, Josue D. Gonzalez Murcia1, James M. Farnham3, Anna R. Damato2, Mariet Allen5, Xue Wang6, Oscar Harari2, Victoria M. Fernandez2, Rita Guerreiro7, Jose Bras7, John Hardy7, Ronald Munger8, Maria Norton9, Celeste Sassi7,10, Andrew Singleton10, Steven G. Younkin5, Dennis W. Dickson5, Todd E. Golde11, Nathan D. Price12, Nilüfer Ertekin-Taner13, Carlos Cruchaga2, Alison M. Goate14, Christopher Corcoran15, JoAnn Tschanz16, Lisa A. Cannon-Albright3,17, John S. K. Kauwe18* and for the Alzheimer’s Disease Neuroimaging Initative Abstract Background: While age and the APOE ε4 allele are major risk factors for Alzheimer’s disease (AD), a small percentage of individuals with these risk factors exhibit AD resilience by living well beyond 75 years of age without any clinical symptoms of cognitive decline. Methods: We used over 200 “AD resilient” individuals and an innovative, pedigree-based approach to identify genetic variants that segregate with AD resilience. First, we performed linkage analyses in pedigrees with resilient individuals and a statistical excess of AD deaths. Second, we used whole genome sequences to identify candidate SNPs in significant linkage regions. Third, we replicated SNPs from the linkage peaks that reduced risk for AD in an independent dataset and in a gene-based test. Finally, we experimentally characterized replicated SNPs. Results: Rs142787485 in RAB10 confers significant protection against AD (p value = 0.0184, odds ratio = 0.5853). -
Supplementary Information – Postema Et Al., the Genetics of Situs Inversus Totalis Without Primary Ciliary Dyskinesia
1 Supplementary information – Postema et al., The genetics of situs inversus totalis without primary ciliary dyskinesia Table of Contents: Supplementary Methods 2 Supplementary Results 5 Supplementary References 6 Supplementary Tables and Figures Table S1. Subject characteristics 9 Table S2. Inbreeding coefficients per subject 10 Figure S1. Multidimensional scaling to capture overall genomic diversity 11 among the 30 study samples Table S3. Significantly enriched gene-sets under a recessive mutation model 12 Table S4. Broader list of candidate genes, and the sources that led to their 13 inclusion Table S5. Potential recessive and X-linked mutations in the unsolved cases 15 Table S6. Potential mutations in the unsolved cases, dominant model 22 2 1.0 Supplementary Methods 1.1 Participants Fifteen people with radiologically documented SIT, including nine without PCD and six with Kartagener syndrome, and 15 healthy controls matched for age, sex, education and handedness, were recruited from Ghent University Hospital and Middelheim Hospital Antwerp. Details about the recruitment and selection procedure have been described elsewhere (1). Briefly, among the 15 people with radiologically documented SIT, those who had symptoms reminiscent of PCD, or who were formally diagnosed with PCD according to their medical record, were categorized as having Kartagener syndrome. Those who had no reported symptoms or formal diagnosis of PCD were assigned to the non-PCD SIT group. Handedness was assessed using the Edinburgh Handedness Inventory (EHI) (2). Tables 1 and S1 give overviews of the participants and their characteristics. Note that one non-PCD SIT subject reported being forced to switch from left- to right-handedness in childhood, in which case five out of nine of the non-PCD SIT cases are naturally left-handed (Table 1, Table S1). -
Molecular Evolution of Voltage-Gated Calcium Channels of L and N Types and Their Genomic Regions
UPTEC X 12 006 Examensarbete 30 hp April 2012 Molecular evolution of voltage-gated calcium channels of L and N types and their genomic regions Jenny Widmark Molecular Biotechnology Programme Uppsala University School of Engineering UPTEC X 12 006 Date of issue 2012-04 Author Jenny Widmark Title (English) Molecular evolution of voltage-gated calcium channels of L and N types and their genomic regions Title (Swedish) Abstract The expansion of the voltage-gated calcium channel alpha 1 subunit families (CACNA1) of L and N types was investigated by combining phylogenetic analyses (neighbour-joining and maximum likelihood) with chromosomal data. Neighbouring gene families were analysed to see if the chromosomal regions duplicated through whole genome doublings in vertebrates. Results show that both types of CACNA1 expanded in two ancient whole genome duplications as parts of larger genomic regions. Many gene families in these regions obtained copies in an additional teleost-specific genome duplication. This diversification of CACNA1 genes probably contributed to evolutionary innovations in nervous system function. Keywords Evolution, vertebrate, voltage-gated calcium channel, whole genome duplication Supervisors Dan Larhammar Uppsala University Scientific reviewer Tatjana Haitina Uppsala University Project name Sponsors Language Security English Classification ISSN 1401-2138 Supplementary bibliographical information Pages 57 Biology Education Centre Biomedical Center Husargatan 3 Uppsala Box 592 S-75124 Uppsala Tel +46 (0)18 4710000 Fax +46 (0)18 471 4687 Molecular evolution of voltage-gated calcium channels of L and N types and their genomic regions Jenny Widmark Populärvetenskaplig sammanfattning I alla celler i en organism finns en och samma uppsättning av arvsmassa (DNA), denna uppsättning kallas för ett genom och i genomet finns alla gener. -
The P53mh Algorithm and Its Application in Detecting P53-Responsive Genes
The p53MH algorithm and its application in detecting p53-responsive genes J. Hoh*†‡, S. Jin§†, T. Parrado*, J. Edington*, A. J. Levine§, and J. Ott* *Laboratories of Statistical Genetics and §Cancer Biology of The Rockefeller University, 1230 York Avenue, New York, NY 10021 Contributed by A. J. Levine, May 6, 2002 A computer algorithm, p53MH, was developed, which identifies overall binding likelihood is needed for a given gene of arbitrary putative p53 transcription factor DNA-binding sites on a genome- size. Three features have been implemented in an algorithm to wide scale with high power and versatility. With the sequences meet the above requirements: binding propensity plots, weighted from the human and mouse genomes, putative p53 DNA-binding scores, and statistical significance for most likely binding sites. elements were identified in a scan of 2,583 human genes and 1,713 This computer algorithm has been used to identify putative mouse orthologs based on the experimental data of el-Deiry et al. binding elements on a genomewide scale. The algorithm, [el-Deiry, W. S., Kern, S. E., Pietenpol, J. A., Kinzler, K. W. & p53MH, uses an optimal scoring system as an indication of the Vogelstein, B. (1992) Nat. Genet. 1, 45–49] and Funk et al. [Funk, percent similarity to the consensus. It can simultaneously screen W. D., Pak, D. T., Karas, R. H., Wright, W. E. & Shay, J. W. (1992) Mol. thousands of genes for degenerate consensus sequences in the Cell. Biol. 12, 2866–2871] (http:͞͞linkage.rockefeller.edu͞p53). The course of only a few minutes. With this, based on the available p53 DNA-binding motif consists of a 10-bp palindrome and most annotated human sequence databases, a White Page-like direc- commonly a second related palindrome linked by a spacer region. -
RABIF/MSS4 Is a Rab-Stabilizing Holdase Chaperone Required for GLUT4 Exocytosis
RABIF/MSS4 is a Rab-stabilizing holdase chaperone required for GLUT4 exocytosis Daniel R. Gulbransona, Eric M. Davisa, Brittany A. Demmitta,b, Yan Ouyanga, Yihong Yec, Haijia Yua,d,1, and Jingshi Shena,1 aDepartment of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309; bInstitute for Behavioral Genetics, University of Colorado, Boulder, CO 80309; cLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; and dJiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China Edited by Jennifer Lippincott-Schwartz, Howard Hughes Medical Institute, Ashburn, VA, and approved August 21, 2017 (received for review July 7, 2017) Rab GTPases are switched from their GDP-bound inactive confor- anabolic hormone insulin facilitates glucose uptake by acutely mation to a GTP-bound active state by guanine nucleotide exchange relocating GLUT4 from intracellular compartments to the cell factors (GEFs). The first putative GEFs isolated for Rabs are RABIF surface (6, 20, 21, 23). Upon the termination of insulin signaling, (Rab-interacting factor)/MSS4 (mammalian suppressor of Sec4) and GLUT4 is retrieved from the plasma membrane through endocy- its yeast homolog DSS4 (dominant suppressor of Sec4). However, tosis and returns to intracellular storage vesicles (6). Importantly, the biological function and molecular mechanism of these molecules the components of GLUT4 exocytosis are also involved in the remained unclear. In a genome-wide CRISPR genetic screen, we regulation of other exocytic pathways such as insulin secretion and isolated RABIF as a positive regulator of exocytosis.