DOCSLIB.ORG

The Role of High Density Lipoprotein Compositional and Functional Heterogeneity in Metabolic Disease

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Role of High Density Lipoprotein Compositional and Functional Heterogeneity in Metabolic Disease The role of high density lipoprotein compositional and functional heterogeneity in metabolic disease By Scott M. Gordon B.S. State University of New York College at Brockport October, 2012 A Dissertation Presented to the Faculty of The University of Cincinnati College of Medicine in partial fulfillment of the requirements for the Degree of Doctor of Philosophy from the Pathobiology and Molecular Medicine graduate program W. Sean Davidson Ph.D. (Chair) David Askew Ph.D. Professor and Thesis Chair Professor Department of Pathology Department of Pathology University of Cincinnati University of Cincinnati Francis McCormack M.D. Gangani Silva Ph.D. Professor Assistant Professor Department of Pathology Department of Pathology University of Cincinnati University of Cincinnati Jason Lu Ph.D. Assistant Professor Division of Bioinformatics Cincinnati Children’s Hospital i Abstract High density lipoproteins (HDL) are complexes of phospholipid, cholesterol and protein that circulate in the blood. Epidemiological studies have demonstrated a strong inverse correlation between plasma levels of HDL associated cholesterol (HDL-C) and the incidence of cardiovascular disease (CVD). Clinically, HDL-C is often measured and used in combination with low density lipoprotein cholesterol (LDL-C) to assess overall cardiovascular health. HDL have been shown to possess a wide variety of functional attributes which likely contribute to this protection including anti-inflammatory and anti- oxidative properties and the ability to remove excess cholesterol from peripheral tissues and deliver it to the liver for excretion, a process known as reverse cholesterol transport. This functional diversity might be explained by the complexity of HDL composition. Recent studies have taken advantage of advances in mass spectrometry technologies to characterize the proteome of total HDL finding that over 50 different proteins can associate with these particles. This adds to a growing body of evidence that supports the global hypothesis of this thesis which is that the total pool of HDL in an individual is composed of numerous subspecies with distinct protein and lipid compositions and therefore will have distinct functional properties. Additionally, we believe that the composition of HDL is dynamic and can change in response to changes in the environment of the blood, as can occur in disease. To test these hypotheses we devised an approach based on three aims. Aim 1: Identify and characterize HDL subspecies based on protein composition. Aim 2: Analyze functional heterogeneity across separated plasma HDL fractions. Aim 3: Examine the effect of type 2 diabetes on HDL subspecies distribution in young adults. To accomplish these goals we have developed novel methods for the separation and fractionation of HDL subspecies from human plasma and their subsequent proteomic and functional analysis. Our findings support the existence of a diverse array of HDL species with distinct functionalities which correlate strongly with specific lipid or protein components of the particle. Additionally, we found that the composition of specific subfractions of HDL are altered in type 2 diabetes and that these fractions can predict vascular health better than LDL-C or HDL-C, suggesting that these may prove to be better biomarkers for cardiovascular risk than the current clinical standard. A detailed understanding of HDL subspeciation will be invaluable in the further development of HDL as a biomarker and therapeutic target not only for cardiovascular disease but a variety of disease states. ii Copyright Notice This dissertation is based, in part, on the following published manuscripts. Permission to include the information contained within these manuscripts was obtained from the publishers (Appendix 1). 1. Gordon, S., Durairaj, A., Lu, J., and Davidson, W.S. HDL Proteomics: Identifying New Drug Targets and Biomarkers by Understanding Functionality. (2010) Cur. Cardiovasc. Risk Reports., 4: 1-8. 2. Gordon, S.M., Jingyuan Deng, L. Jason Lu, and W. Sean Davidson. Proteomic characterization of human plasma high density lipoprotein fractionated by gel filtration chromatography. (2010) J. Proteome Res., Oct. 1; 9(10):5239-49. 3. Gordon, S.M., Hofmann, S., Askew, D., Davidson, W.S. High Density Lipoprotein: It’s Not Just About Lipid Transport Anymore. (2011) Trends in Endocrinology and Metabolism. 22, 9-15. iii Acknowledgements This work was supported by an American Heart Association Pre-doctoral Fellowship, a University Research Council Graduate Student Research Fellowship from the University of Cincinnati and by a pilot grant from the Cincinnati Diabetes and Obesity Center. I want to thank my thesis advisor Sean Davidson for his outstanding guidance and encouragement and for helping me to obtain the best possible opportunities to develop as a successful independent scientist. Adam Rich: My undergraduate research advisor who introduced me to the world of laboratory research and the scientific community. I cannot express enough appreciation for the way you took me in and allowed me to think and grow in your lab. Kathy and Phil Gordon: My amazing parents who have always encouraged me to reach for the stars and told me that there is nothing I cannot accomplish if I put my mind to it and work hard. iv Table of Contents Abstract……………………………………………………………………..………… ii Copyright notice………………………………………………...……………………. iii List of Figures………………………………………………………………………… vii List of Tables…………………………………………………………………………. ix Chapter 1. Introduction and background A. High density lipoproteins 1. Clinical importance of HDL………………………………….. 1 2. Functions of HDL…….…………………………………...….. 4 3. Current measures of HDL subfractions……………….…... 17 4. Applications of modern proteomics to HDL…….……..…... 20 5. Evidence for HDL subspeciation based on protein content ……………………………………………………..…. 24 6. HDL subspeciation and its impact on the treatment of cardiovascular disease……………………………………... 27 B. Goals of thesis research 1. Aim 1: To identify and characterize HDL subspecies based on protein composition…………………………….. 30 2. Aim 2: Analyze functional heterogeneity across separated plasma HDL fractions…………………………. 31 3. Aim 3: Examine the effect of type 2 diabetes on HDL subspecies distribution in young adults…………………… 31 Chapter 2. Proteomic characterization of human plasma high density lipoprotein fractionated by gel filtration chromatography A. Introduction……………………………………………….…..………. 57 B. Experimental………………………………………………….………. 60 C. Results……………………………………………………..…….……. 63 D. Discussion…………………………………………………………….. 69 E. Conclusions…………………………………………………………… 74 Chapter 3. A novel correlation analysis to determine HDL subspecies protein composition A. Introduction……………………………………………………..…….. 91 B. Experimental………………………………………………………….. 92 C. Results………………………………………………………………… 95 D. Discussion……………………………………………………………. 99 v Chapter 4. Using apolipoprotein deficient systems to study HDL composition A. Introduction…………………………………………………………… 114 B. Experimental………………………………………………………….. 116 C. Results………………………………………………………………… 117 D. Discussion…………………………………………………………….. 121 Chapter 5. Functional analysis of HDL subfractions A. Introduction…………………………………………………………... 145 B. Methods…………………..…………………………………………... 146 C. Results………………………………………………………………… 148 D. Discussion……………………………………………………………. 152 Chapter 6. Effects of type 2 diabetes on lipoprotein composition and arterial stiffness in adolescents and young adults A. Introduction…………………………………………………………... 162 B. Methods…………………..…………………………………………… 164 C. Results………………………………………………………………… 168 D. Discussion……………………………………………………………. 174 Chapter 7. Discussion A. Thesis Summary..………………………………………………….... 200 B. Contributions of this work.………………………………………….. 203 C. The future of HDL subspecies research and clinical implications. 207 Appendix I. Reproduction Rights…………………………………………………. x Appendix II. Supplemental Data………………………………………………..…. xiii vi List of Figures Chapter 1. 1-1. The increasing functional heterogeneity of high density lipoprotein. Chapter 2. 2-1. Elution profiles from Superose 6 (2x) and Superdex 200 (3x) size exclusion chromatography configurations. 2-2. SDS PAGE comparison of total HDL preparations derived from ultracentrifugation (UC) and gel filtration (GF) chromatography. 2-3. Ability of calcium silicate hydrate (CSH) to bind ultracentrifugally isolated human plasma lipoproteins. 2-4. Ability of CSH to bind phospholipid-containing particles from fractions collected by gel filtration chromatography. 2-5. Examples of elution profile shifts for proteins upon ether delipidation of fresh human plasma. 2-6. Lipid-associated proteins identified in the plasmas of 3 normolipidemic donors. 2-7. Distribution patterns of common HDL associated proteins across gel filtration fractions. 2-8. Triple Superdex distribution profiles for identified lipid- associated proteins. 2-9. Gene Ontology functional associations of newly identified lipoprotein associated proteins. Chapter 3. 3-1. Correlation strategy for the identification of phospholipid particle subspecies. 3-2. Lipid and protein distribution profiles produced by gel filtration chromatography. 3-3. Lipid and protein distribution profiles produced by anion exchange chromatography. 3-4. Lipid and protein distribution profiles produced by isoelectric focusing. 3-5 Heat map displaying protein distribution patterns by anion exchange chromatography. 3-6. Heat map displaying protein distribution patterns by isoelectric focusing. 3-7. Tracking co-migratory patterns of protein pairs across different
Load more

Recommended publications
  • Genome-Wide Association Study of Increasing Suicidal Ideation During Antidepressant Treatment in the GENDEP Project
    The Pharmacogenomics Journal (2012) 12, 68–77 & 2012 Macmillan Publishers Limited. All rights reserved 1470-269X/12 www.nature.com/tpj ORIGINAL ARTICLE Genome-wide association study of increasing suicidal ideation during antidepressant treatment in the GENDEP project NPerroud1,2,3,RUher1, Suicidal thoughts during antidepressant treatment have been the focus of 1 2,3,4 several candidate gene association studies. The aim of the present genome- MYM Ng , M Guipponi , wide association study was to identify additional genetic variants involved in 5 6 JHauser, N Henigsberg , increasing suicidal ideation during escitalopram and nortriptyline treatment. WMaier7,OMors8, A total of 706 adult participants of European ancestry, treated for major M Gennarelli9, M Rietschel10, depression with escitalopram or nortriptyline over 12 weeks in the Genome- DSouery11, MZ Dernovsek12, Based Therapeutic Drugs for Depression (GENDEP) study were genotyped 13 14 with Illumina Human 610-Quad Beadchips (Illumina, San Diego, CA, USA). AS Stamp ,MLathrop , A total of 244 subjects experienced an increase in suicidal ideation AFarmer1, G Breen1,KJAitchison1, during follow-up. The genetic marker most significantly associated with CM Lewis1,IWCraig1 increasing suicidality (8.28 Â 10À7) was a single-nucleotide polymorphism and P McGuffin1 (SNP; rs11143230) located 30 kb downstream of a gene encoding guanine deaminase (GDA) on chromosome 9q21.13. Two suggestive drug-specific 1MRC Social, Genetic and Developmental Psychiatry associations within KCNIP4 (Kv channel-interacting protein 4; chromosome Centre, Institute of Psychiatry, King’s College 4p15.31) and near ELP3 (elongation protein 3 homolog; chromosome London, London, UK; 2Department of Psychiatry, 8p21.1) were found in subjects treated with escitalopram.
    [Show full text]
  • Identification of the Binding Partners for Hspb2 and Cryab Reveals
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity.
    [Show full text]
  • The Expression of the Human Apolipoprotein Genes and Their Regulation by Ppars
    CORE Metadata, citation and similar papers at core.ac.uk Provided by UEF Electronic Publications The expression of the human apolipoprotein genes and their regulation by PPARs Juuso Uski M.Sc. Thesis Biochemistry Department of Biosciences University of Kuopio June 2008 Abstract The expression of the human apolipoprotein genes and their regulation by PPARs. UNIVERSITY OF KUOPIO, the Faculty of Natural and Environmental Sciences, Curriculum of Biochemistry USKI Juuso Oskari Thesis for Master of Science degree Supervisors Prof. Carsten Carlberg, Ph.D. Merja Heinäniemi, Ph.D. June 2008 Keywords: nuclear receptors; peroxisome proliferator-activated receptor; PPAR response element; apolipoprotein; lipid metabolism; high density lipoprotein; low density lipoprotein. Lipids are any fat-soluble, naturally-occurring molecules and one of their main biological functions is energy storage. Lipoproteins carry hydrophobic lipids in the water and salt-based blood environment for processing and energy supply in liver and other organs. In this study, the genomic area around the apolipoprotein genes was scanned in silico for PPAR response elements (PPREs) using the in vitro data-based computer program. Several new putative REs were found in surroundings of multiple lipoprotein genes. The responsiveness of those apolipoprotein genes to the PPAR ligands GW501516, rosiglitazone and GW7647 in the HepG2, HEK293 and THP-1 cell lines were tested with real-time PCR. The APOA1, APOA2, APOB, APOD, APOE, APOF, APOL1, APOL3, APOL5 and APOL6 genes were found to be regulated by PPARs in direct or secondary manners. Those results provide new insights in the understanding of lipid metabolism and so many lifestyle diseases like atherosclerosis, type 2 diabetes, heart disease and stroke.
    [Show full text]
  • A Gene Expression Resource Generated by Genome-Wide Lacz
    © 2015. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2015) 8, 1467-1478 doi:10.1242/dmm.021238 RESOURCE ARTICLE A gene expression resource generated by genome-wide lacZ profiling in the mouse Elizabeth Tuck1,**, Jeanne Estabel1,*,**, Anika Oellrich1, Anna Karin Maguire1, Hibret A. Adissu2, Luke Souter1, Emma Siragher1, Charlotte Lillistone1, Angela L. Green1, Hannah Wardle-Jones1, Damian M. Carragher1,‡, Natasha A. Karp1, Damian Smedley1, Niels C. Adams1,§, Sanger Institute Mouse Genetics Project1,‡‡, James N. Bussell1, David J. Adams1, Ramiro Ramırez-Soliś 1, Karen P. Steel1,¶, Antonella Galli1 and Jacqueline K. White1,§§ ABSTRACT composite of RNA-based expression data sets. Strong agreement was observed, indicating a high degree of specificity in our data. Knowledge of the expression profile of a gene is a critical piece of Furthermore, there were 1207 observations of expression of a information required to build an understanding of the normal and particular gene in an anatomical structure where Bgee had no essential functions of that gene and any role it may play in the data, indicating a large amount of novelty in our data set. development or progression of disease. High-throughput, large- Examples of expression data corroborating and extending scale efforts are on-going internationally to characterise reporter- genotype-phenotype associations and supporting disease gene tagged knockout mouse lines. As part of that effort, we report an candidacy are presented to demonstrate the potential of this open access adult mouse expression resource, in which the powerful resource. expression profile of 424 genes has been assessed in up to 47 different organs, tissues and sub-structures using a lacZ reporter KEY WORDS: Gene expression, lacZ reporter, Mouse, Resource gene.
    [Show full text]
  • Research Article Characterization of the Equine Skeletal Muscle
    McGivney et al. BMC Genomics 2010, 11:398 http://www.biomedcentral.com/1471-2164/11/398 RESEARCH ARTICLE Open Access CharacterizationResearch article of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training Beatrice A McGivney1, Paul A McGettigan1, John A Browne1, Alexander CO Evans1,3, Rita G Fonseca2, Brendan J Loftus3, Amanda Lohan3, David E MacHugh1,3, Barbara A Murphy1, Lisa M Katz2 and Emmeline W Hill*1 Abstract Background: Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 - untrained, (9 ± 0.5 months old) and T2 - trained (20 ± 0.7 months old). Results: The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by the nuclear genome. Among the 58 genes with decreased expression, MSTN, a negative regulator of muscle growth, had the greatest decrease. Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways.
    [Show full text]
  • Cellular and Molecular Signatures in the Disease Tissue of Early
    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
    [Show full text]
  • System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation
    International Journal of Molecular Sciences Article System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation Nicolas Borisov 1,† , Yaroslav Ilnytskyy 2,3,†, Boseon Byeon 2,3,4,†, Olga Kovalchuk 2,3 and Igor Kovalchuk 2,3,* 1 Moscow Institute of Physics and Technology, 9 Institutsky lane, Dolgoprudny, Moscow Region 141701, Russia; [email protected] 2 Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; [email protected] (Y.I.); [email protected] (B.B.); [email protected] (O.K.) 3 Pathway Rx., 16 Sandstone Rd. S., Lethbridge, AB T1K 7X8, Canada 4 Biomedical and Health Informatics, Computer Science Department, State University of New York, 2 S Clinton St, Syracuse, NY 13202, USA * Correspondence: [email protected] † First three authors contributed equally to this research. Abstract: There are many varieties of Cannabis sativa that differ from each other by composition of cannabinoids, terpenes and other molecules. The medicinal properties of these cultivars are often very different, with some being more efficient than others. This report describes the development of a method and software for the analysis of the efficiency of various cannabis extracts to detect the anti-inflammatory properties of the various cannabis extracts. The method uses high-throughput gene expression profiling data but can potentially use other omics data as well. According to the signaling pathway topology, the gene expression profiles are convoluted into the signaling pathway activities using a signaling pathway impact analysis (SPIA) method. The method was tested by inducing inflammation in human 3D epithelial tissues, including intestine, oral and skin, and then exposing these tissues to various extracts and then performing transcriptome analysis.
    [Show full text]
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • Identification and Prioritization Genes
    Original Article 2015, Vol: 3, Issue: 1, Pages: 18-23 Bioinformatics useful tool in study of genes associated with diseases Research in Molecular Medicine DOI: 10.7508/rmm.2015.01.004 Identifying and prioritizing genes related to Familial hypercholesterolemia QTLs using gene ontology and protein interaction networks Ali Kazemi-Pour 1, Bahram Goliaei 2*, Hamid Pezeshk 3, Behjat Kalantari khandani 4 1 PhD student of Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 2 Professor of Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 3 Professor of statistics, Science College, University of Tehran, Tehran, Iran. 4 Assistant Professor of Internal Medicine, Kerman University of Medical Sciences, Kerman, Iran. Received: 17 Aug 2014 Abstract Revised : 4 Sep 2014 Background: Gene identification represents the first step to a better understanding of the physiological role of the underlying protein and disease Accepted: 10 Sep 2014 pathways, which in turn serves as a starting point for developing therapeutic interventions. Familial hypercholesterolemia is a hereditary metabolic disorder Corresponding Authors: Bahram Goliaei characterized by high low-density lipoprotein cholesterol levels. Institute of Biochemistry and Hypercholesterolemia is a quantitative trait that is controlled by interactions Biophysics, University of Tehran, among several quantitative trait loci. Many biological data is presented in the Tehran, Iran. context of biological networks and evaluation of biological networks is considered Phone: +98-2161113356 E-mail: [email protected] as the essential key to understanding complex biological systems. Materials and Methods: In this research, we used combination of information about quantitative trait loci of hypercholesterolemia with information of gene ontology and protein–protein interaction network for identification of genes associated with hypercholesterolemia.
    [Show full text]
  • Microarray Analysis Provides New Insights Into the Function of Apolipoprotein O in Hepg2 Cell Line Chen-Lu Wu, Shui-Ping Zhao* and Bi-Lian Yu*
    Wu et al. Lipids in Health and Disease 2013, 12:186 http://www.lipidworld.com/content/12/1/186 RESEARCH Open Access Microarray analysis provides new insights into the function of apolipoprotein O in HepG2 cell line Chen-Lu Wu, Shui-Ping Zhao* and Bi-Lian Yu* Abstract Background: Apolipoprotein O (apoO) is a new member of the apolipoprotein family. However, data on its physiological functions are limited and inconsistent. Using a microarray expression analysis, this study explored the function of apoO in liver cells. Methods: HepG2 cells were treated either with oleic acid or tumor necrosis factor-α for 24 h. mRNA and protein expression of apoO were assessed by quantitative real-time PCR (qRT-PCR) and Western blot respectively. An efficient lentiviral siRNA vector targeting the human apoO gene was designed and constructed. The gene expression profile of HepG2 human hepatocellular carcinoma cells transfected with the apoO silencing vector was investigated using a whole-genome oligonucleotide microarray. The expression levels of some altered genes were validated using qRT-PCR. Results: ApoO expression in HepG2 cells was dramatically affected by lipid and inflammatory stimuli. A total of 282 differentially expressed genes in apoO-silenced HepG2 cells were identified by microarray analysis. These genes included those participating in fatty acid metabolism, such as ACSL4, RGS16, CROT and CYP4F11, and genes participating in the inflammatory response, such as NFKBIZ, TNFSF15, USP2, IL-17, CCL23, NOTCH2, APH-1B and N2N. The gene Uncoupling protein 2 (UCP2), which is involved in both these metabolic pathways, demonstrated significant changes in mRNA level after transfection.
    [Show full text]
  • Fibrinolysis Influences SARS-Cov-2 Infection in Ciliated Cells
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.07.425801; this version posted January 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Fibrinolysis influences SARS-CoV-2 infection in ciliated cells 2 3 Yapeng Hou1, Yan Ding1, Hongguang Nie1, *, Hong-Long Ji2 4 5 1Department of Stem Cells and Regenerative Medicine, College of Basic Medical Science, China Medical 6 University, Shenyang, Liaoning 110122, China. 2Department of Cellular and Molecular Biology, University 7 of Texas Health Science Center at Tyler, Tyler, TX 75708, USA. 8 9 *Address correspondence to [email protected] 10 11 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.07.425801; this version posted January 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 12 Abstract 13 Rapid spread of COVID-19 has caused an unprecedented pandemic worldwide, and an inserted furin site 14 in SARS-CoV-2 spike protein (S) may account for increased transmissibility. Plasmin, and other host 15 proteases, may cleave the furin site of SARS-CoV-2 S protein and subunits of epithelial sodium channels ( 16 ENaC), resulting in an increment in virus infectivity and channel activity. As for the importance of ENaC in 17 the regulation of airway surface and alveolar fluid homeostasis, whether SARS-CoV-2 will share and 18 strengthen the cleavage network with ENaC proteins at the single-cell level is urgently worthy of consideration.
    [Show full text]
  • Specificity of a Polyclonal Fecal Elastase ELISA for CELA3
    RESEARCH ARTICLE Specificity of a Polyclonal Fecal Elastase ELISA for CELA3 Frank Ulrich Weiss, Christoph Budde, Markus M. Lerch* University Medicine Greifswald, Department of Medicine A, Ferdinand Sauerbruch-Str., D-17475 Greifswald, Germany * [email protected] a11111 Abstract Introduction Elastase is a proteolytic pancreatic enzyme that passes through the gastrointestinal tract undergoing only limited degradation. ELISA tests to determine stool elastase concentra- tions have therefore been developed for the diagnosis of exocrine pancreatic insufficiency. OPEN ACCESS Five different isoforms of pancreatic elastase (CELA1, CELA2A, CELA2B, CELA3A, Citation: Weiss FU, Budde C, Lerch MM (2016) CELA3B) are encoded in the human genome. We have investigated three different poly- Specificity of a Polyclonal Fecal Elastase ELISA for CELA3. PLoS ONE 11(7): e0159363. doi:10.1371/ clonal antisera that are used in a commercial fecal elastase ELISA to determine their speci- journal.pone.0159363 ficity for different pancreatic elastase isoforms. Editor: Keping Xie, The University of Texas MD Anderson Cancer Center, UNITED STATES Material and Methods Received: October 9, 2015 Different polyclonal rabbit antisera against human elastase peptides (BIOSERV Diagnos- Accepted: July 2, 2016 tics GmbH, Germany) were tested by Western blot analysis of human pancreatic juice, in HEK-293 cells expressing Elastase constructs, and in the protein content of porcine pancre- Published: July 26, 2016 atin, used for treatment of exocrine pancreatic insufficiency. Copyright: © 2016 Weiss et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits Results unrestricted use, distribution, and reproduction in any In human pancreatic juice the polyclonal antisera detected proteins at the corresponding medium, provided the original author and source are size of human pancreatic elastase isoforms (~29kDa).
    [Show full text]