A Focus on Retinol Metabolism" (2011)
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Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
AGPAT2 Gene 1-Acylglycerol-3-Phosphate O-Acyltransferase 2
AGPAT2 gene 1-acylglycerol-3-phosphate O-acyltransferase 2 Normal Function The AGPAT2 gene provides instructions for making an enzyme that is found in many of the body's cells and tissues. It plays a critical role in the growth and development of adipocytes, which are cells that store fats for energy. Adipocytes are the major component of the body's fatty (adipose) tissue. The AGPAT2 enzyme is part of a chemical pathway in many cells that produces two important types of fats (lipids): glycerophospholipids and triacylglycerols. Glycerophospholipids are the major component of cell membranes and are involved in chemical signaling within cells. Triacylglycerols (also known as triglycerides) are fat molecules that are stored in adipocytes for later conversion to energy. The AGPAT2 enzyme is responsible for a particular chemical reaction in the production of these two types of lipids. Specifically, the enzyme helps convert a molecule called lysophosphatidic acid (LPA) to another molecule, phosphatidic acid (PA). Additional reactions convert phosphatidic acid to glycerophospholipids and triacylglycerols. Health Conditions Related to Genetic Changes Congenital generalized lipodystrophy At least 26 mutations in the AGPAT2 gene have been identified in people with congenital generalized lipodystrophy (also called Berardinelli-Seip congenital lipodystrophy) type 1. This rare condition is characterized by an almost total absence of adipose tissue and a very muscular appearance. A shortage of adipose tissue leads to multiple health problems, including high levels of triglycerides circulating in the bloodstream (hypertriglyceridemia) and diabetes mellitus. The AGPAT2 gene mutations that cause congenital generalized lipodystrophy type 1 greatly reduce or eliminate the activity of the AGPAT2 enzyme. -
Biomolecules
biomolecules Article The Vitamin D Receptor Regulates Glycerolipid and Phospholipid Metabolism in Human Hepatocytes Teresa Martínez-Sena 1, Polina Soluyanova 1, Carla Guzmán 1, José Manuel Valdivielso 2 , José Vicente Castell 1,3,4 and Ramiro Jover 1,3,4,* 1 Experimental Hepatology Unit, IIS Hospital La Fe, 46026 Valencia, Spain; [email protected] (T.M.-S.); [email protected] (P.S.); [email protected] (C.G.); [email protected] (J.V.C.) 2 Vascular and Renal Translational Research Group, Experimental Medicine Department, IRBLleida, 25196 Lleida, Spain; [email protected] 3 Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain 4 Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), ISCIII, 28029 Madrid, Spain * Correspondence: [email protected]; Tel.: +34-96124-6653 Received: 21 February 2020; Accepted: 20 March 2020; Published: 24 March 2020 Abstract: The vitamin D receptor (VDR) must be relevant to liver lipid metabolism because VDR deficient mice are protected from hepatosteatosis. Therefore, our objective was to define the role of VDR on the overall lipid metabolism in human hepatocytes. We developed an adenoviral vector for human VDR and performed transcriptomic and metabolomic analyses of cultured human hepatocytes upon VDR activation by vitamin D (VitD). Twenty percent of the VDR responsive genes were related to lipid metabolism, including MOGAT1, LPGAT1, AGPAT2, and DGAT1 (glycerolipid metabolism); CDS1, PCTP, and MAT1A (phospholipid metabolism); and FATP2, SLC6A12, and AQP3 (uptake of fatty acids, betaine, and glycerol, respectively). They were rapidly induced (4–6 h) upon VDR activation by 10 nM VitD or 100 µM lithocholic acid (LCA). -
Supplemental Table 1. List of Candidate Gene Filters Used in the Analysis of Exome Sequencing. MYOPATHY NEUROPATHY MND ABHD5
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Supplemental table 1. List of candidate gene filters used in the analysis of exome sequencing. MYOPATHY NEUROPATHY MND ABHD5 AAAS AAAS ACADL AARS1 AARS1 ACADM ABCA1 AGT ACADS ABCD1 ALAD ACADVL ABHD12 ALS2 ACTA1 ADCY6 ANG ADSSL1 AFG3L2 APEX1 AGL AIFM1 APOE AGPAT2 AMACR AR AGRN ANG ASAH1 AIRE AP1S1 ATM ALDOA APOA1 ATP7A ALG14 APTX ATXN2 ALG2 ARHGEF10 ATXN3 ALG3 ARL6IP1 B4GALT6 ANKRD2 ARSA BCL11B ANO5 ASAH1 BCL6 ASCC1 ATL1 BICD2 ATGL ATL3 BSCL2 ATP2A1 ATM C19orf12 ATRN ATXN1 C9orf72 B3GALNT2 ATXN10 CCS B3GNT2 ATXN2 CDH13 BAG3 ATXN3 CDH22 BIN1 ATXN7 CHCHD10 BSCL2 B2M CHMP2B BVES B4GALNT1 CNTF CACNA1S BAG3 CNTN4 CAPN3 BCKDHB CNTN6 CASQ1 BSCL2 CRIM1 CAV1 C12orf65 CRYM CAV3 C9orf72 CSNK1G3 CAVIN1 CLP1 CST3 CCDC78 CNTNAP1 CUL4B CDKN1C COX10 CYP2D6 CFL2 COX6A1 DAO Grunseich C, et al. J Neurol Neurosurg Psychiatry 2021;0:1–11. doi: 10.1136/jnnp-2020-325437 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry CHAT CPOX DCAF15 CHCHD10 CRYAB DCTN1 CHD7 CTDP1 DIAPH3 CHKB CTSA DISC1 CHN1 CYP27A1 DNAJB2 CHRM3 DARS2 DOC2B CHRNA1 DDHD1 DPP6 CHRNB1 DGUOK DYNC1H1 CHRND DHH EFEMP1 CHRNE DHTKD1 ELP3 CIDEC DMD EPHA4 CLCN1 DNAJB2 EWSR1 CLN3 DNAJC3 EXOSC3 CNBP DNM2 FBLN5 CNTN1 DYNC1H1 FBXO38 COA3 EGR2 FEZF2 COL12A1 EMD FGGY COL13A1 ERCC6 FIG4 COL6A ERCC8 FUS COL6A1 FAH GARS1 COL6A2 FAM126A GBE1 COL6A3 FBLN5 GMPPA COL9A3 FGD4 GRB14 COLQ FGF14 GRN COX10 FIG4 HEXA COX15 FLNC HFE CPT2 FLRT1 HINT1 CRAT FLVCR1 HSPB1 CRPPA FMR1 HSPB3 CRYAB FUS HSPB8 CTNS FXN IGHMBP2 DAG1 GALC ITPR2 DECR1 GAN KDR DES GARS1 KIFAP3 DGUOK GBA2 KLHL9 DIH1 GBE1 LAMA2 DMD GDAP1 LAS1L DMPK GJB1 LIF DNAJB6 GJB3 LIPC DNAJC19 GLA LOX Grunseich C, et al. -
An Oxysterol Sensor and a Major Playerin the Control of Lipogenesis Simon Ducheix, J.M.A
Liver X Receptor: an oxysterol sensor and a major playerin the control of lipogenesis Simon Ducheix, J.M.A. Lobaccaro, Pascal G.P. Martin, Hervé Guillou To cite this version: Simon Ducheix, J.M.A. Lobaccaro, Pascal G.P. Martin, Hervé Guillou. Liver X Receptor: an oxysterol sensor and a major playerin the control of lipogenesis. Chemistry and Physics of Lipids, Elsevier, 2011, 164 (6), pp.500-14. 10.1016/j.chemphyslip.2011.06.004. hal-02651993 HAL Id: hal-02651993 https://hal.inrae.fr/hal-02651993 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Chemistry and Physics of Lipids 164 (2011) 500–514 Contents lists available at ScienceDirect Chemistry and Physics of Lipids journal homepage: www.elsevier.com/locate/chemphyslip Review Liver X Receptor: an oxysterol sensor and a major player in the control of lipogenesis S. Ducheix a, J.M.A. Lobaccaro b, P.G. Martin a, H. Guillou a,∗ a Integrative Toxicology and Metabolism, UR 66, ToxAlim, INRA, 31 027 Toulouse Cedex 3, France b Clermont Université, CNRS Unité Mixte de Recherche 6247 Génétique, Reproduction et Développement, Université Blaise Pascal, Centre de Recherche en Nutrition Humaine d’Auvergne, BP 10448, F-63000 Clermont-Ferrand, France article info abstract Article history: De novo fatty acid biosynthesis is also called lipogenesis. -
Imbim Annual Report 2015
Department of Medical Biochemistry and Microbiology IMBIM ANNUAL REPORT 2015 DEPARTMENT OF MEDICAL BIOCHEMISTRY AND MICROBIOLOGY ANNUAL REPORT 2015 Pictures taken by Helena Öhrvik The role of copper in mast cell granule homeostasis Ctr2 is a protein involved in cellular transport of copper. Upper panels: staining for tryptase, a mast cell granule protease, in tryptase (Mcpt6)-deficient (negative control), Ctr2-/- and wild type (WT) mast cells. Note that the absence of Ctr2 causes upregulated expression of tryptase. Lower panels: staining of Ctr2-/- and WT mast cells with toluidine blue, a proteoglycan- binding dye. Note increased toluidine blue staining of Ctr2-/- mast cells, indicating increased proteoglycan content of granules. Öhrvik, H., Logeman, B., Noguchi, G., Eriksson, I., Kjellén, L., Thiele, D.J., Pejler, G. (2015) Ctr2 regulates mast cell maturation by affecting the storage and expression of tryptase and proteoglycans. J. Immunol. 195, 3654-364. Edited by Veronica Hammar ISBN no 978-91-979531-8-4 PREFACE Another year has passed with both small and large successes for the laboratory. The Department has a stable staff consisting of some 150 people. Including project workers, post doc etc we are around 250 persons that spend our daily work hours at the Department. Fortunately the granting situation for the IMBIM researchers improved considerably during 2015. Many of the small and medium sized research groups received grants that will help them continue to excel during the coming years. In addition Dan Andersson, Leif Andersson, Per Jemth, and a couple of scientists at ICM, received a hefty 47 milj kr grant from “Knut och Alice Wallenbergs Stiftelse” to support their research on the evolution of new genes and proteins. -
Transcriptional Regulation Profiling Reveals Disrupted Lipid Metabolism in Failing Hearts with a Pathogenic Phospholamban Mutation
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.30.402792; this version posted December 1, 2020. 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. Transcriptional regulation profiling reveals disrupted lipid metabolism in failing hearts with a pathogenic phospholamban mutation Jiayi Pei1,2,3*, Renee G.C. Maas1,2*, Ema Nagyova1,4, Johannes M.I.H. Gho1, Christian Snijders Blok1,2, Iris van Adrichem1,2, Jorg J.A. Calis1,2, René van Es1, Shahrzad Sepehrkhouy5, Dries Feyen6, Noortje van den Dungen4, Nico Lansu4, Nicolaas de Jonge1, Hester M. den Ruijter1, Manon M.H. Huibers5, Roel A. de Weger5, Linda W. van Laake1, Marianne C. Verhaar2,3, Peter van Tintelen7, Frank G. van Steenbeek1,2,8, Alain van Mil1,2, Jan W. Buikema1,2, Boudewijn Burgering9, Ioannis Kararikes6, Mark Mercola6, Pieter A. Doevendans1,10, Joost Sluijter1,2, Aryan Vink5, Caroline Cheng2,3, Michal Mokry2,4,11*, Folkert W. Asselbergs1,9,12,13*#, Magdalena Harakalova1,2*# *equal contribution; #corresponding authors 1 Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands 2 Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, The Netherlands 3 Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht (UMCU), The Netherlands 4 Epigenomics facility, University Medical Center Utrecht, Utrecht, The -
Complete Account of the Selection Process
Complete account of the selection process Andreas Hoppe. October 17, 2012 Contents 1 Principles 1 1.1 Selection of functions . 1 1.2 Selection of genes . 2 2 Selection in detail 3 2.1 Collagens . 4 2.2 Ethanol degradation . 5 2.3 Sphinganine-1P synthesis . 6 2.4 Tyrosine degradation . 7 2.5 Panthetheine synthesis . 8 2.6 Inositol synthesis . 9 2.7 Urea synthesis . 9 2.8 Bilirubin conjugation . 10 2.9 Cholesterol synthesis . 10 2.10 Bile acid synthesis and excretion . 12 2.11 b-hydroxybutyrate . 13 2.12 Glycolysis . 13 2.13 Triglycerides . 14 1 Principles 1.1 Selection of functions The selection process was based on the result of the ModeScore computation of the most regulated metabolic functions, in particular (with decreasing order of importance) • the comparison of the control and the TGFb series at the 24h time point (C/T 24h), • the comparison of the 1h to the 24h time point in the control series (C1h/24h), • the comparison of the 1h to the 24h time point in the TGFb series (T1h/24h), • the comparison of the 1h to the 6h time point in the control series (C1h/6h) in conjunction with the comparison of the 6h to the 24h time point in the control series (C6h/24h), and • the comparison of the control and the TGFb series at the 6h time point (C/T 6h), • the comparison of the 1h to the 6h time point in the control series (T1h/24h) in conjunction with the comparison of the 6h to the 24h time point in the TGFb series (T6h/24h) — not shown in the diagrams below. -
Inheritest 500 PLUS
Inheritest® 500 PLUS 525 genes Specimen ID: 00000000010 Container ID: H0651 Control ID: Acct #: LCA-BN Phone: SAMPLE REPORT, F-630049 Patient Details Specimen Details Physician Details DOB: 01/01/1991 Date Collected: 08/05/2019 12:00 (Local) Ordering: Age (yyy/mm/dd): 028/07/04 Date Received: 08/06/2019 Referring: Gender: Female Date Entered: 08/06/2019 ID: Patient ID: 00000000010 Date Reported: 08/21/2019 15:29 (Local) NPI: Ethnicity: Unknown Specimen Type: Blood Lab ID: MNEGA Indication: Carrier screening Genetic Counselor: None SUMMARY: POSITIVE POSITIVE RESULTS DISORDER (GENE) RESULTS INTERPRETATION Spinal muscular atrophy AT RISK AT RISK to be a silent carrier (2+0). For ethnic-specific risk (SMN1) 2 copies of SMN1; positive for revisions see Methods/Limitations. Genetic counseling is NMID: NM_000344 c.*3+80T>G SNP recommended. Risk: AT INCREASED RISK FOR AFFECTED PREGNANCY. See Additional Clinical Information. NEGATIVE RESULTS DISORDER (GENE) RESULTS INTERPRETATION Cystic fibrosis NEGATIVE This result reduces, but does not eliminate the risk to be a (CFTR) carrier. NMID: NM_000492 Risk: NOT at an increased risk for an affected pregnancy. Fragile X syndrome NEGATIVE: Not a carrier of a fragile X expansion. (FMR1) 29 and 36 repeats NMID: NM_002024 Risk: NOT at an increased risk for an affected pregnancy. ALL OTHER DISORDERS NEGATIVE This result reduces, but does not eliminate the risk to be a carrier. Risk: The individual is NOT at an increased risk for having a pregnancy that is affected with one of the disorders covered by this test. For partner's gene-specific risks, visit www.integratedgenetics.com. -
Characterizing Thyroid Hormone Mediated Action on Gene
Characterizing thyroid hormone mediated action on gene expression in mice: mechanistic insight into thyroid hormone response elements, thyroid hormone receptor-binding sites, and microRNAs by Martin A. Paquette A thesis submitted to the Faculty of Graduate and Postdoctoral Affairs in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Carleton University Ottawa, Ontario ©2013 Martin A. Paquette ABSTRACT Thyroid hormone (TH) exerts its effects by binding to the TH receptor (TR), which binds to TH response elements (TREs) to regulate target gene expression. Disruption of TH action can have detrimental health effects. The precise molecular mechanisms involved in TH mediated gene expression remain unclear. The overall objectives of this thesis were to: i) characterize global gene and microRNA (miRNA) expression in early response to TH perturbation in mouse liver; ii) identify TREs and TR-binding sites found throughout the mouse genome; and iii) compare TRE half-site organizations and their ability to drive gene expression. Transcriptional profiling of mRNA liver samples from TH disrupted mice enabled the identification of genes that were under direct TH-regulation. TREs in the promoter region of Tor1a, Hectd3, Slc25a45 and 2310003H01Rik were validated in vitro, adding four genes to the battery of only 13 known TRE- containing mouse genes. Hepatic miRNAs were also found to be significantly altered following perturbations in TH levels. In vitro analyses confirmed TH regulation of miR-206. Moreover, Mup1 and Gpd2 were confirmed to be targeted by miR-206 in response to TH, demonstrating that miRNAs can act as master regulators of the TH response pathway. -
Supplemental Materials
The infection-tolerant mammalian reservoir of Lyme disease and other zoonoses broadly counters the inflammatory effects of endotoxin Supplemental Materials Figures S1-S5 Tables S1-S20 Figure S1. Digital photograph of two adult Peromyscus leucopus with exudative conjunctivitis and huddled together. The animals had received 10 mg/gm body of Escherichia coli lipopolysaccharide intraperitoneally the day before. Figure S2. Species- and tissue-specific responses to LPS. Independent differential gene expression analysis of RNA-seq data were performed for blood, spleen, and liver tissues of P. leucopus and M. musculus collected 4 h after injection with LPS or buffer alsone as control. These are represented as volcano plots with range- adjusted scales for the log2-transformed fold-changes on x-axes and log10-transformed FDR p values on y- axes. Colors of symbols denote the following: red, up-regulated gene with absolute fold-change > 4.0 and p value < 0.05; purple, down-regulated gene with absolute fold-change > 4.0 and p value < 0.05; and gray, all others. Numbers at the top left and right corners in each plot respresent numbers of down- and up-regulated genes, respectively. Figure 3 is same data with constant scales for x- and y-axes across the plots. Numerical values for each gene in the 6 datasets are provided in Tables S4-S9. Figure S3. Correlation of IL-10 and IL-10 P. leucopus and M. musculus from RNA-seq of spleen and of Figure 6B and TaBle S14. The scatter plot is log10 values of normalized unique reads of one coding sequence against another for each of the four groups, as defined in the legend for Figure 6 and indicated By different symBols. -
Gene Resides on the Telomeric End of the 11Q13 Amplicon and Is Expressed in Lipogenic Breast Cancers: Implications for Control of Tumor Metabolism
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 6989–6994, June 1998 Medical Sciences The ‘‘Spot 14’’ gene resides on the telomeric end of the 11q13 amplicon and is expressed in lipogenic breast cancers: Implications for control of tumor metabolism JOEL T. MONCUR*†,JONATHAN P. PARK‡,VINCENT A. MEMOLI‡,T.K.MOHANDAS‡, AND WILLIAM B. KINLAW*§ Dartmouth Medical School, Departments of *Medicine, †Physiology, and ‡Pathology, 1 Medical Center Drive, Lebanon, NH 03756 Communicated by William T. Wickner, Dartmouth Medical School, Hanover, NH, April 10, 1998 (received for review January 27, 1998) ABSTRACT Enhanced long chain fatty acid synthesis mechanism underlying enhanced expression of lipogenic en- may occur in breast cancer, where it is necessary for tumor zymes in the tumors is unknown. growth and predicts a poor prognosis. ‘‘Spot 14’’ (S14) is a We localized the human S14 gene (THRSP) to the long arm carbohydrate- and thyroid hormone-inducible nuclear protein of chromosome 11 (11q13.5) (10), which has been confirmed specific to liver, adipose, and lactating mammary tissues that independently (11). Amplification at 11q13 occurs in '20% of functions to activate genes encoding the enzymes of fatty acid breast cancers, and this amplification predicts a poor prognosis synthesis. Amplification of chromosome region 11q13, where (12, 13). It is believed that 11q13 amplification results in the S14 gene (THRSP) resides, also predicts a poor prognosis overexpression of genes that are critical for tumor growth. We in breast tumors. We localized the S14 gene between markers therefore considered the possibility that the S14 gene is D11S906 and D11S937, at the telomeric end of the amplified amplified and overexpressed in breast tumors and that this region at 11q13, and found that it was amplified and expressed could result in increased tumor lipogenesis.