Metabolic Impact of the Glycerol Channels AQP7 and AQP9 in Adipose Tissue and Liver
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
Aquaporin Channels in the Heart—Physiology and Pathophysiology
International Journal of Molecular Sciences Review Aquaporin Channels in the Heart—Physiology and Pathophysiology Arie O. Verkerk 1,2,* , Elisabeth M. Lodder 2 and Ronald Wilders 1 1 Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; [email protected] 2 Department of Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; [email protected] * Correspondence: [email protected]; Tel.: +31-20-5664670 Received: 29 March 2019; Accepted: 23 April 2019; Published: 25 April 2019 Abstract: Mammalian aquaporins (AQPs) are transmembrane channels expressed in a large variety of cells and tissues throughout the body. They are known as water channels, but they also facilitate the transport of small solutes, gasses, and monovalent cations. To date, 13 different AQPs, encoded by the genes AQP0–AQP12, have been identified in mammals, which regulate various important biological functions in kidney, brain, lung, digestive system, eye, and skin. Consequently, dysfunction of AQPs is involved in a wide variety of disorders. AQPs are also present in the heart, even with a specific distribution pattern in cardiomyocytes, but whether their presence is essential for proper (electro)physiological cardiac function has not intensively been studied. This review summarizes recent findings and highlights the involvement of AQPs in normal and pathological cardiac function. We conclude that AQPs are at least implicated in proper cardiac water homeostasis and energy balance as well as heart failure and arsenic cardiotoxicity. However, this review also demonstrates that many effects of cardiac AQPs, especially on excitation-contraction coupling processes, are virtually unexplored. -
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. -
Supplementary Figure S4
18DCIS 18IDC Supplementary FigureS4 22DCIS 22IDC C D B A E (0.77) (0.78) 16DCIS 14DCIS 28DCIS 16IDC 28IDC (0.43) (0.49) 0 ADAMTS12 (p.E1469K) 14IDC ERBB2, LASP1,CDK12( CCNE1 ( NUTM2B SDHC,FCGR2B,PBX1,TPR( CD1D, B4GALT3, BCL9, FLG,NUP21OL,TPM3,TDRD10,RIT1,LMNA,PRCC,NTRK1 0 ADAMTS16 (p.E67K) (0.67) (0.89) (0.54) 0 ARHGEF38 (p.P179Hfs*29) 0 ATG9B (p.P823S) (0.68) (1.0) ARID5B, CCDC6 CCNE1, TSHZ3,CEP89 CREB3L2,TRIM24 BRAF, EGFR (7p11); 0 ABRACL (p.R35H) 0 CATSPER1 (p.P152H) 0 ADAMTS18 (p.Y799C) 19q12 0 CCDC88C (p.X1371_splice) (0) 0 ADRA1A (p.P327L) (10q22.3) 0 CCNF (p.D637N) −4 −2 −4 −2 0 AKAP4 (p.G454A) 0 CDYL (p.Y353Lfs*5) −4 −2 Log2 Ratio Log2 Ratio −4 −2 Log2 Ratio Log2 Ratio 0 2 4 0 2 4 0 ARID2 (p.R1068H) 0 COL27A1 (p.G646E) 0 2 4 0 2 4 2 EDRF1 (p.E521K) 0 ARPP21 (p.P791L) ) 0 DDX11 (p.E78K) 2 GPR101, p.A174V 0 ARPP21 (p.P791T) 0 DMGDH (p.W606C) 5 ANP32B, p.G237S 16IDC (Ploidy:2.01) 16DCIS (Ploidy:2.02) 14IDC (Ploidy:2.01) 14DCIS (Ploidy:2.9) -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 Log Ratio Log Ratio Log Ratio Log Ratio 12DCIS 0 ASPM (p.S222T) Log Ratio Log Ratio 0 FMN2 (p.G941A) 20 1 2 3 2 0 1 2 3 2 ERBB3 (p.D297Y) 2 0 1 2 3 20 1 2 3 0 ATRX (p.L1276I) 20 1 2 3 2 0 1 2 3 0 GALNT18 (p.F92L) 2 MAPK4, p.H147Y 0 GALNTL6 (p.E236K) 5 C11orf1, p.Y53C (10q21.2); 0 ATRX (p.R1401W) PIK3CA, p.H1047R 28IDC (Ploidy:2.0) 28DCIS (Ploidy:2.0) 22IDC (Ploidy:3.7) 22DCIS (Ploidy:4.1) 18IDC (Ploidy:3.9) 18DCIS (Ploidy:2.3) 17q12 0 HCFC1 (p.S2025C) 2 LCMT1 (p.S34A) 0 ATXN7L2 (p.X453_splice) SPEN, p.P677Lfs*13 CBFB 1 2 3 4 5 6 7 8 9 10 11 -
IL-4-Induced Hysteresis in Naïve T Cell Activation
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.31.275842; this version posted September 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. IL-4-induced hysteresis in naïve T cell activation Alexandre P. Meli1, Yaqiu Wang1, Dimitri A. de Kouchkovsky1, Yong Kong2, Malay K. Basu3, Sourav Ghosh4,5,* and Carla V. Rothlin1,5,* 1Department of Immunobiology School of Medicine Yale University 300 Cedar Street New Haven, CT 06520, USA 2Department of Biostatistics School of Public Health Yale University 60 College Street New Haven, CT 06520, USA 3Department of Pathology University of Alabama at Birmingham 619 South 19th Street Birmingham, AL 35233, USA 4Department of Neurology School of Medicine Yale University 300 Cedar Street New Haven, CT 06520, USA 5Department of Pharmacology School of Medicine Yale University 333 Cedar Street New Haven, CT 06520, USA *equal contribution, co-corresponding authors All correspondence should be addressed to: [email protected] or [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.08.31.275842; this version posted September 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. Abstract: Naïve T cells are generally considered to be a homogeneous population, but for their unique T cell receptors (TCRs). Naïve T cells are activated within a specific cytokine milieu upon interaction with antigen-presenting cells through cognate TCR::MHC-peptide interaction and co-stimulation. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Ion Channels 3 1
r r r Cell Signalling Biology Michael J. Berridge Module 3 Ion Channels 3 1 Module 3 Ion Channels Synopsis Ion channels have two main signalling functions: either they can generate second messengers or they can function as effectors by responding to such messengers. Their role in signal generation is mainly centred on the Ca2 + signalling pathway, which has a large number of Ca2+ entry channels and internal Ca2+ release channels, both of which contribute to the generation of Ca2 + signals. Ion channels are also important effectors in that they mediate the action of different intracellular signalling pathways. There are a large number of K+ channels and many of these function in different + aspects of cell signalling. The voltage-dependent K (KV) channels regulate membrane potential and + excitability. The inward rectifier K (Kir) channel family has a number of important groups of channels + + such as the G protein-gated inward rectifier K (GIRK) channels and the ATP-sensitive K (KATP) + + channels. The two-pore domain K (K2P) channels are responsible for the large background K current. Some of the actions of Ca2 + are carried out by Ca2+-sensitive K+ channels and Ca2+-sensitive Cl − channels. The latter are members of a large group of chloride channels and transporters with multiple functions. There is a large family of ATP-binding cassette (ABC) transporters some of which have a signalling role in that they extrude signalling components from the cell. One of the ABC transporters is the cystic − − fibrosis transmembrane conductance regulator (CFTR) that conducts anions (Cl and HCO3 )and contributes to the osmotic gradient for the parallel flow of water in various transporting epithelia. -
Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer
Author Manuscript Published OnlineFirst on July 6, 2020; DOI: 10.1158/0008-5472.CAN-19-2269 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Title. Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer Authors. Chen Dai1,2*, Verodia Charlestin1,2*, Man Wang1,2, Zachary T. Walker1,2, Maria Cristina Miranda-Vergara1,2, Beth A. Facchine1,2, Junmin Wu1,2, William J. Kaliney2, Norman J. Dovichi1,2, Jun Li2,3, and Laurie E. Littlepage1,2 Affiliations. 1Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 2Harper Cancer Research Institute, South Bend, IN 46617 3Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556 *Authors contributed equally Running title. Aquaporin-7 is a metabolic regulator in breast cancer Keywords. Aquaporin, breast cancer, tumor metabolism, correlation-based network analysis Corresponding Author. Laurie Littlepage, Ph.D., Harper Cancer Research Institute, University of Notre Dame, 1234 N Notre Dame Avenue, South Bend, IN 46617; Phone: (574) 631-4804 Fax: (574) 631-1165 Email: [email protected] Conflict of interest disclosure statement. The authors disclose no potential conflicts of interest. 1 Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on July 6, 2020; DOI: 10.1158/0008-5472.CAN-19-2269 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Abstract The complex yet interrelated connections between cancer metabolism, gene expression, and oncogenic driver genes have the potential to identify novel biomarkers and drug targets with prognostic and therapeutic value. -
Protein Expression in Mammalian Cell Lines After Lowlevel Metal Exposure
Montana Tech Library Digital Commons @ Montana Tech Graduate Theses & Non-Theses Student Scholarship Spring 2021 PROTEIN EXPRESSION IN MAMMALIAN CELL LINES AFTER LOWLEVEL METAL EXPOSURE Sydney Jennings Follow this and additional works at: https://digitalcommons.mtech.edu/grad_rsch PROTEIN EXPRESSION IN MAMMALIAN CELL LINES AFTER LOW- LEVEL METAL EXPOSURE by Sydney Jennings A thesis submitted in partial fulfillment of the requirements for the degree of Interdisciplinary Masters of Science Montana Tech 2021 ii Abstract Mining in Butte, Montana has been ongoing since the mid-19th century. The US Environmental Protection Agency (EPA) added the Butte Area to the National Priority List in 1983, designating it a Superfund site. Butte is currently part of the largest EPA Superfund site in the United States. The EPA lists arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg) as metal contaminants of concern for residents living in proximity to the Butte Area Superfund site. However, very limited human biomonitoring has been conducted in Butte and studies that have been published focus on Pb and, to a lesser extent, As. No synergistic, antagonistic, or additive studies have been conducted, even though it is widely accepted that the exposure in Butte is a metal mixture scenario, rather than single element exposure. Metals that are trace micronutrients, such as copper (Cu), manganese (Mn), and zinc (Zn) have been largely unrecognized as possibly having negative health effects on residents of Butte, despite the fact the metals have been historically released into the soil, water, and air through active blasting and crushing of ore and are known to be potential neurotoxins. -
Aquaglyceroporin AQP9: Solute Permeation and Metabolic Control of Expression in Liver
Aquaglyceroporin AQP9: Solute permeation and metabolic control of expression in liver Jennifer M. Carbrey*†, Daniel A. Gorelick-Feldman*†, David Kozono*, Jeppe Praetorius‡, Søren Nielsen‡, and Peter Agre*§¶ Departments of *Biological Chemistry and §Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205; and ‡Water and Salt Research Center, University of Aarhus, DK-8000 Aarhus, Denmark Contributed by Peter Agre, December 30, 2002 Aquaglyceroporins form the subset of the aquaporin water chan- We undertook studies to define the permeation of proteoli- nel family that is permeable to glycerol and certain small, un- posomes reconstituted with purified rat AQP9 protein and to charged solutes. AQP9 has unusually broad solute permeability provide evidence that expression of AQP9 protein is altered in and is expressed in hepatocyte plasma membranes. Proteolipo- rats during fasting and insulin deficiency. Our studies indicate somes reconstituted with expressed, purified rat AQP9 protein that AQP9 facilitates hepatocyte glycerol influx and urea efflux, were compared with simple liposomes for solute permeability. At establishing a greater functional repertoire for AQP9 as a solute .pH 7.5, AQP9 proteoliposomes exhibited Hg2؉-inhibitible glycerol channel with minor water transport capacity and urea permeabilities that were increased 63-fold and 90-fold over background. -Hydroxybutyrate permeability was not in- Materials and Methods creased above background, and osmotic water permeability was Plasmid Construction. Standard methods were used (10). pXG- only minimally elevated. During starvation, the liver takes up ev1-AQP9 was constructed with AQP9 cDNA prepared from rat  glycerol for gluconeogenesis. Expression of AQP9 in liver was liver total RNA and inserted into the BglII site of pX G-ev1  induced up to 20-fold in rats fasted for 24–96 h, and the AQP9 level (11). -
Comparative Analysis of Sequences, Polymorphisms and Topology of Yeasts Aquaporins and Aquaglyceroporins
FEMS Yeast Research, 16, 2016, fow025 doi: 10.1093/femsyr/fow025 Advance Access Publication Date: 20 March 2016 Minireview MINIREVIEW Comparative analysis of sequences, polymorphisms Downloaded from https://academic.oup.com/femsyr/article/16/3/fow025/2467777 by guest on 30 September 2021 and topology of yeasts aquaporins and aquaglyceroporins Farzana Sabir1,2,∗,†, Maria C. Loureiro-Dias1 and Catarina Prista1 1LEAF, Instituto Superior de Agronomia, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal and 2Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal ∗Corresponding author: LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal. Tel: (+351)-213653207; Fax: (+351)-213653195; E-mail: [email protected] One sentence summary: This review summarizes a detailed analysis of water and glycerol channels in yeasts and explores the relationship between their existence and adaptation of yeasts in various ecological niches. Editor: Jens Nielsen †Farzana Sabir, http://orcid.org/0000-0002-0181-989X ABSTRACT Efficient homeostasis of water and glycerol is a prerequisite for osmoregulation and other aspects of yeasts life. The cellular status of these molecules is often associated with functional presence of aquaporins and aquaglyceroporins. The present study provides a detailed updated analysis of aquaporins and aquaglyceroporins in 47 yeast species. A comprehensive analysis of aquaporins and aquaglyceroporins in 38 strains of Saccharomyces cerevisiae from different ecological niches is also presented. The functionality of specific aquaporins in yeasts has been associated with their adaptation requirements in different environmental conditions. In the present study, various inactivating mutations in aquaporin sequences were found in strains of S. -
Prolonged Starvation Causes Up-Regulation of AQP1 in Adipose Tissue Capillaries of AQP7 Knock-Out Mice
International Journal of Molecular Sciences Article Prolonged Starvation Causes Up-Regulation of AQP1 in Adipose Tissue Capillaries of AQP7 Knock-Out Mice Mariusz T. Skowronski 1,*, Agnieszka Skowronska 2, Aleksandra Rojek 3, Michal K. Oklinski 3 and Søren Nielsen 3 1 Department of Animal Physiology, University of Warmia and Mazury in Olsztyn, Olsztyn 10-752, Poland 2 Department of Human Physiology, University of Warmia and Mazury in Olsztyn, Olsztyn 10-752, Poland; [email protected] 3 Department of Health Science and Technology, Aalborg University, Aalborg 9220, Denmark; [email protected] (A.R.); [email protected] (M.K.O.); [email protected] (S.N.) * Correspondence: [email protected]; Tel.: +48-89-523-4226 Academic Editor: Kenichi Ishibashi Received: 11 May 2016; Accepted: 6 July 2016; Published: 22 July 2016 Abstract: Aquaporins (AQPs) are membrane proteins involved in the regulation of cellular transport and the balance of water and glycerol and cell volume in the white adipose tissue (WAT). In our previous study, we found the co-expression of the AQP1 water channel and AQP7 in the mouse WAT. In our present study, we aimed to find out whether prolonged starvation influences the AQP1 expression of AQP7 knock-out mice (AQP7 KO) in the WAT. To resolve this hypothesis, immunoperoxidase, immunoblot and immunogold microscopy were used. AQP1 expression was found with the use of immunohistochemistry and was confirmed by immunogold microscopy in the vessels of mouse WAT of all studied groups. Semi-quantitative immunoblot and quantitative immunogold microscopy showed a significant increase (by 2.5- to 3-fold) in the abundance of AQP1 protein expression in WAT in the 72 h starved AQP7 KO mice as compared to AQP7+/+ (p < 0.05) and AQP7´/´ (p < 0.01) controls, respectively.