Activation of the Endogenous Renin-Angiotensin- Aldosterone System Or Aldosterone Administration Increases Urinary Exosomal Sodium Channel Excretion

Total Page:16

File Type:pdf, Size:1020Kb

Activation of the Endogenous Renin-Angiotensin- Aldosterone System Or Aldosterone Administration Increases Urinary Exosomal Sodium Channel Excretion CLINICAL RESEARCH www.jasn.org Activation of the Endogenous Renin-Angiotensin- Aldosterone System or Aldosterone Administration Increases Urinary Exosomal Sodium Channel Excretion † † Ying Qi,* Xiaojing Wang, Kristie L. Rose,* W. Hayes MacDonald,* Bing Zhang, ‡ | Kevin L. Schey,* and James M. Luther § Departments of *Biochemistry, †Bioinformatics, ‡Division of Clinical Pharmacology, Department of Medicine, §Division of Nephrology, Department of Medicine, and |Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee ABSTRACT Urinary exosomes secreted by multiple cell types in the kidney may participate in intercellular signaling and provide an enriched source of kidney-specific proteins for biomarker discovery. Factors that alter the exosomal protein content remain unknown. To determine whether endogenous and exogenous hormones modify urinary exosomal protein content, we analyzed samples from 14 mildly hypertensive patients in a crossover study during a high-sodium (HS, 160 mmol/d) diet and low-sodium (LS, 20 mmol/d) diet to activate the endogenous renin-angiotensin-aldosterone system. We further analyzed selected exosomal protein content in a separate cohort of healthy persons receiving intravenous aldosterone (0.7 mg/kg per hour for 10 hours) versus vehicle infusion. The LS diet increased plasma renin activity and aldosterone concentration, whereas aldosterone infusion increased only aldosterone concentration. Protein analysis of paired urine exosome samples by liquid chromatography-tandem mass spectrometry–based multidimen- sional protein identification technology detected 2775 unique proteins, of which 316 exhibited signifi- cantly altered abundance during LS diet. Sodium chloride cotransporter (NCC) and a-andg-epithelial sodium channel (ENaC) subunits from the discovery set were verified using targeted multiple reaction monitoring mass spectrometry quantified with isotope-labeled peptide standards. Dietary sodium restric- tion or acute aldosterone infusion similarly increased urine exosomal gENaC[112–122] peptide concentra- tions nearly 20-fold, which correlated with plasma aldosterone concentration and urinary Na/K ratio. Urine exosomal NCC and aENaC concentrations were relatively unchanged during these interventions. We conclude that urinary exosome content is altered by renin-angiotensin-aldosterone system activation. Urinary measurement of exosomal gENaC[112–122] concentration may provide a useful biomarker of ENaC activation in future clinical studies. J Am Soc Nephrol 27: 646–656, 2016. doi: 10.1681/ASN.2014111137 Urinary exosomes are small (approximately 100 nm activity are unknown. Further characterization of diameter) vesicles excreted by multiple cell types the urinary exosome protein response to these along the nephron and urogenital tract that provide a unique source of kidney-enriched pro- teins.1,2 Urinary exosomes contain RNA and pro- Received November 25, 2014. Accepted April 22, 2015. teins, including multiple sodium channels and Published online ahead of print. Publication date available at transporters, and they may contribute to physio- www.jasn.org. 1–10 logic processes in the kidney. Whether proteins Correspondence: Dr. James M. Luther, Vanderbilt University within urinary exosomes are altered by dietary fac- Medical Center2200 Pierce Avenue, 560 RRB, Nashville, TN tors or exogenous hormones and whether these 37232-6602. Email: [email protected] changes are useful in determining physiologic Copyright © 2016 by the American Society of Nephrology 646 ISSN : 1046-6673/2702-646 J Am Soc Nephrol 27: 646–656, 2016 www.jasn.org CLINICAL RESEARCH modifying factors would inform their use in future biomarker We previously identified .3000 unique proteins from hu- discovery efforts. man urinary exosomes using multidimensional protein iden- Urinary exosomes are formed in cells lining the nephron by tification technology (MudPIT).5 In the present study, we formation of endocytic vesicles that may eventually be released tested the hypothesis that RAAS activation during a low- into the urinary space by the process of exocytosis.11 The exo- sodium (LS) diet and during exogenous aldosterone infusion some content includes membrane and soluble proteins as well alters the urinary exosome proteomic profile. We extended these as RNA, all of which may be relatively protected from degra- findings using a more targeted, sensitive, and quantitative dation in the urine by the vesicular lipid bilayer. The role of approach to investigate the profile of ENaC and NCC, which exosomes in human physiology is an area of intense investi- are known to play an essential role in renal sodium and po- gation, but within the kidney they may transport their con- tassium homeostasis. tents intercellularly, signal fibrotic responses, and perform innate immune functions.7–9 Much interest has focused on urinary exosomes as a source for biomarker discovery in hu- RESULTS mans due to the relative enrichment of membrane proteins.11 Validation of a urinary biomarker would be supported by Participant Characteristics and Effects of Dietary predictable alterations during physiologic stimulation or in- Sodium Restriction hibition. Potential approaches in humans could use dietary, We assessed the urinary exosome protein cargo using matched pharmacologic, or hormonal modification. urine samples from 14 patients during a high-sodium (HS) The renin-angiotensin-aldosterone system (RAAS) is acti- and a low-sodium (LS) diet to activate the endogenous RAAS vated in response to dietary sodium restriction, which helps and increase renal sodium reabsorption. In a separate crossover maintain long-term BP by modifying renal sodium and water study, aldosterone (0.7 mg/kg per hour) and vehicle were in- handling.12 The RAAS stimulates sodium reabsorption in part fused intravenously overnight (10 pm–8 am) as described pre- via aldosterone, leading to epithelial sodium channel (ENaC) viously,14 and urine was collected from 1 am to 7 am for and sodium chloride cotransporter (NCC) activation, which exosome isolation and analysis. Participant characteristics can be inhibited by potassium sparing (e.g., amiloride) and are presented in Table 1. During the LS diet, plasma renin thiazide diuretics, respectively.13 Because no direct measures activity and plasma aldosterone increased and urinary so- of renal ENaC activity exist in humans, it has been estimated dium excretion (198.5621.0 for HS diet versus 18.662.1 by urinary sodium-to-potassium ratio in prior studies. So- mmol/d for LS diet; P,0.001) and urinary sodium-to-potas- dium channel peptides and novel sodium channel phosphor- sium ratio (2.2060.18 versus 0.2960.05, respectively; ylation sites have been identified by proteomic analysis of P,0.001) decreased as anticipated. Urinary creatinine con- urinary exosomal proteins,1 but no studies have investigated centration (0.8460.12 mg/ml for HS diet versus 0.9560.17 their physiologic role or the dynamic changes during RAAS mg/ml for LS diet; P=0.24), creatinine excretion rate (1.596 activation in humans. 0.10 g/d versus 1.6360.13 g/d; P=0.77), urinary exosomal Table 1. Participant characteristics and physiologic effects of dietary sodium restriction Dietary Study Aldosterone Characteristic P Value P Value HS LS HS+Vehicle HS+Aldosterone Screening measurements Age (yr) 42.963.0 44.967.8 Men/women (n/n)7/72/2 Race (white/black) (n/n) 10/4 4/0 Height (m) 1.7460.033 1.7165.5 Weight (kg) 90.967.8 98.366.4 Body mass index (kg/m2) 29.561.6 33.862.1 Creatinine (mg/dl) 0.8960.04 0.7960.09 Serum sodium (mEq/L) 139.260.49 139.560.65 Serum potassium (mEq/L) 4.060.08 3.860.10 Pre- and post-dietary measures Systolic BP (mmHg) 136.064.1 131.463.4 0.32 111.865.5 108.668.2 0.56 Diastolic BP (mmHg) 81.563.3 79.162.0 0.36 60.563.9 58.163.4 0.47 Heart rate (beats/min) 64.562.4 67.862.8 0.004 60.365.5 57.964.7 0.27 Plasma aldosterone (ng/dl) 7.6960.81 16.161.8 ,0.001 7.561.2 83.5627.9 0.06 Plasma renin activity (ng AngI/ml per hour 0.8760.20 2.9260.49 ,0.001 1.0860.22 1.8760.31 0.04 Unless otherwise noted, values are the mean6SD. J Am Soc Nephrol 27: 646–656, 2016 RAAS Alters Urinary Exosomes 647 CLINICAL RESEARCH www.jasn.org protein excretion (50.467.2 mg protein versus 54.266.2 mg and kallikrein-related peptidase 10, among others. These pro- protein; P=0.58), diastolic BP, and systolic BP were not sig- teins are responsible for the enriched GO terms, extracellular nificantly changed by LS diet. matrix organization, extracellular structure organization, and regulation of membrane protein ectodomain proteolysis in Dietary Sodium Restriction Alters Urinary Exosomal the biologic process category; serine-type peptidase activity, Protein Expression extracellular matrix structural constituent, serine hydrolase Paired urine exosome samples from 14 patients during the LS activity, and serine-type endopeptidase activity in the molec- and HS diets were analyzed by MudPIT. We identified a total of ular function category; and extracellular-related terms in the 1,514,909 tryptic peptides, representing 34,208 unique pep- cellular component category. For the downregulated proteins, tides with scores above the minimum peptide identity thresh- the abundance of ribosomal proteins observed at lower levels olds (see Concise Methods section). After removal of proteins in the HS samples are responsible for the endoplasmic retic- with low total spectral counts (,10 spectral counts across 28 ulum (ER)- and translation-related GO terms and the macro- samples), 2775 proteins remained (Supplemental Table 1). molecular complex and non-membrane bound organelle Dietary sodium restriction significantly altered the expression terms in Figure 2. of 316 of 2775 (11.4%) urinary exosome proteins after adjust- ment for multiple comparisons. Of these, 113 (4.1%) in- creased and 203 (7.3%) decreased during LS diet. Hierarchical clustering demonstrated a visible distribution pattern of pro- teins clustered with dietary sodium intake (Figure 1). A high- resolution figure with protein ID annotation is available in the Supplemental Material.
Recommended publications
  • PSPC1 Potentiates IGF1R Expression to Augment Cell Adhesion and Motility
    1 Supplementary information 2 PSPC1 potentiates IGF1R expression to augment cell 3 adhesion and motility 4 Hsin-Wei Jen1,2 , De-Leung Gu 2, Yaw-Dong Lang 2 and Yuh-Shan Jou 1,2,* 5 1 Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 6 2 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan 7 * Author to whom correspondence should be addressed 8 Cells 2020, 9, x; doi: FOR PEER REVIEW www.mdpi.com/journal/cells Cells 2020, 9, x FOR PEER REVIEW 2 of 10 9 10 11 Supplementary Figure S1: Expression of IGF1R and integrin in PSPC1-expressing or PSPC1-depleted 12 HCC cells by Western blotting analysis 13 (A) Detection of IGF1R protein levels in three PSPC1-knockdown cells Huh7, HepG2 and Mahlavu. (B) 14 Detection of selected integrin expression in PSPC1-overexpressing or PSPC1-depleted HCC cells by using 15 their total cell lysates immunoblotted with specific integrin antibodies as shown. 16 17 18 Supplementary Figure S2: PSPC1-modulated IGF1R downstream signaling in HCC cells. Cells 2020, 9, x FOR PEER REVIEW 3 of 10 19 (A, B) Immunoblotting of IGF1R expression in PSPC1-overexpressing SK-Hep1 and PLC5 cells 20 treated with IGF1R shRNAs. (C, D) Cell migration and adhesion were measured in PSPC1- 21 knockdown Hep3B cells rescued with exogenous expression of IGF1R. Exogenous expression of 22 IGF1R in PSPC1-knockdown Hep3B cells were then applied for detection of altered AKT/ERK 23 signaling including (E) total PSPC1, IGF1R, AKT, ERK, p-IGF1R, p-AKT(S473), and 24 p-ERK(T202/Y204) as well as altered FAK/Src signaling including (F) total FAK, Src, p-FAK(Y397) 25 and p-Src(Y416) by immunoblotting assay.
    [Show full text]
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
    [Show full text]
  • 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.
    [Show full text]
  • Defining Functional Interactions During Biogenesis of Epithelial Junctions
    ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
    [Show full text]
  • Β-Catenin Knockdown Affects Mitochondrial Biogenesis and Lipid Metabolism in Breast Cancer Cells
    ORIGINAL RESEARCH published: 27 July 2017 doi: 10.3389/fphys.2017.00544 β-Catenin Knockdown Affects Mitochondrial Biogenesis and Lipid Metabolism in Breast Cancer Cells Daniele Vergara 1, 2 †, Eleonora Stanca 1, 2 †, Flora Guerra 1, Paola Priore 3, Antonio Gaballo 3, Julien Franck 4, Pasquale Simeone 5, Marco Trerotola 6, Stefania De Domenico 7, Isabelle Fournier 4, Cecilia Bucci 1, Michel Salzet 4, Anna M. Giudetti 1* and Michele Maffia 1, 2* 1 Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy, 2 Laboratory of Clinical Proteomic, “Giovanni Paolo II” Hospital, Lecce, Italy, 3 CNR NANOTEC - Institute of Nanotechnology, Lecce, Italy, 4 University of Lille, Institut national de la santé et de la recherche médicale, U-1192 - Laboratoire Protéomique, Réponse Edited by: Inflammatoire et Spectrométrie de Masse-PRISM, Lille, France, 5 Unit of Cytomorphology, CeSI-MeT and Department of Andrei Surguchov, Medicine and Aging Sciences, School of Medicine and Health Sciences, University “G. d’Annunzio,” Chieti, Italy, 6 Unit of Kansas University of Medical Center Cancer Pathology, CeSI-MeT and Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio,” Research Institute, United States Chieti, Italy, 7 C.N.R. Unit of Lecce, Institute of Food Production Sciences, Lecce, Italy Reviewed by: Kamal Datta, β-catenin plays an important role as regulatory hub in several cellular processes including Georgetown University, United States Silvana Gaetani, cell adhesion, metabolism, and epithelial mesenchymal transition. This is mainly achieved Sapienza Università di Roma, Italy by its dual role as structural component of cadherin-based adherens junctions, and as Clizia Chinello, University of Milano-Bicocca, Italy a key nuclear effector of the Wnt pathway.
    [Show full text]
  • Steroid-Dependent Regulation of the Oviduct: a Cross-Species Transcriptomal Analysis
    University of Kentucky UKnowledge Theses and Dissertations--Animal and Food Sciences Animal and Food Sciences 2015 Steroid-dependent regulation of the oviduct: A cross-species transcriptomal analysis Katheryn L. Cerny University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Cerny, Katheryn L., "Steroid-dependent regulation of the oviduct: A cross-species transcriptomal analysis" (2015). Theses and Dissertations--Animal and Food Sciences. 49. https://uknowledge.uky.edu/animalsci_etds/49 This Doctoral Dissertation is brought to you for free and open access by the Animal and Food Sciences at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Animal and Food Sciences by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known.
    [Show full text]
  • Supplementary Materials
    1 Supplementary Materials: Supplemental Figure 1. Gene expression profiles of kidneys in the Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice. (A) A heat map of microarray data show the genes that significantly changed up to 2 fold compared between Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice (N=4 mice per group; p<0.05). Data show in log2 (sample/wild-type). 2 Supplemental Figure 2. Sting signaling is essential for immuno-phenotypes of the Fcgr2b-/-lupus mice. (A-C) Flow cytometry analysis of splenocytes isolated from wild-type, Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice at the age of 6-7 months (N= 13-14 per group). Data shown in the percentage of (A) CD4+ ICOS+ cells, (B) B220+ I-Ab+ cells and (C) CD138+ cells. Data show as mean ± SEM (*p < 0.05, **p<0.01 and ***p<0.001). 3 Supplemental Figure 3. Phenotypes of Sting activated dendritic cells. (A) Representative of western blot analysis from immunoprecipitation with Sting of Fcgr2b-/- mice (N= 4). The band was shown in STING protein of activated BMDC with DMXAA at 0, 3 and 6 hr. and phosphorylation of STING at Ser357. (B) Mass spectra of phosphorylation of STING at Ser357 of activated BMDC from Fcgr2b-/- mice after stimulated with DMXAA for 3 hour and followed by immunoprecipitation with STING. (C) Sting-activated BMDC were co-cultured with LYN inhibitor PP2 and analyzed by flow cytometry, which showed the mean fluorescence intensity (MFI) of IAb expressing DC (N = 3 mice per group). 4 Supplemental Table 1. Lists of up and down of regulated proteins Accession No.
    [Show full text]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Identification of the Key Micrornas and Mirna- Mrna Interaction Networks During the Ovarian Development of Hens
    Article Identification of the Key microRNAs and miRNA- mRNA Interaction Networks During the Ovarian Development of Hens Jing Li †, Chong Li †, Qi Li, Wen-Ting Li, Hong Li, Guo-Xi Li, Xiang-Tao Kang, Xiao-Jun Liu and Ya-Dong Tian * College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; [email protected] (J.L.); [email protected] (C.L.); [email protected] (Q.L.); [email protected] (W.-T.L.); [email protected] (H.L.); [email protected] (G.-X.L.); [email protected] (X.-T.K.); [email protected] (X.-J.L.) * Correspondence: [email protected] † These two authors contributed equally to this work. Received: 27 July 2020; Accepted: 15 September 2020; Published: date Supplementary Material Animals 2020, 10, x; doi: www.mdpi.com/journal/animals Animals 2020, 10, x 2 of 24 Table 1. The list of the interaction network, the expression levels and Pearson’s correlation coefficient of DE miRNAs and DE mRNAs. Expression Level ( TPM) Expression Level ( FPKM) sRNA Transcript Id Gene Id Gene Name Correlatio 15W 20W 30W 68W 15W 20W 30W 68W gga-miR-1560-3p 3.253 6.030 4.295 2.565 ENSGALT00000087050 ENSGALG00000005902 RAB7A 17.832 0.031 6.674 0.077 -0.324 gga-miR-143-3p 25118.987 49390.256 87681.664 32277.275 ENSGALT00000069072 ENSGALG00000041760 CLTCL1 2.189 0.000 1.321 1.252 -0.268 gga-miR-7472-5p 0.054 0.264 0.466 0.000 ENSGALT00000066785 ENSGALG00000014582 CADM1 6.810 2.342 0.000 0.000 -0.394 gga-miR-7472-5p 0.054 0.264 0.466 0.000 ENSGALT00000033172 ENSGALG00000008121 CYP17A1 722.987
    [Show full text]
  • Investigation of Candidate Genes and Mechanisms Underlying Obesity
    Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between
    [Show full text]
  • 1 Supporting Information for a Microrna Network Regulates
    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
    [Show full text]
  • Proteomic and Metabolomic Analyses of Mitochondrial Complex I-Deficient
    THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 24, pp. 20652–20663, June 8, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Proteomic and Metabolomic Analyses of Mitochondrial Complex I-deficient Mouse Model Generated by Spontaneous B2 Short Interspersed Nuclear Element (SINE) Insertion into NADH Dehydrogenase (Ubiquinone) Fe-S Protein 4 (Ndufs4) Gene*□S Received for publication, November 25, 2011, and in revised form, April 5, 2012 Published, JBC Papers in Press, April 25, 2012, DOI 10.1074/jbc.M111.327601 Dillon W. Leong,a1 Jasper C. Komen,b1 Chelsee A. Hewitt,a Estelle Arnaud,c Matthew McKenzie,d Belinda Phipson,e Melanie Bahlo,e,f Adrienne Laskowski,b Sarah A. Kinkel,a,g,h Gayle M. Davey,g William R. Heath,g Anne K. Voss,a,h René P. Zahedi,i James J. Pitt,j Roman Chrast,c Albert Sickmann,i,k Michael T. Ryan,l Gordon K. Smyth,e,f,h b2 a,h,m,n3 David R. Thorburn, and Hamish S. Scott Downloaded from From the aMolecular Medicine Division, gImmunology Division, and eBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, the bMurdoch Childrens Research Institute, Royal Children’s Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia, the cDépartement de Génétique Médicale, Université de Lausanne, 1005 Lausanne, Switzerland, the dCentre for Reproduction and Development, Monash Institute of Medical Research, Clayton, Victoria 3168, Australia, the hDepartment of Medical Biology
    [Show full text]