Metabolic Adaptation of White Adipose Tissue to Nutritional and Environmental Challenges
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Surface Glycoproteomic Analysis of Hepatocellular Carcinoma Cells by Affinity Enrichment and Mass Spectrometric Identification
Glycoconj J (2012) 29:411–424 DOI 10.1007/s10719-012-9420-3 Surface glycoproteomic analysis of hepatocellular carcinoma cells by affinity enrichment and mass spectrometric identification Wei Mi & Wei Jia & Zhaobin Zheng & Jinglan Wang & Yun Cai & Wantao Ying & Xiaohong Qian Received: 14 April 2012 /Revised: 5 June 2012 /Accepted: 12 June 2012 /Published online: 1 July 2012 # Springer Science+Business Media, LLC 2012 Abstract Cell surface glycoproteins are one of the most surface-capturing (CSC) technique was an approach specif- frequently observed phenomena correlated with malignant ically targeted at membrane glycoproteins involving the growth. Hepatocellular carcinoma (HCC) is one of the most affinity capture of membrane glycoproteins using glycan malignant tumors in the world. The majority of hepatocel- biotinylation labeling on intact cell surfaces. To characterize lular carcinoma cell surface proteins are modified by glyco- the cell surface glycoproteome and probe the mechanism of sylation in the process of tumor invasion and metastasis. tumor invasion and metastasis of HCC, we have modified Therefore, characterization of cell surface glycoproteins can and evaluated the cell surface-capturing strategy, and ap- provide important information for diagnosis and treatment plied it for surface glycoproteomic analysis of hepatocellu- of liver cancer, and also represent a promising source of lar carcinoma cells. In total, 119 glycosylation sites on 116 potential diagnostic biomarkers and therapeutic targets for unique glycopeptides were identified, corresponding to 79 hepatocellular carcinoma. However, cell surface glycopro- different protein species. Of these, 65 (54.6 %) new pre- teins of HCC have been seldom identified by proteomics dicted glycosylation sites were identified that had not pre- approaches because of their hydrophobic nature, poor solu- viously been determined experimentally. -
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. -
Microarchitecture of the Dyad
Cardiovascular Research (2013) 98, 169–176 SPOTLIGHT REVIEW doi:10.1093/cvr/cvt025 Microarchitecture of the dyad David R.L. Scriven, Parisa Asghari, and Edwin D.W. Moore* Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3 Received 12 December 2012; revised 2 February 2013; accepted 4 February 2013; online publish-ahead-of-print 11 February 2013 Downloaded from https://academic.oup.com/cardiovascres/article/98/2/169/278625 by guest on 23 September 2021 Abstract This review highlights recent and ongoing discoveries that are transforming the previously held view of dyad structure and function. New data show that dyads vary greatly in both structure and in their associated molecules. Dyads can contain varying numbers of type 2 ryanodine receptor (RYR2) clusters that range in size from one to hundreds of tetramers and they can adopt numerous orientations other than the expected checkerboard. The association of Cav1.2 with RYR2, which defines the couplon, is not absolute, leading to a number of scenarios such as dyads without couplons and those in which only a fraction of the clusters are in couplons. Different dyads also vary in the transporters and exchangers with which they are associated producing functional differences that amplify their structural diversity. The essential role of proteins, such as junctophilin-2, calsequestrin, triadin, and junctin that main- tain both the functional and structural integrity of the dyad have recently been elucidated giving a new mechanistic understanding of heart diseases, such as arrhythmias, hypertension, failure, and sudden cardiac death. -
Figure S1. DMD Module Network. the Network Is Formed by 260 Genes from Disgenet and 1101 Interactions from STRING. Red Nodes Are the Five Seed Candidate Genes
Figure S1. DMD module network. The network is formed by 260 genes from DisGeNET and 1101 interactions from STRING. Red nodes are the five seed candidate genes. Figure S2. DMD module network is more connected than a random module of the same size. It is shown the distribution of the largest connected component of 10.000 random modules of the same size of the DMD module network. The green line (x=260) represents the DMD largest connected component, obtaining a z-score=8.9. Figure S3. Shared genes between BMD and DMD signature. A) A meta-analysis of three microarray datasets (GSE3307, GSE13608 and GSE109178) was performed for the identification of differentially expressed genes (DEGs) in BMD muscle biopsies as compared to normal muscle biopsies. Briefly, the GSE13608 dataset included 6 samples of skeletal muscle biopsy from healthy people and 5 samples from BMD patients. Biopsies were taken from either biceps brachii, triceps brachii or deltoid. The GSE3307 dataset included 17 samples of skeletal muscle biopsy from healthy people and 10 samples from BMD patients. The GSE109178 dataset included 14 samples of controls and 11 samples from BMD patients. For both GSE3307 and GSE10917 datasets, biopsies were taken at the time of diagnosis and from the vastus lateralis. For the meta-analysis of GSE13608, GSE3307 and GSE109178, a random effects model of effect size measure was used to integrate gene expression patterns from the two datasets. Genes with an adjusted p value (FDR) < 0.05 and an │effect size│>2 were identified as DEGs and selected for further analysis. A significant number of DEGs (p<0.001) were in common with the DMD signature genes (blue nodes), as determined by a hypergeometric test assessing the significance of the overlap between the BMD DEGs and the number of DMD signature genes B) MCODE analysis of the overlapping genes between BMD DEGs and DMD signature genes. -
Regulatory Micrornas in Brown, Brite and White Adipose Tissue
cells Review Regulatory microRNAs in Brown, Brite and White Adipose Tissue Seley Gharanei 1,2, Kiran Shabir 3 , James E. Brown 3,4, Martin O. Weickert 1,2,5 , 1,2 1,2,3, 1,2,3, , Thomas M. Barber , Ioannis Kyrou y and Harpal S. Randeva * y 1 Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry CV2 2DX, UK; [email protected] (S.G.); [email protected] (M.O.W.); [email protected] (T.M.B.); [email protected] (I.K.) 2 Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK 3 Aston Medical Research Institute, Aston Medical School, College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK; [email protected] (K.S.); [email protected] (J.E.B.) 4 School of Biosciences, College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK 5 Centre of Applied Biological & Exercise Sciences, Faculty of Health & Life Sciences, Coventry University, Coventry CV1 5FB, UK * Correspondence: [email protected] Joint senior authors; contributed equally to the manuscript. y Received: 30 September 2020; Accepted: 13 November 2020; Published: 16 November 2020 Abstract: MicroRNAs (miRNAs) constitute a class of short noncoding RNAs which regulate gene expression by targeting messenger RNA, inducing translational repression and messenger RNA degradation. This regulation of gene expression by miRNAs in adipose tissue (AT) can impact on the regulation of metabolism and energy homeostasis, particularly considering the different types of adipocytes which exist in mammals, i.e., white adipocytes (white AT; WAT), brown adipocytes (brown AT; BAT), and inducible brown adipocytes in WAT (beige or brite or brown-in-white adipocytes). -
Transcriptional Control of Tissue-Resident Memory T Cell Generation
Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells. -
Absence of Triadin, a Protein of the Calcium Release Complex, Is Responsible for Cardiac Arrhythmia with Sudden Death in Human
Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human. Nathalie Roux-Buisson, Marine Cacheux, Anne Fourest-Lieuvin, J. Fauconnier, Julie Brocard, Isabelle Denjoy, Philippe Durand, Pascale Guicheney, Florence Kyndt, Antoine Leenhardt, et al. To cite this version: Nathalie Roux-Buisson, Marine Cacheux, Anne Fourest-Lieuvin, J. Fauconnier, Julie Brocard, et al.. Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human.. Human Molecular Genetics, Oxford University Press (OUP), 2012, 21 (12), pp.2759-67. 10.1093/hmg/dds104. inserm-00763211 HAL Id: inserm-00763211 https://www.hal.inserm.fr/inserm-00763211 Submitted on 10 Dec 2012 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. HMG Advance Access published March 29, 2012 Human Molecular Genetics, 2012 1–9 doi:10.1093/hmg/dds104 Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human Nathalie Roux-Buisson1,2,3,4,{, Marine Cacheux1,4,{, Anne Fourest-Lieuvin1,4,5, Jeremy Fauconnier6,7,8,9, Julie Brocard1,4, Isabelle Denjoy10, Philippe Durand11, Pascale Guicheney12,13, Florence Kyndt14,15,16, Antoine Leenhardt10, Herve´ Le Marec14,16,17, Vincent Lucet18, Philippe Mabo19, Vincent Probst14,16,17, Nicole Monnier1,2, Pierre F. -
Mir-29C Is Downregulated in Gastric Carcinomas and Regulates Cell
Matsuo et al. Molecular Cancer 2013, 12:15 http://www.molecular-cancer.com/content/12/1/15 RESEARCH Open Access MiR-29c is downregulated in gastric carcinomas and regulates cell proliferation by targeting RCC2 Mitsuhiro Matsuo1†, Chisato Nakada1†, Yoshiyuki Tsukamoto1*, Tsuyoshi Noguchi2, Tomohisa Uchida1, Naoki Hijiya1, Keiko Matsuura1 and Masatsugu Moriyama1 Abstract Background: Previously, using miRNA microarray, we have found that miR-29c is significantly downregulated in advanced gastric carcinoma. In the present study, we investigated whether miR-29c functions as a tumor- suppressor miRNA in gastric carcinoma cells. For this purpose, we verified the downregulation of miR-29c in gastric carcinoma tissues, and assessed the biological effect of miR-29c on gastric carcinoma cells. Results: In miR-29c-transfected cells, both proliferation and colony formation ability on soft agar were significantly decreased. Although apoptosis was not induced, BrdU incorporation and the proportion of cells positive for phospho-histone H3 (S10) were significantly decreased in miR-29c-transfected cells, indicating that miR-29c may be involved in the regulation of cell proliferation. To explain the mechanism of growth suppression by miR-29c, we explored differentially expressed genes (>2-fold) in miR-29c-transfected cells in comparison with negative control transfected cells using microarray. RCC2, PPIC and CDK6 were commonly downregulated in miR-29c-transfected MKN45, MKN7 and MKN74 cells, and all of the genes harbored miR-29c target sequences in the 3’-UTR of their mRNA. RCC2 and PPIC were actually upregulated in gastric carcinoma tissues, and therefore both were identified as possible targets of miR-29c in gastric carcinoma. -
New Insights Into the Secretory Functions of Brown Adipose Tissue
243 2 Journal of J Villarroya et al. Secretory functions of brown 243:2 R19–R27 Endocrinology adipose tissue REVIEW New insights into the secretory functions of brown adipose tissue Joan Villarroya, Rubén Cereijo, Aleix Gavaldà-Navarro, Marion Peyrou, Marta Giralt and Francesc Villarroya Departament de Bioquímica i Biomedicina Molecular and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain CIBER Fisiopatología de la Obesidad y Nutrición, Barcelona, Catalonia, Spain Correspondence should be addressed to F Villarroya: [email protected] Abstract In recent years, an important secretory role of brown adipose tissue (BAT) has emerged, Key Words which is consistent, to some extent, with the earlier recognition of the important f brown adipose tissue secretory role of white fat. The so-called brown adipokines or ‘batokines’ may play an f brown adipokine autocrine role, which may either be positive or negative, in the thermogenic function f batokine of brown adipocytes. Additionally, there is a growing recognition of the signalling f thermogenesis molecules released by brown adipocytes that target sympathetic nerve endings (such as neuregulin-4 and S100b protein), vascular cells (e.g., bone morphogenetic protein-8b), and immune cells (e.g., C-X-C motif chemokine ligand-14) to promote the tissue remodelling associated with the adaptive BAT recruitment in response to thermogenic stimuli. Moreover, existing indications of an endocrine role of BAT are being confirmed through the release of brown adipokines acting on other distant tissues and organs; a recent example is the recognition that BAT-secreted fibroblast growth factor-21 and myostatin target the heart and skeletal muscle, respectively. -
Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Author Manuscript Published OnlineFirst on June 13, 2019; DOI: 10.1158/2159-8290.CD-19-0094 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts Ela Elyada1,2, Mohan Bolisetty3,4,14, Pasquale Laise5,14, William F. Flynn3,14, Elise T. Courtois3, Richard A. Burkhart6, Jonathan A. Teinor6, Pascal Belleau1, Giulia Biffi1,2, Matthew S. Lucito1,2, Santhosh Sivajothi3, Todd D. Armstrong6, Dannielle D. Engle1,2,7, Kenneth H. Yu8, Yuan Hao1, Christopher L. Wolfgang6, Youngkyu Park1,2, Jonathan Preall1, Elizabeth M. Jaffee6, Andrea Califano5,9-12, Paul Robson3,13 and David A. Tuveson1,2. 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA 2Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA. 3The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA 4Bristol-Myers Squibb, Pennington, NJ, USA 5Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA 6Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. 7Salk institute for Biological Studies, La Jolla, CA 92037 8Memorial Sloan Kettering Cancer Center, New York, NY, USA 9Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA 10J.P. Sulzberger Columbia Genome Center, Columbia University, New York, NY 10032, USA 11Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA 12Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA 13Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA 14Equal contribution Running title Antigen-presenting CAFs in PDAC Keywords Single-cell analysis, pancreatic cancer, CAFs, MHC class II, heterogeneity *Co-corresponding authors: David A. -
Human Skeletal Muscles Replaced to a High Degree by White Adipose Tissue
Okajimas Folia Anat. Jpn.,Replacement 87(4): 165–170, of muscle February, by fat 2011165 Human skeletal muscles replaced to a high degree by white adipose tissue By Keisuke INA1, Hirokazu KITAMURA1, Takayuki MASAKI2, Shuji TATSUKAWA1, Hironobu YOSHIMATSU2 and Yoshihisa FUJIKURA1 1 Department of Molecular Anatomy, Faculty of Medicine, Oita University 2 Department of Internal Medicine 1, Faculty of Medicine, Oita University, 1-1, Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan –Received for Publication, August 28, 2010– Key Words: fatty degeneration, skeletal muscle, diabetes mellitus, renal failure, hypothyroidism Summary: Extreme replacement of skeletal muscles by adipose tissue was found in an 86-year old Japanese male cadaver during dissection practice for medical students at Oita University School of Medicine. Especially, the bilateral sartorius muscles looked overall like adipose tissue. The man had suffered from diabetes mellitus, renal failure, hypertension and hy- pothyroidism before his death. He was also an alcohol drinker. He had been bedridden late in life. The cause of death was renal failure. In microscopy, the adipose tissue-like sartorius muscle was shown to consist of leptin-positive adipocytes with a small number of degenerated muscle fibers. Fatty replacement, or fatty degeneration, appears to result from endocrine and metabolic disorders, and being bedridden leads to muscle atrophy and damage, although the origin of the adipocytes which emerged in the degenerated muscles is unknown. Introduction tally denerved muscle atrophy (Dulor et al., 19984)). A recent report has demonstrated that, when a muscle There are two distinct types of fat accumulation in is injured, the event which subsequently occurs is either skeletal muscles: intramyocellular fat deposits and extra- myocyte regeneration or fatty degeneration, depending myocellular adipocyte accumulation. -
Triadin, a Linker for Calsequestrin and the Ryanodine Receptor
Triadin, a Linker for Calsequestrin and the Ryanodine Receptor Wei Guo,* Annelise 0. Jorgensen,' and Kevin P. Campbell* *Howard Hughes Medical Institute, Department of Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, Iowa 52242, and *Departmentof Anatomy and Cell Biology, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Introduction Protein components of the triad junction play essential roles in muscle excitation- contraction coupling (EC coupling). Considerable research has been performed on the identification and characterization of proteins that regulate calcium storage and release from the sarcoplasmic reticulum (McPherson and Campbell, 1993; Franzini- Armstrong and Jorgensen, 1994). Key proteins characterized include the dihydro- pyridine receptor; the voltage sensor and L-type calcium channel in t-tubules; the ryanodine receptor/Ca2+-releasechannel in the terminal cisternae of the sarcoplas- mic reticulum; and calsequestrin, a moderate-affinity, high-capacity calcium-bind- ing protein located in the lumen of the junctional sarcoplasmic reticulum. Study of these proteins has been instrumental to our understanding of the molecular mecha- nisms of EC coupling. Recent research from our laboratory has focused on triadin, an abundant transmembrane protein in the junctional sarcoplasmic reticulum. Here, we briefly review recent results on the structure of triadin and its interactions with other protein components of the junctional complex in skeletal and cardiac muscle. Identification of Triadin Using purified skeletal muscle triads, we generated a library of monoclonal anti- bodies against different proteins of the junctional sarcoplasmic reticulum (Camp- bell et al., 1987). Several monoclonal antibodies recognize a protein of 94 kD (now called triadin) on reducing SDS-PAGE (Fig.