Hypoxia-Inducible Factor–1Α–Dependent Induction of Mir122 Enhances Hepatic Ischemia Tolerance
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Hypoxia and Oxygen-Sensing Signaling in Gene Regulation and Cancer Progression
International Journal of Molecular Sciences Review Hypoxia and Oxygen-Sensing Signaling in Gene Regulation and Cancer Progression Guang Yang, Rachel Shi and Qing Zhang * Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; [email protected] (G.Y.); [email protected] (R.S.) * Correspondence: [email protected]; Tel.: +1-214-645-4671 Received: 6 October 2020; Accepted: 29 October 2020; Published: 31 October 2020 Abstract: Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression. The key molecules of the hypoxia/oxygen-sensing signaling include the transcriptional regulator hypoxia-inducible factor (HIF) which widely controls oxygen responsive genes, the central members of the 2-oxoglutarate (2-OG)-dependent dioxygenases, such as prolyl hydroxylase (PHD or EglN), and an E3 ubiquitin ligase component for HIF degeneration called von Hippel–Lindau (encoding protein pVHL). In this review, we summarize the current knowledge about the canonical hypoxia signaling, HIF transcription factors, and pVHL. In addition, the role of 2-OG-dependent enzymes, such as DNA/RNA-modifying enzymes, JmjC domain-containing enzymes, and prolyl hydroxylases, in gene regulation of cancer progression, is specifically reviewed. We also discuss the therapeutic advancement of targeting hypoxia and oxygen sensing pathways in cancer. Keywords: hypoxia; PHDs; TETs; JmjCs; HIFs 1. Introduction Molecular oxygen serves as a co-factor in many biochemical processes and is fundamental for aerobic organisms to maintain intracellular ATP levels [1,2]. -
Interplay Between Epigenetics and Metabolism in Oncogenesis: Mechanisms and Therapeutic Approaches
OPEN Oncogene (2017) 36, 3359–3374 www.nature.com/onc REVIEW Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches CC Wong1, Y Qian2,3 and J Yu1 Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment. In this review, we summarized the recent discoveries linking epigenetics and metabolism and their underlying roles in tumorigenesis; and highlighted the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these abnormalities in cancer. Oncogene (2017) 36, 3359–3374; doi:10.1038/onc.2016.485; published online 16 January 2017 INTRODUCTION metabolic genes have also been identified as driver genes It has been appreciated since the early days of cancer research mutated in some cancers, such as isocitrate dehydrogenase 1 16 17 that the metabolic profiles of tumor cells differ significantly from and 2 (IDH1/2) in gliomas and acute myeloid leukemia (AML), 18 normal cells. Cancer cells have high metabolic demands and they succinate dehydrogenase (SDH) in paragangliomas and fuma- utilize nutrients with an altered metabolic program to support rate hydratase (FH) in hereditary leiomyomatosis and renal cell 19 their high proliferative rates and adapt to the hostile tumor cancer (HLRCC). -
Mutant IDH, (R)-2-Hydroxyglutarate, and Cancer
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer Julie-Aurore Losman1 and William G. Kaelin Jr.1,2,3 1Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA; 2Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Mutations in metabolic enzymes, including isocitrate whether altered cellular metabolism is a cause of cancer dehydrogenase 1 (IDH1) and IDH2, in cancer strongly or merely an adaptive response of cancer cells in the face implicate altered metabolism in tumorigenesis. IDH1 of accelerated cell proliferation is still a topic of some and IDH2 catalyze the interconversion of isocitrate and debate. 2-oxoglutarate (2OG). 2OG is a TCA cycle intermediate The recent identification of cancer-associated muta- and an essential cofactor for many enzymes, including tions in three metabolic enzymes suggests that altered JmjC domain-containing histone demethylases, TET cellular metabolism can indeed be a cause of some 5-methylcytosine hydroxylases, and EglN prolyl-4-hydrox- cancers (Pollard et al. 2003; King et al. 2006; Raimundo ylases. Cancer-associated IDH mutations alter the enzymes et al. 2011). Two of these enzymes, fumarate hydratase such that they reduce 2OG to the structurally similar (FH) and succinate dehydrogenase (SDH), are bone fide metabolite (R)-2-hydroxyglutarate [(R)-2HG]. Here we tumor suppressors, and loss-of-function mutations in FH review what is known about the molecular mechanisms and SDH have been identified in various cancers, in- of transformation by mutant IDH and discuss their im- cluding renal cell carcinomas and paragangliomas. -
Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen, -
Egln2 Associates with the NRF1PGC1 Complex and Controls
Article EglN2 associates with the NRF1-PGC1a complex and controls mitochondrial function in breast cancer Jing Zhang1,†, Chengyang Wang2,†, Xi Chen3, Mamoru Takada1, Cheng Fan1, Xingnan Zheng1, Haitao Wen1,4, Yong Liu1, Chenguang Wang5, Richard G Pestell6, Katherine M Aird7, William G Kaelin Jr8,9, Xiaole Shirley Liu10 & Qing Zhang1,11,* Abstract Introduction The EglN2/PHD1 prolyl hydroxylase is an important oxygen sensor The presence of hypoxic cells in the tumor microenvironment was contributing to breast tumorigenesis. Emerging studies suggest proposed by Thomlinson and Gray more than 50 years ago that there is functional cross talk between oxygen sensing and (Thomlinson & Gray, 1955). These hypoxic cells confer radio- or mitochondrial function, both of which play an essential role for chemotherapeutic resistance and therefore are hypothesized to be sustained tumor growth. However, the potential link between under selection for aggressive malignancy during the course of EglN2 and mitochondrial function remains largely undefined. cancer development (Brown & Wilson, 2004). One central question Here, we show that EglN2 depletion decreases mitochondrial is how hypoxic cancer cells sense their oxygen availability, adapt to respiration in breast cancer under normoxia and hypoxia, which the stressful environment, and proliferate out of control. The key correlates with decreased mitochondrial DNA in a HIF1/2a- proteins mediating oxygen sensing in these cells mainly involve independent manner. Integrative analyses of gene expression proteins that are responsible for the hydroxylation of hypoxia- profile and genomewide binding of EglN2 under hypoxic condi- inducible factor (HIF), namely the prolyl hydroxylases EglN1-3. As a tions reveal nuclear respiratory factor 1 (NRF1) motif enrichment key EglN enzyme substrate, HIF1a is hydroxylated on prolines 402 in EglN2-activated genes, suggesting NRF1 as an EglN2 binding and 564 under normoxic conditions. -
Application to Acetaminophen Anaïs Michaut, Dounia Le Guillou, Caroline Moreau, Simon Bucher, Mitchell R
A cellular model to study drug-induced liver injury in nonalcoholic fatty liver disease: application to acetaminophen Anaïs Michaut, Dounia Le Guillou, Caroline Moreau, Simon Bucher, Mitchell R. Mcgill, Sophie Martinais, Thomas Gicquel, Isabelle Morel, Marie-Anne Robin, Hartmut Jaeschke, et al. To cite this version: Anaïs Michaut, Dounia Le Guillou, Caroline Moreau, Simon Bucher, Mitchell R. Mcgill, et al.. A cellular model to study drug-induced liver injury in nonalcoholic fatty liver disease: applica- tion to acetaminophen. Toxicology and Applied Pharmacology, Elsevier, 2016, 292, pp.40-55. 10.1016/j.taap.2015.12.020. hal-01255826 HAL Id: hal-01255826 https://hal-univ-rennes1.archives-ouvertes.fr/hal-01255826 Submitted on 29 Jan 2016 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. ACCEPTED MANUSCRIPT A cellular model to study drug-induced liver injury in nonalcoholic fatty liver disease: application to acetaminophen Anaïs Michauta, Dounia Le Guilloua, Caroline Moreaua,b, Simon Buchera, Mitchell R. McGillc, Sophie Martinaisa, Thomas Gicquela,b, Isabelle Morela,b, Marie-Anne Robina, Hartmut Jaeschkec, and Bernard Fromentya,* aINSERM, U991, Université de Rennes 1, Rennes, France, bService de Biochimie et Toxicologie, CHU Pontchaillou, Rennes, France, cDepartment of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA *To whom correspondenceACCEPTED should be addressed MANUSCRIPT at INSERM U991, Université de Rennes 1, 35043 Rennes Cedex, France. -
Original Article Colonic Mucosal Gene Expression in Irritable Bowel Syndrome Rats by the Liquid Chip Technology
Int J Clin Exp Pathol 2016;9(10):10751-10755 www.ijcep.com /ISSN:1936-2625/IJCEP0036079 Original Article Colonic mucosal gene expression in irritable bowel syndrome rats by the liquid chip technology Guanqun Chao1, Yingying Wang2, Shuo Zhang2 1Department of Family Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Zhejiang, China; 2Department of Gastroenterology, The First Affiliated Hospital, Zhejiang Chinese Medical University, Zhejiang, China Received July 18, 2016; Accepted August 27, 2016; Epub October 1, 2016; Published October 15, 2016 Abstract: Background: Irritable bowel syndrome (IBS) is one of the most frequent GI disorders. The etiology and pathogenesis underlying IBS are currently unclear. Gene influence a number of chronic disease processes and may also be involved in regulating disease activity in gastrointestinal disorders, but few studies of IBS have focused on gene expression. Objective: The objective of this study was to screen the differentially expressed colonic mucosal genes in IBS rats to build the expression profile of genes in the colon of IBS rats. Methods: Twenty SD rats were divided randomly into two groups: the rats of control group were normal rats; the rats of model group were induced by conditioned stimulus and unconditioned stimulus. The rats’ visceral sensitivity was evaluated by abdominal with- draw reaction. Then we screened differential expression of colonic mucosal gene by the liquid chip technology and verified by RT-PCR technology. Results: The IBS model was successfully established. Compared with control group, the dose of injection water was decreased in model group (P<0.01). We screened htr4, htr1a, 2rl3, nos1, Calca, npy, crhr2, il1b, p2rx3, nos2, tph1, crhr1, hmox1, trpv1, Vip, f2rl, tgfb1, htr3a, slc6a4, tff2, aqp8 from the colon, but we found that only the expression of nos1, il1b, htr3a in model group was up-regulated (P<0.05). -
Integrative Genomics Identifies New Genes Associated with Severe COPD and Emphysema Phuwanat Sakornsakolpat1,2, Jarrett D
Sakornsakolpat et al. Respiratory Research (2018) 19:46 https://doi.org/10.1186/s12931-018-0744-9 RESEARCH Open Access Integrative genomics identifies new genes associated with severe COPD and emphysema Phuwanat Sakornsakolpat1,2, Jarrett D. Morrow1, Peter J. Castaldi1,3, Craig P. Hersh1,4, Yohan Bossé5, Edwin K. Silverman1,4, Ani Manichaikul6 and Michael H. Cho1,4* Abstract Background: Genome-wide association studies have identified several genetic risk loci for severe chronic obstructive pulmonary disease (COPD) and emphysema. However, these studies do not fully explain disease heritability and in most cases, fail to implicate specific genes. Integrative methods that combine gene expression data with GWAS can provide more power in discovering disease-associated genes and give mechanistic insight into regulated genes. Methods: We applied a recently described method that imputes gene expression using reference transcriptome data to genome-wide association studies for two phenotypes (severe COPD and quantitative emphysema) and blood and lung tissue gene expression datasets. We further tested the potential causality of individual genes using multi-variant colocalization. Results: We identified seven genes significantly associated with severe COPD, and five genes significantly associated with quantitative emphysema in whole blood or lung. We validated results in independent transcriptome databases and confirmed colocalization signals for PSMA4, EGLN2, WNT3, DCBLD1, and LILRA3. Three of these genes were not located within previously reported GWAS loci for either phenotype. We also identified genetically driven pathways, including those related to immune regulation. Conclusions: An integrative analysis of GWAS and gene expression identified novel associations with severe COPD and quantitative emphysema, and also suggested disease-associated genes in known COPD susceptibility loci. -
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 -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses 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 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Endocrine Abstracts Vol 65
Endocrine Abstracts November 2019 Volume 65 ISSN 1479-6848 (online) Society for Endocrinology BES 2019 11–13 November 2019, Brighton published by Online version available at bioscientifica www.endocrine-abstracts.org Volume 65 Endocrine Abstracts November 2019 Society for Endocrinology BES 2019 11–13 November 2019, Brighton VOLUME EDITORS The abstracts submitted were marked by the Abstract Marking panel, selected by the Programme Organising Committee. Programme Committee D Bassett (Programme Secretary) (London) Laura Matthews (Leeds) Andrew Childs (Programme Co-ordinator) (London) Carla Moran (Cambridge) Nils Krone (Programme Co-ordinator) (Sheffield) Annice Mukherjee (Salford) Helen Simpson (Programme Co-ordinator) (London) Francesca Spiga (Bristol) Davide Calebiro (Birmingham) Jeremy Tomlinson (Oxford) Ben Challis (Cambridge) Jennifer Walsh (Sheffield) Mandy Drake (Edinburgh) Abstract Marking Panel Ramzi Ajjan (Leeds) Neil Gittoes (Birmingham) John Newell-Price (Sheffield) Richard Anderson (Edinburgh) Helena Gleeson (Birmingham) Mark Nixon (Edinburgh) Ruth Andrew (Edinburgh) Philippa Hanson (London) Finbarr O’Harte (Ulster) Weibke Arlt (Birmingham) Martin Hewison (Birmingham) Adrian Park (Cambridge) Mo Aye (Hull) Claire Higham (Manchester) Simon Pearce (Newcastle) Tom Barber (Warwick) Steve Hillier (Edinburgh) Andrew Powlson (Cambridge) Duncan Bassett (London) Andy James (Newcastle) Teresa Rea (Belfast) Roger Brown (Edinburgh) Channa Jayasena (London) Martin Read (Birmingham) Paul Carroll (London) Niki Karavitaki (Oxford) Aled Rees (Cardiff) -
Areca Catechu-(Betel-Nut)-Induced Whole Transcriptome Changes Associated With
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.233932; this version posted August 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Areca catechu-(Betel-nut)-induced whole transcriptome changes associated with 2 diabetes, obesity and metabolic syndrome in a human monocyte cell line 3 4 Short title: Betel-nut induced whole transcriptome changes 5 6 7 Shirleny Cardoso1¶ , B. William Ogunkolade1¶, Rob Lowe2, Emanuel Savage3, Charles A 8 Mein3, Barbara J Boucher1, Graham A Hitman1* 9 10 11 1Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of 12 Medicine and Dentistry, Queen Mary University of London, United Kingdom 13 14 2Omnigen Biodata Ltd, Cambridge, United Kingdom 15 16 3Barts and The London Genome Centre, Blizard Institute, Queen Mary University of London, 17 United Kingdom 18 19 * Corresponding author 20 Email: [email protected] 21 22 ¶These authors contributed equally to the work 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.233932; this version posted August 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 25 Abstract 26 Betel-nut consumption is the fourth most common addictive habit globally and there is good 27 evidence to link it with obesity, type 2 diabetes and the metabolic syndrome.