Eif6 Coordinates Insulin Sensitivity and Lipid Metabolism by Coupling Translation to Transcription
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Deep Learning–Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer Kumardeep Chaudhary1, Olivier B
Published OnlineFirst October 5, 2017; DOI: 10.1158/1078-0432.CCR-17-0853 Statistics in CCR Clinical Cancer Research Deep Learning–Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer Kumardeep Chaudhary1, Olivier B. Poirion1, Liangqun Lu1,2, and Lana X. Garmire1,2 Abstract Identifying robust survival subgroups of hepatocellular car- index (C-index) ¼ 0.68]. More aggressive subtype is associated cinoma (HCC) will significantly improve patient care. Current- with frequent TP53 inactivation mutations, higher expression ly, endeavor of integrating multi-omicsdatatoexplicitlypredict of stemness markers (KRT19 and EPCAM)andtumormarker HCC survival from multiple patient cohorts is lacking. To fill BIRC5, and activated Wnt and Akt signaling pathways. We this gap, we present a deep learning (DL)–based model on HCC validated this multi-omics model on five external datasets of that robustly differentiates survival subpopulations of patients various omics types: LIRI-JP cohort (n ¼ 230, C-index ¼ 0.75), in six cohorts. We built the DL-based, survival-sensitive model NCI cohort (n ¼ 221, C-index ¼ 0.67), Chinese cohort (n ¼ on 360 HCC patients' data using RNA sequencing (RNA-Seq), 166, C-index ¼ 0.69), E-TABM-36 cohort (n ¼ 40, C-index ¼ miRNA sequencing (miRNA-Seq), and methylation data from 0.77), and Hawaiian cohort (n ¼ 27, C-index ¼ 0.82). This TheCancerGenomeAtlas(TCGA),whichpredictsprognosis is the first study to employ DL to identify multi-omics features as good as an alternative model where genomics and clinical linked to the differential survival of patients with HCC. Given data are both considered. This DL-based model provides two its robustness over multiple cohorts, we expect this workflow to optimal subgroups of patients with significant survival differ- be useful at predicting HCC prognosis prediction. -
Small-Molecule Inhibition of 6-Phosphofructo-2-Kinase Activity Suppresses Glycolytic Flux and Tumor Growth
110 Small-molecule inhibition of 6-phosphofructo-2-kinase activity suppresses glycolytic flux and tumor growth Brian Clem,1,3 Sucheta Telang,1,3 Amy Clem,1,3 reduces the intracellular concentration of Fru-2,6-BP, Abdullah Yalcin,1,2,3 Jason Meier,2 glucose uptake, and growth of established tumors in vivo. Alan Simmons,1,3 Mary Ann Rasku,1,3 Taken together, these data support the clinical development Sengodagounder Arumugam,1,3 of 3PO and other PFKFB3 inhibitors as chemotherapeutic William L. Dean,2,3 John Eaton,1,3 Andrew Lane,1,3 agents. [Mol Cancer Ther 2008;7(1):110–20] John O. Trent,1,2,3 and Jason Chesney1,2,3 Departments of 1Medicine and 2Biochemistry and Molecular Introduction Biology and 3Molecular Targets Group, James Graham Brown Neoplastic transformation causes a marked increase in Cancer Center, University of Louisville, Louisville, Kentucky glucose uptake and catabolic conversion to lactate, which forms the basis for the most specific cancer diagnostic 18 Abstract examination—positron emission tomography of 2- F- fluoro-2-deoxyglucose (18F-2-DG) uptake (1). The protein 6-Phosphofructo-1-kinase, a rate-limiting enzyme of products of several oncogenes directly increase glycolytic glycolysis, is activated in neoplastic cells by fructose-2,6- flux even under normoxic conditions, a phenomenon bisphosphate (Fru-2,6-BP), a product of four 6-phospho- originally termed the Warburg effect (2, 3). For example, fructo-2-kinase/fructose-2,6-bisphosphatase isozymes c-myc is a transcription factor that promotes the expression (PFKFB1-4). The inducible PFKFB3 isozyme is constitu- of glycolytic enzyme mRNAs, and its expression is increased tively expressed by neoplastic cells and required for the in several human cancers regardless of the oxygen pressure high glycolytic rate and anchorage-independent growth of (4, 5). -
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. -
Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6
Research Collection Doctoral Thesis Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6 Author(s): Voigts-Hoffmann, Felix Publication Date: 2012 Permanent Link: https://doi.org/10.3929/ethz-a-007303759 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library ETH Zurich Dissertation No. 20189 Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6 A dissertation submitted to ETH ZÜRICH for the degree of Doctor of Sciences (Dr. sc. ETH Zurich) presented by Felix Voigts-Hoffmann MSc Molecular Biotechnology, Universität Heidelberg born April 11, 1981 citizen of Göttingen, Germany accepted on recommendation of Prof. Dr. Nenad Ban (Examiner) Prof. Dr. Raimund Dutzler (Co-examiner) Prof. Dr. Rudolf Glockshuber (Co-examiner) 2012 blank page ii Summary Ribosomes are large complexes of several ribosomal RNAs and dozens of proteins, which catalyze the synthesis of proteins according to the sequence encoded in messenger RNA. Over the last decade, prokaryotic ribosome structures have provided the basis for a mechanistic understanding of protein synthesis. While the core functional centers are conserved in all kingdoms, eukaryotic ribosomes are much larger than archaeal or bacterial ribosomes. Eukaryotic ribosomal rRNA and proteins contain extensions or insertions to the prokaryotic core, and many eukaryotic proteins do not have prokaryotic counterparts. Furthermore, translation regulation and ribosome biogenesis is much more complex in eukaryotes, and defects in components of the translation machinery are associated with human diseases and cancer. -
Enzyme DHRS7
Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d. -
Exploring the Non-Canonical Functions of Metabolic Enzymes Peiwei Huangyang1,2 and M
© 2018. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2018) 11, dmm033365. doi:10.1242/dmm.033365 REVIEW SPECIAL COLLECTION: CANCER METABOLISM Hidden features: exploring the non-canonical functions of metabolic enzymes Peiwei Huangyang1,2 and M. Celeste Simon1,3,* ABSTRACT A key finding from studies of metabolic enzymes is the existence The study of cellular metabolism has been rigorously revisited over the of mechanistic links between their nuclear localization and the past decade, especially in the field of cancer research, revealing new regulation of transcription. By modulating gene expression, insights that expand our understanding of malignancy. Among these metabolic enzymes themselves facilitate adaptation to rapidly insights isthe discovery that various metabolic enzymes have surprising changing environments. Furthermore, they can directly shape a ’ activities outside of their established metabolic roles, including in cell s epigenetic landscape (Kaelin and McKnight, 2013). the regulation of gene expression, DNA damage repair, cell cycle Strikingly, several metabolic enzymes exert completely distinct progression and apoptosis. Many of these newly identified functions are functions in different cellular compartments. Nuclear fructose activated in response to growth factor signaling, nutrient and oxygen bisphosphate aldolase, for example, directly interacts with RNA ́ availability, and external stress. As such, multifaceted enzymes directly polymerase III to control transcription (Ciesla et al., 2014), -
Stearoyl-Coa Desaturase 1 As a Therapeutic Target for the Treatment of Cancer
cancers Review Stearoyl-CoA Desaturase 1 as a Therapeutic Target for the Treatment of Cancer Zuzanna Tracz-Gaszewska and Pawel Dobrzyn * Laboratory of Molecular Medical Biochemistry, Nencki Institute of Experimental Biology Polish Academy of Sciences, 02-093 Warsaw, Poland * Correspondence: [email protected] Received: 5 June 2019; Accepted: 3 July 2019; Published: 5 July 2019 Abstract: A distinctive feature of cancer cells of various origins involves alterations of the composition of lipids, with significant enrichment in monounsaturated fatty acids. These molecules, in addition to being structural components of newly formed cell membranes of intensely proliferating cancer cells, support tumorigenic signaling. An increase in the expression of stearoyl-CoA desaturase 1 (SCD1), the enzyme that converts saturated fatty acids to D9-monounsaturated fatty acids, has been observed in a wide range of cancer cells, and this increase is correlated with cancer aggressiveness and poor outcomes for patients. Studies have demonstrated the involvement of SCD1 in the promotion of cancer cell proliferation, migration, metastasis, and tumor growth. Many studies have reported a role for this lipogenic factor in maintaining the characteristics of cancer stem cells (i.e., the population of cells that contributes to cancer progression and resistance to chemotherapy). Importantly, both the products of SCD1 activity and its direct impact on tumorigenic pathways have been demonstrated. Based on these findings, SCD1 appears to be a significant player in the development of malignant disease and may be a promising target for anticancer therapy. Numerous chemical compounds that exert inhibitory effects on SCD1 have been developed and preclinically tested. The present review summarizes our current knowledge of the ways in which SCD1 contributes to the progression of cancer and discusses opportunities and challenges of using SCD1 inhibitors for the treatment of cancer. -
Adiponectin Regulates Expression of Hepatic Genes Critical for Glucose and Lipid Metabolism
Adiponectin regulates expression of hepatic genes critical for glucose and lipid metabolism Qingqing Liua, Bingbing Yuana, Kinyui Alice Loa,b, Heide Christine Pattersona,c,d, Yutong Sune, and Harvey F. Lodisha,b,1 aWhitehead Institute for Biomedical Research, Cambridge, MA 02142; bDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; cDepartment of Pathology, Brigham and Women’s Hospital, Boston, MA 02115; dInstitut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany; and eDepartment of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030 Contributed by Harvey F. Lodish, July 23, 2012 (sent for review May 30, 2012) The effects of adiponectin on hepatic glucose and lipid metabolism mediated by a master regulator of hepatic gene expression, the at transcriptional level are largely unknown. We profiled hepatic transcription factor (TF) Hnf4a. gene expression in adiponectin knockout (KO) and wild-type (WT) mice by RNA sequencing. Compared with WT mice, adiponectin KO Results mice fed a chow diet exhibited decreased mRNA expression of rate- Rate-limiting enzymes catalyze the slowest or irreversible steps limiting enzymes in several important glucose and lipid metabolic in metabolic pathways, which makes them the targets of tran- pathways, including glycolysis, tricarboxylic acid cycle, fatty-acid scriptional regulation and/or posttranslational modifications activation and synthesis, triglyceride synthesis, and cholesterol such as phosphorylation in the regulation of metabolism (7). synthesis. In addition, binding of the transcription factor Hnf4a to Because adiponectin plays an important role in energy metabo- DNAs encoding several key metabolic enzymes was reduced in KO lism, our analysis on hepatic gene expression in adiponectin KO mice, suggesting that adiponectin might regulate hepatic gene and WT mice was specifically focused on the expression levels of expression via Hnf4a. -
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 -
Loss of Sbds in Shwachman-Diamond Syndrome Murine Model Leads to Reduction of 80S Ribosomes and Altered Transcript Binding
Loss of Sbds in Shwachman-Diamond Syndrome Murine Model Leads to Reduction of 80S Ribosomes and Altered Transcript Binding by Hongrui Liu A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Molecular Genetics University of Toronto © Copyright by Hongrui Liu 2016 Loss of Sbds in Shwachman-Diamond Syndrome Murine Model Leads to Reduction of 80S Ribosomes and Altered Transcript Binding Hongrui Liu Doctor of Philosophy Department of Molecular Genetics University of Toronto 2016 Abstract Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease characterized by growth retardation, exocrine pancreatic dysfunction, skeletal dysplasia, cognitive impairment and bone marrow failure. SDS is caused by mutations in SBDS (Shwachman- Bodian-Diamond syndrome). A recent model proposes that SBDS/Sbds functions together with EFL1/Efl1 to release EIF6/Eif6 from the pre-60S complex, enabling ribosomal subunit joining for translation initiation. To assess the protein synthesis deficiency that has been detected in SDS, I examined ribosomal profiles of murine fetal organs with the SDS-associated missense mutation, R126T (SbdsR126T/R126T). The SDS organ extracts revealed reduced 80S monosomes and preserved polysomes, with no ribosomal subunit imbalance compared to matched controls. Further, Eif6 was found to bind to both the 60S and 80S ribosome complexes in mutants in contrast to only 60S complexes in controls. To investigate these changes and to learn how the SDS translatome is affected, total and polysomal mRNAs of mutant and control samples were studied using cDNA microarray analyses. By comparing individual polysomal transcripts ii to respective total transcript levels, I found 799 transcripts (of 18,936 analyzed) with altered polysome loading in mutant fetal livers, with 634 being increased. -
The Role of the Rare Variants in the Genes Encoding the Alpha-Ketoglutarate Dehydrogenase in Alzheimer’S Disease
life Article The Role of the Rare Variants in the Genes Encoding the Alpha-Ketoglutarate Dehydrogenase in Alzheimer’s Disease Dora Csaban 1, Klara Pentelenyi 1, Renata Toth-Bencsik 1, Anett Illes 2, Zoltan Grosz 1, Andras Gezsi 3 and Maria Judit Molnar 1,* 1 Institute of Genomic Medicine and Rare Disorders, Semmelweis University, H-1082 Budapest, Hungary; [email protected] (D.C.); pentelenyi.klara@ med.semmelweis-univ.hu (K.P.); [email protected] (R.T.-B.); [email protected] (Z.G.) 2 PentaCore Laboratory Budapest, H-1094 Budapest, Hungary; [email protected] 3 Department of Measurement and Information Systems, Budapest University of Technology and Economics, H-1117 Budapest, Hungary; [email protected] * Correspondence: [email protected] Abstract: There is increasing evidence that several mitochondrial abnormalities are present in the brains of patients with Alzheimer’s disease (AD). Decreased alpha-ketoglutarate dehydrogenase complex (αKGDHc) activity was identified in some patients with AD. The αKGDHc is a key enzyme in the Krebs cycle. This enzyme is very sensitive to the harmful effect of reactive oxygen species, which gives them a critical role in the Alzheimer and mitochondrial disease research area. Previously, several genetic risk factors were described in association with AD. Our aim was to analyze the associations of rare damaging variants in the genes encoding αKGDHc subunits and AD. The three genes (OGDH, DLST, DLD) encoding αKGDHc subunits were sequenced from different brain regions Citation: Csaban, D.; Pentelenyi, K.; of 11 patients with histologically confirmed AD and the blood of further 35 AD patients. -
Eif6 Promotes the Malignant Progression of Human
Sun et al. J Transl Med (2021) 19:216 https://doi.org/10.1186/s12967-021-02877-4 Journal of Translational Medicine RESEARCH Open Access eIF6 promotes the malignant progression of human hepatocellular carcinoma via the mTOR signaling pathway Liping Sun1†, Shuguang Liu3, Xiaopai Wang4, Xuefeng Zheng5, Ya Chen1 and Hong Shen1,2* Abstract Background: Eukaryotic translation initiation factor 6 (eIF6) has a crucial function in the maturation of 60S ribosomal subunits, and it controls the initiation of protein translation. Although emerging studies indicate that eIF6 is aberrantly expressed in various types of cancers, the functions and underlying molecular mechanisms of eIF6 in the pathological progression of hepatocellular carcinoma (HCC) remain unclear. This study aimed to evaluate the potential diagnostic and prognostic value of eIF6 in patients with HCC. Methods: HCC samples enrolled from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and our cohort were used to explore the role and mechanism of eIF6 in HCC. The diagnostic power of eIF6 was verifed by receiver operating characteristic curve (ROC) analysis and its prognostic value was assessed by Kaplan–Meier analysis, and then related biological functions of eIF6 were determined in vitro and in vivo cancer models. In addition, poten- tial molecular mechanism of eIF6 in HCC was unveiled by the gene set enrichment analysis and western blot assay. Results: We demonstrated that eIF6 expression was markedly increased in HCC, and elevated eIF6 expression cor- related with pathological progression of HCC. Besides, eIF6 served as not only a new diagnostic biomarker but also an independent risk factor for OS in HCC patients.