A Role for PFK-2/Fbpase-2 As Distinct from Fructose 2,6-Bisphosphate In
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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. -
Upregulation of Peroxisome Proliferator-Activated Receptor-Α And
Upregulation of peroxisome proliferator-activated receptor-α and the lipid metabolism pathway promotes carcinogenesis of ampullary cancer Chih-Yang Wang, Ying-Jui Chao, Yi-Ling Chen, Tzu-Wen Wang, Nam Nhut Phan, Hui-Ping Hsu, Yan-Shen Shan, Ming-Derg Lai 1 Supplementary Table 1. Demographics and clinical outcomes of five patients with ampullary cancer Time of Tumor Time to Age Differentia survival/ Sex Staging size Morphology Recurrence recurrence Condition (years) tion expired (cm) (months) (months) T2N0, 51 F 211 Polypoid Unknown No -- Survived 193 stage Ib T2N0, 2.41.5 58 F Mixed Good Yes 14 Expired 17 stage Ib 0.6 T3N0, 4.53.5 68 M Polypoid Good No -- Survived 162 stage IIA 1.2 T3N0, 66 M 110.8 Ulcerative Good Yes 64 Expired 227 stage IIA T3N0, 60 M 21.81 Mixed Moderate Yes 5.6 Expired 16.7 stage IIA 2 Supplementary Table 2. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of an ampullary cancer microarray using the Database for Annotation, Visualization and Integrated Discovery (DAVID). This table contains only pathways with p values that ranged 0.0001~0.05. KEGG Pathway p value Genes Pentose and 1.50E-04 UGT1A6, CRYL1, UGT1A8, AKR1B1, UGT2B11, UGT2A3, glucuronate UGT2B10, UGT2B7, XYLB interconversions Drug metabolism 1.63E-04 CYP3A4, XDH, UGT1A6, CYP3A5, CES2, CYP3A7, UGT1A8, NAT2, UGT2B11, DPYD, UGT2A3, UGT2B10, UGT2B7 Maturity-onset 2.43E-04 HNF1A, HNF4A, SLC2A2, PKLR, NEUROD1, HNF4G, diabetes of the PDX1, NR5A2, NKX2-2 young Starch and sucrose 6.03E-04 GBA3, UGT1A6, G6PC, UGT1A8, ENPP3, MGAM, SI, metabolism -
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). -
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Published OnlineFirst February 12, 2018; DOI: 10.1158/0008-5472.CAN-17-2215 Cancer Metabolism and Chemical Biology Research RSK Regulates PFK-2 Activity to Promote Metabolic Rewiring in Melanoma Thibault Houles1, Simon-Pierre Gravel2,Genevieve Lavoie1, Sejeong Shin3, Mathilde Savall1, Antoine Meant 1, Benoit Grondin1, Louis Gaboury1,4, Sang-Oh Yoon3, Julie St-Pierre2, and Philippe P. Roux1,4 Abstract Metabolic reprogramming is a hallmark of cancer that includes glycolytic flux in melanoma cells, suggesting an important role for increased glucose uptake and accelerated aerobic glycolysis. This RSK in BRAF-mediated metabolic rewiring. Consistent with this, phenotypeisrequiredtofulfill anabolic demands associated with expression of a phosphorylation-deficient mutant of PFKFB2 aberrant cell proliferation and is often mediated by oncogenic decreased aerobic glycolysis and reduced the growth of melanoma drivers such as activated BRAF. In this study, we show that the in mice. Together, these results indicate that RSK-mediated phos- MAPK-activated p90 ribosomal S6 kinase (RSK) is necessary to phorylation of PFKFB2 plays a key role in the metabolism and maintain glycolytic metabolism in BRAF-mutated melanoma growth of BRAF-mutated melanomas. cells. RSK directly phosphorylated the regulatory domain of Significance: RSK promotes glycolytic metabolism and the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2 (PFKFB2), growth of BRAF-mutated melanoma by driving phosphory- an enzyme that catalyzes the synthesis of fructose-2,6-bisphosphate lation of an important glycolytic enzyme. Cancer Res; 78(9); during glycolysis. Inhibition of RSK reduced PFKFB2 activity and 2191–204. Ó2018 AACR. Introduction but recently developed therapies that target components of the MAPK pathway have demonstrated survival advantage in pati- Melanoma is the most aggressive form of skin cancer and arises ents with BRAF-mutated tumors (7). -
Interaction of 6-Phosphofructo-2-Kinase/Fructose-2,6- Bisphosphatase (PFK-2/Fbpase-2) with Glucokinase Activates Glucose Phospho
Interaction of 6-Phosphofructo-2-Kinase/Fructose-2,6- Bisphosphatase (PFK-2/FBPase-2) With Glucokinase Activates Glucose Phosphorylation and Glucose Metabolism in Insulin-Producing Cells Laura Massa,1 Simone Baltrusch,1 David A. Okar,2,3 Alex J. Lange,2 Sigurd Lenzen,1 and Markus Tiedge1 The bifunctional enzyme 6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase (PFK-2/FBPase-2) was re- cently identified as a new intracellular binding partner he enzyme glucokinase (GK) plays a pivotal role for glucokinase (GK). Therefore, we studied the impor- in the recognition of glucose in pancreatic tance of this interaction for the activity status of GK -cells and the regulation of glucose metabolism and glucose metabolism in insulin-producing cells by Tin the liver (1–7). In pancreatic -cells, GK acts overexpression of the rat liver and pancreatic islet as a glucose sensor and catalyzes the rate-limiting step for isoforms of PFK-2/FBPase-2. PFK-2/FBPase-2 overex- initiation of glucose-induced insulin secretion (6). GK is pression in RINm5F-GK cells significantly increased the regulated in a complex manner in pancreatic -cells by GK activity by 78% in cells expressing the islet isoform, posttranslational modifications of the enzyme protein that by 130% in cells expressing the liver isoform, and by mainly depend on the intracellular glucose concentration 116% in cells expressing a cAMP-insensitive liver S32A/ (8–13). These posttranslational mechanisms of GK activity H258A double mutant isoform. Only in cells overex- regulation are comprised of conformational changes pressing the wild-type liver PFK-2/FBPase-2 isoform (14,15), sulfhydryl-group conversions (16–18), and inter- was the increase of GK activity abolished by forskolin,  apparently due to the regulatory site for phosphoryla- actions with -cell matrix proteins (13,19), insulin gran- tion by a cAMP-dependent protein kinase. -
New Nucleotide Sequence Data on the EMBL File Server
.=) 1991 Oxford University Press Nucleic Acids Research, Vol. 19, No. 2 413 New nucleotide sequence data on the EMBL File Server October 30, 1990 to November 13, 1990 New nucleotide sequence data, available from the EMBL File Server, (see Stoehr, P.J. and Omond, R.A. (1989) Nucleic Acids Res., 17 (16), 6763 -6764), are reported below. Availability of all the newest sequence data is the result of collaboration between.the EMBL Data Library and GenBank' , and data are supplied regularly by both groups. Updates to existing data are not reported here. This report has been prepared by the EMBL Data Library. PRIMATES: Human casein kinase II alpha subunit mRNA, complete cds. Human specific HS5 DNA Lozeman F.J., Litchfield D.W., Piening C., Takio K., Walsh Ueda S., Washio K., Kurosaki K.; K.A., Krebs E.G.; Genomics 8:7-12(1990). X17579 Biochemistry 29:8436-8447(1990). M55268 Human mRNA for heat shock protein HSP27 Human mRNA for actin-binding protein (ABP-280) Carper S.W., Rocheleau T.A., Storm F.K.; Gorlin J.B., Yamin R., Egan S., Stewart M., Stossel T.P., Nucleic Acids Res. 18:6457-6457(1990). X54079 Kwiatkowski D.J., Hartwig J.H.; J. Cell Biol. 111:1089-1105(1990). X53416 Human Ig germline H-chain D-region Dxpl and Dxp'1 genes, 3' Human amiloride-binding protein, complete cds. end. Barbry P., Champe M., Chassande O., Munemitsu S., Champigny Huang C., Stollar B.David.; G., Lingueglia E., Maes P., Frelin C., Tartar A., Ullrich A., Unpublished. M37485 Lazdunski M.; Proc. Natl. Acad. -
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), -
Cdna Sequence and Tissue Expression Analysis of Glucokinase from Liver of Grass Carp (Ctenopharyngodon Idella )
African Journal of Biotechnology Vol. 11(3), pp. 534-542, 10 January, 2012 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB11.3174 ISSN 1684–5315 © 2012 Academic Journals Full Length Research Paper cDNA sequence and tissue expression analysis of glucokinase from liver of grass carp (Ctenopharyngodon idella ) CHENG Han-liang*, JI Nan-jing, PENG Yong-xing, SHEN Xin, XU Jian-he, DONG Zhi-guo and WU Chen-chen Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang 222005, People’s Republic of China. Accepted 19 December, 2011 A full-length cDNA coding glucokinase (GK) was cloned from the liver of grass carp ( Ctenopharyngodon idella ) by reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends methods. The cDNA obtained was 2066 bp exclusive of poly (A) residues with a 1431 bp open reading frame encoding 476 amino acids. The GK protein has a calculated molecular weight of 53.7 kDa and isoelectric point of 5.11. Some conserved functional sites were found including one conserved hexokinase signature sequence Leu 156 -Phe 181 ; two N-linked glycosylation sites Asn 176 and Asn 214 ; one cell attachment sequence Arg 202 -Asp 204 ; one glycosaminoglycan attachment site Ser455 -Gly 458 . The amino acid sequence has a high similarity to GK of other species, the percent identity compared with topmouth culter, common carp, human and rat are 98.1, 96.8, 80.3 and 79.8%, respectively. Tissue distribution of GK mRNA in brain, mesenteric adipose tissue, spleen, white muscle and liver of grass carp was analyzed by SYBR real-time fluorescence quantitative RT-PCR method using β-actin as an internal control for cDNA normalization. -
Understanding the Central Role of Citrate in the Metabolism of Cancer Cells and Tumors: an Update
International Journal of Molecular Sciences Review Understanding the Central Role of Citrate in the Metabolism of Cancer Cells and Tumors: An Update Philippe Icard 1,2,3,*, Antoine Coquerel 1,4, Zherui Wu 5 , Joseph Gligorov 6, David Fuks 7, Ludovic Fournel 3,8, Hubert Lincet 9,10 and Luca Simula 11 1 Medical School, Université Caen Normandie, CHU de Caen, 14000 Caen, France; [email protected] 2 UNICAEN, INSERM U1086 Interdisciplinary Research Unit for Cancer Prevention and Treatment, Normandie Université, 14000 Caen, France 3 Service de Chirurgie Thoracique, Hôpital Cochin, Hôpitaux Universitaires Paris Centre, APHP, Paris-Descartes University, 75014 Paris, France; [email protected] 4 INSERM U1075, COMETE Mobilités: Attention, Orientation, Chronobiologie, Université Caen, 14000 Caen, France 5 School of Medicine, Shenzhen University, Shenzhen 518000, China; [email protected] 6 Oncology Department, Tenon Hospital, Pierre et Marie Curie University, 75020 Paris, France; [email protected] 7 Service de Chirurgie Digestive et Hépato-Biliaire, Hôpital Cochin, Hôpitaux Universitaires Paris Centre, APHP, Paris-Descartes University, 75014 Paris, France; [email protected] 8 Descartes Faculty of Medicine, University of Paris, Paris Center, 75006 Paris, France 9 INSERM U1052, CNRS UMR5286, Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; [email protected] 10 ISPB, Faculté de Pharmacie, Université Lyon 1, 69373 Lyon, France 11 Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Citation: Icard, P.; Coquerel, A.; Wu, University of Paris, 75014 Paris, France; [email protected] Z.; Gligorov, J.; Fuks, D.; Fournel, L.; * Correspondence: [email protected] Lincet, H.; Simula, L. -
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. -
Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6 -
Vitamin K2 Promotes PI3K/AKT/HIF-1Α-Mediated
www.nature.com/scientificreports OPEN Vitamin K2 promotes PI3K/AKT/ HIF-1α-mediated glycolysis that leads to AMPK-dependent autophagic cell death in bladder cancer cells Fengsen Duan1, Chunlei Mei2, Luhao Yang2, Junyan Zheng2, Huiai Lu1, Yanzhi Xia1, Stacy Hsu4, Huageng Liang3 ✉ & Ling Hong1 ✉ Vitamin K2 has been shown to exert remarkable anticancer activity. However, the detailed mechanism remains unclear. Here, our study was the frst to show that Vitamin K2 signifcantly promoted the glycolysis in bladder cancer cells by upregulating glucose consumption and lactate production, whereas inhibited TCA cycle by reducing the amounts of Acetyl-CoA. Moreover, suppression of PI3K/ AKT and HIF-1α attenuated Vitamin K2-increased glucose consumption and lactate generation, indicating that Vitamin K2 promotes PI3K/AKT and HIF-1α-mediated glycolysis in bladder cancer cells. Importantly, upon glucose limitation, Vitamin K2-upregulated glycolysis markedly induced metabolic stress, along with AMPK activation and mTORC1 pathway suppression, which subsequently triggered AMPK-dependent autophagic cell death. Intriguingly, glucose supplementation profoundly abrogated AMPK activation and rescued bladder cancer cells from Vitamin K2-triggered autophagic cell death. Furthermore, both inhibition of PI3K/AKT/HIF-1α and attenuation of glycolysis signifcantly blocked Vitamin K2-induced AMPK activation and subsequently prevented autophagic cell death. Collectively, these fndings reveal that Vitamin K2 could induce metabolic stress and trigger AMPK-dependent autophagic cell death in bladder cancer cells by PI3K/AKT/HIF-1α-mediated glycolysis promotion. Cancer cells, including bladder carcinoma cells, display the altered metabolism, compared to normal cells1. One of the most metabolic shifs in cancer cells is the aberrant glucose metabolism.