Metabolic Interplay Between the Immune System and Melanoma Cells: Therapeutic Implications
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Screening Differentially Expressed Genes of Pancreatic Cancer Between Mongolian and Han People Using Bioinformatics Technology
Screening differentially expressed genes of pancreatic cancer between Mongolian and Han people using bioinformatics technology Jiasheng Xu First Aliated Hospital of Nanchang University Kaili Liao Second Aliated Hospital of Nanchang University ZHONGHUA FU First Aliated Hospital of Nanchang University ZHENFANG XIONG ( [email protected] ) The First Aliated Hospital of Nanchang University https://orcid.org/0000-0003-2062-9204 Research article Keywords: Pancreatic ductal cell carcinoma; Affymetrix gene expression prole; Gene differential expression; GO analysis; Pathway analysis; Mongolian Posted Date: October 14th, 2019 DOI: https://doi.org/10.21203/rs.2.11118/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at BMC Cancer on April 9th, 2020. See the published version at https://doi.org/10.1186/s12885-020-06722-7. Page 1/19 Abstract Objective: To screen and analyze differentially expressed genes in pancreatic carcinoma tissues taken from Mongolian and Han patients by Affymetrix Genechip. Methods: Pancreatic ductal cell carcinoma tissues were collected from the Mongolian and Han patients undergoing resection in the Second Aliated Hospital of Nanchang University from March 2015 to May 2018 and the total RNA was extracted. Differentially expressed genes were selected from the total RNA qualied by Nanodrop 2000 and Agilent 2100 using Affymetrix and a cartogram was drawn; The gene ontology (GO) analysis and Pathway analysis were used for the collection and analysis of biological information of these differentially expressed genes. Finally, some differentially expressed genes were veried by real-time PCR. Results: Through the microarray analysis of gene expression, 970 differentially expressed genes were detected by comparing pancreatic cancer tissue samples between Mongolian and Han patients. -
Cori Cycle Activity in Man
Cori cycle activity in man Christine Waterhouse, Julian Keilson J Clin Invest. 1969;48(12):2359-2366. https://doi.org/10.1172/JCI106202. Research Article 12 subjects have been studied after an overnight fast with trace amounts of pyruvate-3-14C and glucose-6-14C. Blood disappearance curves and incorporation of the pyruvate-3-14C label into blood glucose have been determined. By the use of transfer functions which allow processes with many different chemical steps to be examined as a unit, we have determined the per cent of pyruvate and presumably lactate which is regenerated into glucose. 8 of the 12 subjects showed that 7-23 mg/kg per hr are recycled, while 4 subjects fell well outside this range. Correlation of increased activity was not good with any demonstrated metabolic abnormality (diabetes or obesity), and it is suggested from clinical observation of the subjects that anxiety may play a role. Find the latest version: https://jci.me/106202/pdf Cori Cycle Activity in Man CHRISTIE WATERHOUSE and JULLAN KEISON From the Department of Medicine, University of Rochester School of Medicine and Dentistry and the Department of Statistics, University of Rochester College of Arts and Sciences, Rochester, New York 14620 ABSTRACT 12 subjects have been studied after an glucose derived from lactate and pyruvate. The analysis overnight fast with trace amounts of pyruvate-3-'4C and itself also views glucose as distributed in a homogeneous glucose-6-'4C. Blood disappearance curves and incorpora- pool within the body, thus neglecting the early portion tion of the pyruvate-3-14C label into blood glucose have of the glucose 'C disappearance curve. -
An in Cellulo-Derived Structure of PAK4 in Complex with Its Inhibitor Inka1
ARTICLE Received 27 May 2015 | Accepted 21 Sep 2015 | Published 26 Nov 2015 DOI: 10.1038/ncomms9681 OPEN An in cellulo-derived structure of PAK4 in complex with its inhibitor Inka1 Yohendran Baskaran1,*, Khay C. Ang1,2,*, Praju V. Anekal1, Wee L. Chan1, Jonathan M. Grimes3,4, Ed Manser1,5,6 & Robert C. Robinson1,2 PAK4 is a metazoan-specific kinase acting downstream of Cdc42. Here we describe the structure of human PAK4 in complex with Inka1, a potent endogenous kinase inhibitor. Using single mammalian cells containing crystals 50 mm in length, we have determined the in cellulo crystal structure at 2.95 Å resolution, which reveals the details of how the PAK4 catalytic domain binds cellular ATP and the Inka1 inhibitor. The crystal lattice consists only of PAK4– PAK4 contacts, which form a hexagonal array with channels of 80 Å in diameter that run the length of the crystal. The crystal accommodates a variety of other proteins when fused to the kinase inhibitor. Inka1–GFP was used to monitor the process crystal formation in living cells. Similar derivatives of Inka1 will allow us to study the effects of PAK4 inhibition in cells and model organisms, to allow better validation of therapeutic agents targeting PAK4. 1 Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Proteos Building, 61 Biopolis Drive, 8-15, Singapore 138673, Singapore. 2 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore. 3 Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. -
Phospho-PAK4 (Ser474)/PAK5 (Ser602)/PAK6 (Ser560) Antibody Detects Endogenous 12
Revision 1 C 0 2 - t Phospho-PAK4 (Ser474)/PAK5 a e r o t (Ser602)/PAK6 (Ser560) Antibody S Orders: 877-616-CELL (2355) [email protected] Support: 877-678-TECH (8324) 1 4 Web: [email protected] 2 www.cellsignal.com 3 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source: UniProt ID: Entrez-Gene Id: WB H M GP Endogenous 72 (PAK4). 82 Rabbit Q9NQU5, Q9P286, O96013 56924, 57144, 10298 (PAK6). 90 (PAK5). p y g y p y Product Usage Information pivotal role in regulating the activity and function of PAK4 (10). PAK family members are widely expressed, and often overexpressed in human cancer (11,12). Application Dilution 1. Knaus, U.G. and Bokoch, G.M. (1998) Int. J. Biochem. Cell Biol. 30, 857-62. 2. Daniels, R.H. et al. (1998) EMBO J. 17, 754-64. Western Blotting 1:1000 3. King, C.C. et al. (2000) J. Biol. Chem. 275, 41201-9. 4. Manser, E. et al. (1997) Mol. Cell. Biol. 17, 1129-43. Storage 5. Gatti, A. et al. (1999) J. Biol. Chem. 274, 8022-8. 6. Lei, M. et al. (2000) Cell 102, 387-97. Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA and 50% 7. Chong, C. et al. (2001) J. Biol. Chem. 276, 17347-53. glycerol. Store at –20°C. Do not aliquot the antibody. 8. Zhao, Z. et al. (2000) Mol. Cell. Biol. 20, 3906-17. 9. -
Screening of Potential Genes and Transcription Factors Of
ANIMAL STUDY e-ISSN 1643-3750 © Med Sci Monit, 2018; 24: 503-510 DOI: 10.12659/MSM.907445 Received: 2017.10.08 Accepted: 2018.01.01 Screening of Potential Genes and Transcription Published: 2018.01.25 Factors of Postoperative Cognitive Dysfunction via Bioinformatics Methods Authors’ Contribution: ABE 1 Yafeng Wang 1 Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical Study Design A AB 1 Ailan Huang University, Nanning, Guangxi, P.R. China Data Collection B 2 Department of Gynecology, People’s Hospital of Guangxi Zhuang Autonomous Statistical Analysis C BEF 1 Lixia Gan Region, The First Affiliated Hospital of Guangxi Medical University, Nanning, Data Interpretation D BCF 1 Yanli Bao Guangxi, P.R. China Manuscript Preparation E BDF 1 Weilin Zhu 3 Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical Literature Search F University, Nanning, Guangxi, P.R. China Funds Collection G EF 1 Yanyan Hu AE 1 Li Ma CF 2 Shiyang Wei DE 3 Yuyan Lan Corresponding Author: Yafeng Wang, e-mail: [email protected] Source of support: Departmental sources Background: The aim of this study was to explore the potential genes and transcription factors involved in postoperative cognitive dysfunction (POCD) via bioinformatics analysis. Material/Methods: GSE95070 miRNA expression profiles were downloaded from Gene Expression Omnibus database, which in- cluded five hippocampal tissues from POCD mice and controls. Moreover, the differentially expressed miRNAs (DEMs) between the two groups were identified. In addition, the target genes of DEMs were predicted using Targetscan 7.1, followed by protein-protein interaction (PPI) network construction, functional enrichment anal- ysis, pathway analysis, and prediction of transcription factors (TFs) targeting the potential targets. -
Transcriptome Analysis of Human Diabetic Kidney Disease
ORIGINAL ARTICLE Transcriptome Analysis of Human Diabetic Kidney Disease Karolina I. Woroniecka,1 Ae Seo Deok Park,1 Davoud Mohtat,2 David B. Thomas,3 James M. Pullman,4 and Katalin Susztak1,5 OBJECTIVE—Diabetic kidney disease (DKD) is the single cases, mild and then moderate mesangial expansion can be leading cause of kidney failure in the U.S., for which a cure has observed. In general, diabetic kidney disease (DKD) is not yet been found. The aim of our study was to provide an considered a nonimmune-mediated degenerative disease unbiased catalog of gene-expression changes in human diabetic of the glomerulus; however, it has long been noted that kidney biopsy samples. complement and immunoglobulins sometimes can be de- — tected in diseased glomeruli, although their role and sig- RESEARCH DESIGN AND METHODS Affymetrix expression fi arrays were used to identify differentially regulated transcripts in ni cance is not clear (4). 44 microdissected human kidney samples. The DKD samples were The understanding of DKD has been challenged by multi- significant for their racial diversity and decreased glomerular ple issues. First, the diagnosis of DKD usually is made using filtration rate (~20–30 mL/min). Stringent statistical analysis, using clinical criteria, and kidney biopsy often is not performed. the Benjamini-Hochberg corrected two-tailed t test, was used to According to current clinical practice, the development of identify differentially expressed transcripts in control and diseased albuminuria in patients with diabetes is sufficient to make the glomeruli and tubuli. Two different Web-based algorithms were fi diagnosis of DKD (5). We do not understand the correlation used to de ne differentially regulated pathways. -
Glycolysis and Gluconeogenesis
CC7_Unit 2.3 Glycolysis and Gluconeogenesis Glucose occupies a central position in the metabolism of plants, animals and many microorganisms. In animals, glucose has four major fates as shown in figure 1. The organisms that do not have access to glucose from other sources must make it. Plants make glucose by photosynthesis. Non-photosynthetic cells make glucose from 3 and 4 carbon precursors by the process of gluconeogenesis. Glycolysis is the process of enzymatic break down of one molecule of glucose (6 carbon) into two pyruvate molecules (3 carbon) with the concomitant net production of two molecules of ATP. The complete glycolytic pathway was elucidated by 1940, largely through the pioneering cotributions of Gustav Embden, Otto Meyerhof, Carl Neuberg, Jcob Parnad, Otto Wrburg, Gerty Cori and Carl Cori. Glycolysis is also known as Embden-Meyerhof pathway. • Glycolysis is an almost universal central pathway of glucose catabolism. • Glycolysis is anaerobic process. During glycolysis some of the free energy is released and conserved in the form of ATP and NADH. • Anaerobic microorganisms are entirely dependent on glycolysis. • In most of the organisms, the pyruvate formed by glycolysis is further metabolised via one of the three catabolic routes. 1) Under aerobic conditions, glucose is oxidized all the way to C02 and H2O. 2) Under anaerobic conditions, the pyruvic acid can be fermented to lactic acid or to 3) ethanol plus CO2 as shown in figure 2. • Glycolytic breakdown of glucose is the sole source of metabolic energy in some mammalian tissues and cells (RBCs, Brain, Renal medulla and Sperm cell). Glycolysis occurs in TEN steps. -
Proximity Proteomics Identifies PAK4 As a Component of Afadin–Nectin
ARTICLE https://doi.org/10.1038/s41467-021-25011-w OPEN Proximity proteomics identifies PAK4 as a component of Afadin–Nectin junctions Yohendran Baskaran 1,5, Felicia Pei-Ling Tay2,5, Elsa Yuen Wai Ng1, Claire Lee Foon Swa 3, Sheena Wee 3, ✉ Jayantha Gunaratne3 & Edward Manser 1,4 Human PAK4 is an ubiquitously expressed p21-activated kinase which acts downstream of Cdc42. Since PAK4 is enriched in cell-cell junctions, we probed the local protein environment 1234567890():,; around the kinase with a view to understanding its location and substrates. We report that U2OS cells expressing PAK4-BirA-GFP identify a subset of 27 PAK4-proximal proteins that are primarily cell-cell junction components. Afadin/AF6 showed the highest relative biotin labelling and links to the nectin family of homophilic junctional proteins. Reciprocally >50% of the PAK4-proximal proteins were identified by Afadin BioID. Co-precipitation experiments failed to identify junctional proteins, emphasizing the advantage of the BioID method. Mechanistically PAK4 depended on Afadin for its junctional localization, which is similar to the situation in Drosophila. A highly ranked PAK4-proximal protein LZTS2 was immuno- localized with Afadin at cell-cell junctions. Though PAK4 and Cdc42 are junctional, BioID analysis did not yield conventional cadherins, indicating their spatial segregation. To identify cellular PAK4 substrates we then assessed rapid changes (12’) in phospho-proteome after treatment with two PAK inhibitors. Among the PAK4-proximal junctional proteins seventeen PAK4 sites were identified. We anticipate mammalian group II PAKs are selective for the Afadin/nectin sub-compartment, with a demonstrably distinct localization from tight and cadherin junctions. -
8. 2020-New METABOLISM in CANCER CELLS-Students
METABOLIC ALTERATIONS IN CANCER CELLS METABOLIC CHARACTERISTICS OF CANCER CELLS Increased GLYCOLYTIC ACTIVITY (Warburg Effect) Increased production of LACTATE Loss of PASTEUR’S EFFECT (Oxygen inhibition of glycolysis) INCREASED CONSUMPTION Cox4- of GLUTAMINE 2 INCREASED PROTEIN SYNTHESIS DECREASED PROTEOLYSIS DECREASED SYNTHESIS OF FATTY ACIDS (increased lipolysis from host adipose tissue) ENERGETIC METABOLISM IN TUMOURS • WARBURG EFFECT • In the 1920s, Otto Warburg observed that tumor cells consume a large amount of glucose, much • more than normal cells, and convert most of it to lactic acid. This phenomenon, now known as the • ‘Warburg effect,’ is the foundation of one of the earliest general concepts of cancer: that a • fundamental disturbance of cellular metabolic activity is at the root of tumor formation and growth. Biography Otto Heinrich Warburg: • Born-October 8, 1883 in Germany • Died-August 1, 1970 in Berlin, Germany • Son of physicist Emil Warburg • Otto was a German physiologist and medical doctor. • He won a Nobel prize in Physiology and Medicine for his Warburg effect in 1931. • He was one of the twentieth century's leading biochemist One of his Lectures… • "Cancer, above all other diseases, has countless secondary causes. But, even for cancer, there is only one prime cause. Summarized in a few words, the prime cause of cancer is the replacement of the respiration of oxygen in normal body cells by a fermentation of sugar… " -- Dr. Otto H. Warburg in Lecture The Warburg hypothesis The prime cause of cancer is the replacement of the respiration of oxygen…by a fermentation of sugar…” Injury of respiration Aerobic glycolysis De-differentiation Normal cell Phase I Phase II Phase III Cancer cell The Warburg Effect • Pyruvate is an end-product of glycolysis, and is oxidized within the mitochondria. -
PAK4 Signaling in Health and Disease
Won et al. Experimental & Molecular Medicine (2019) 51:11 https://doi.org/10.1038/s12276-018-0204-0 Experimental & Molecular Medicine REVIEW ARTICLE Open Access PAK4signalinginhealthanddisease: defining the PAK4–CREB axis So-Yoon Won1,Jung-JinPark1,Eun-YoungShin1 and Eung-Gook Kim1 Abstract p21-Activated kinase 4 (PAK4), a member of the PAK family, regulates a wide range of cellular functions, including cell adhesion, migration, proliferation, and survival. Dysregulation of its expression and activity thus contributes to the development of diverse pathological conditions. PAK4 plays a pivotal role in cancer progression by accelerating the epithelial–mesenchymal transition, invasion, and metastasis. Therefore, PAK4 is regarded as an attractive therapeutic target in diverse types of cancers, prompting the development of PAK4-specific inhibitors as anticancer drugs; however, these drugs have not yet been successful. PAK4 is essential for embryonic brain development and has a neuroprotective function. A long list of PAK4 effectors has been reported. Recently, the transcription factor CREB has emerged as a novel effector of PAK4. This finding has broad implications for the role of PAK4 in health and disease because CREB-mediated transcriptional reprogramming involves a wide range of genes. In this article, we review the PAK4 signaling pathways involved in prostate cancer, Parkinson’s disease, and melanogenesis, focusing in particular on the PAK4-CREB axis. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction kinase domain of all PAK family members is located at the p21-Activated kinase (PAK) was initially identified as an C-terminus. In the inactive state, group I PAKs are effector of Rho GTPases that play a central role in reor- homodimers, and group II PAKs are monomers. -
Identification of Key Genes and Pathways for Alzheimer's Disease
Biophys Rep 2019, 5(2):98–109 https://doi.org/10.1007/s41048-019-0086-2 Biophysics Reports RESEARCH ARTICLE Identification of key genes and pathways for Alzheimer’s disease via combined analysis of genome-wide expression profiling in the hippocampus Mengsi Wu1,2, Kechi Fang1, Weixiao Wang1,2, Wei Lin1,2, Liyuan Guo1,2&, Jing Wang1,2& 1 CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China 2 Department of Psychology, University of Chinese Academy of Sciences, Beijing 10049, China Received: 8 August 2018 / Accepted: 17 January 2019 / Published online: 20 April 2019 Abstract In this study, combined analysis of expression profiling in the hippocampus of 76 patients with Alz- heimer’s disease (AD) and 40 healthy controls was performed. The effects of covariates (including age, gender, postmortem interval, and batch effect) were controlled, and differentially expressed genes (DEGs) were identified using a linear mixed-effects model. To explore the biological processes, func- tional pathway enrichment and protein–protein interaction (PPI) network analyses were performed on the DEGs. The extended genes with PPI to the DEGs were obtained. Finally, the DEGs and the extended genes were ranked using the convergent functional genomics method. Eighty DEGs with q \ 0.1, including 67 downregulated and 13 upregulated genes, were identified. In the pathway enrichment analysis, the 80 DEGs were significantly enriched in one Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, GABAergic synapses, and 22 Gene Ontology terms. These genes were mainly involved in neuron, synaptic signaling and transmission, and vesicle metabolism. These processes are all linked to the pathological features of AD, demonstrating that the GABAergic system, neurons, and synaptic function might be affected in AD. -
Biological Chemistry I: Endings to Glycolysis
Chemistry 5.07SC Biological Chemistry Fall Semester, 2013 I Lecture 15/16 Endings to Glycolysis: how to regenerate NAD+ and reversible conversion of P to alanine. I. There are three endings to glycolysis. We will look at each transformation and the energetic consequences. 1. Homolactate fermentation which occurs in muscle under anaerobic conditions. 2. Ethanol production which occurs in yeast under anaerobic conditions and is central to the beer and wine industry. 3. AcetylCoA production in aerobic metabolism and a segway into the TCA cycle. 4. We will also discuss conversion of pyruvate to alanine using Vitamin B6, pyridoxal phosphate. PLP is central to all amino acid metabolism and reversible conversion of α- ketoacids and amino acids is central to feeding intermediates into/ and removal of intermediates from the TCA cycle. 1. Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate (P) to lactate (L) using NADH as the cofactor: This ending of the glycolysis pathway is utilized when the demand for ATP is high and the O2 supply is low. Anaerobic glycolysis can continue at high rates for 1 to 3 min. Generation of ATP by this mechanism is much faster than the O/P pathway. In muscles, lactic acid is the end product produced and is transported through the blood to the liver, where it can be converted back to pyruvate and used to make glucose. Lactic acid requires a transporter in muscles and is coupled to H+ transport. Contrary to general belief, it is not lactic acid buildup that causes muscle fatigue and soreness; this phenotype occurs on too long a time scale.