NMU Is a Poor Prognostic Biomarker in Patients with Lung Adenocarcinoma
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An Evolutionary Based Strategy for Predicting Rational Mutations in G Protein-Coupled Receptors
Ecology and Evolutionary Biology 2021; 6(3): 53-77 http://www.sciencepublishinggroup.com/j/eeb doi: 10.11648/j.eeb.20210603.11 ISSN: 2575-3789 (Print); ISSN: 2575-3762 (Online) An Evolutionary Based Strategy for Predicting Rational Mutations in G Protein-Coupled Receptors Miguel Angel Fuertes*, Carlos Alonso Department of Microbiology, Centre for Molecular Biology “Severo Ochoa”, Spanish National Research Council and Autonomous University, Madrid, Spain Email address: *Corresponding author To cite this article: Miguel Angel Fuertes, Carlos Alonso. An Evolutionary Based Strategy for Predicting Rational Mutations in G Protein-Coupled Receptors. Ecology and Evolutionary Biology. Vol. 6, No. 3, 2021, pp. 53-77. doi: 10.11648/j.eeb.20210603.11 Received: April 24, 2021; Accepted: May 11, 2021; Published: July 13, 2021 Abstract: Capturing conserved patterns in genes and proteins is important for inferring phenotype prediction and evolutionary analysis. The study is focused on the conserved patterns of the G protein-coupled receptors, an important superfamily of receptors. Olfactory receptors represent more than 2% of our genome and constitute the largest family of G protein-coupled receptors, a key class of drug targets. As no crystallographic structures are available, mechanistic studies rely on the use of molecular dynamic modelling combined with site-directed mutagenesis data. In this paper, we hypothesized that human-mouse orthologs coding for G protein-coupled receptors maintain, at speciation events, shared compositional structures independent, to some extent, of their percent identity as reveals a method based in the categorization of nucleotide triplets by their gross composition. The data support the consistency of the hypothesis, showing in ortholog G protein-coupled receptors the presence of emergent shared compositional structures preserved at speciation events. -
Ligand-Specific Signaling Profiles and Resensitization Mechanisms of the Neuromedin U2 Receptor
1521-0111/94/1/674–688$35.00 https://doi.org/10.1124/mol.117.111070 MOLECULAR PHARMACOLOGY Mol Pharmacol 94:674–688, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Ligand-Specific Signaling Profiles and Resensitization Mechanisms of the Neuromedin U2 Receptor Khaled Alhosaini,1 Omar Bahattab,2 Heider Qassam, R. A. John Challiss, and Gary B. Willars Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom Received November 8, 2017; accepted April 24, 2018 Downloaded from ABSTRACT The structurally related, but distinct neuropeptides, neuromedin resensitization is faster following NmU compared with NmS U (NmU) and neuromedin S (NmS) are ligands of two G protein- exposure, but is similar if endothelin-converting enzyme-1 coupled NmU receptors (NMU1 and NMU2). Hypothalamic activity is inhibited or knocked down. Although acute activation NMU2 regulates feeding behavior and energy expenditure and of extracellular signal-regulated kinase (ERK) is also similar, has therapeutic potential as an anti-obesity target, making an activation by NMU2 is longer lasting if NmS is the ligand. understanding of its signaling and regulation of particular in- Furthermore, when cells are briefly challenged before removal molpharm.aspetjournals.org terest. NMU2 binds both NmU and NmS with high affinity, of free, but not receptor-bound ligand, activation of ERK and p38 resulting in receptor-ligand co-internalization. We have investi- mitogen-activated protein kinase by NmS is more sustained. gated whether receptor trafficking events post-internalization However, only NmU responses are potentiated and extended by are biased by the ligand bound and can therefore influence endothelin-converting enzyme-1 inhibition. -
Adenylyl Cyclase 2 Selectively Regulates IL-6 Expression in Human Bronchial Smooth Muscle Cells Amy Sue Bogard University of Tennessee Health Science Center
University of Tennessee Health Science Center UTHSC Digital Commons Theses and Dissertations (ETD) College of Graduate Health Sciences 12-2013 Adenylyl Cyclase 2 Selectively Regulates IL-6 Expression in Human Bronchial Smooth Muscle Cells Amy Sue Bogard University of Tennessee Health Science Center Follow this and additional works at: https://dc.uthsc.edu/dissertations Part of the Medical Cell Biology Commons, and the Medical Molecular Biology Commons Recommended Citation Bogard, Amy Sue , "Adenylyl Cyclase 2 Selectively Regulates IL-6 Expression in Human Bronchial Smooth Muscle Cells" (2013). Theses and Dissertations (ETD). Paper 330. http://dx.doi.org/10.21007/etd.cghs.2013.0029. This Dissertation is brought to you for free and open access by the College of Graduate Health Sciences at UTHSC Digital Commons. It has been accepted for inclusion in Theses and Dissertations (ETD) by an authorized administrator of UTHSC Digital Commons. For more information, please contact [email protected]. Adenylyl Cyclase 2 Selectively Regulates IL-6 Expression in Human Bronchial Smooth Muscle Cells Document Type Dissertation Degree Name Doctor of Philosophy (PhD) Program Biomedical Sciences Track Molecular Therapeutics and Cell Signaling Research Advisor Rennolds Ostrom, Ph.D. Committee Elizabeth Fitzpatrick, Ph.D. Edwards Park, Ph.D. Steven Tavalin, Ph.D. Christopher Waters, Ph.D. DOI 10.21007/etd.cghs.2013.0029 Comments Six month embargo expired June 2014 This dissertation is available at UTHSC Digital Commons: https://dc.uthsc.edu/dissertations/330 Adenylyl Cyclase 2 Selectively Regulates IL-6 Expression in Human Bronchial Smooth Muscle Cells A Dissertation Presented for The Graduate Studies Council The University of Tennessee Health Science Center In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy From The University of Tennessee By Amy Sue Bogard December 2013 Copyright © 2013 by Amy Sue Bogard. -
Consensus Molecular Subtype Differences Linking Colon Adenocarcinoma and Obesity Revealed by a Cohort Transcriptomic Analysis
medRxiv preprint doi: https://doi.org/10.1101/2021.08.31.21262900; this version posted September 2, 2021. 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. It is made available under a CC-BY-NC-ND 4.0 International license . Title: Consensus molecular subtype differences linking colon adenocarcinoma and obesity revealed by a cohort transcriptomic analysis Short Title: Obesity and colon cancer Michael W. Greene1*, Peter T. Abraham2, Peyton C. Kuhlers1,3, Elizabeth A. Lipke2, Martin J. Heslin4, Stanley T. Wijaya1 and Ifeoluwa Odeniyi1 1Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA 2Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA 3Department of Biostatistics, University of North Carolina at Chapel Hill, NC 27599, USA 4Mitchell Cancer Institute, The University of South Alabama, Mobile, AL 36604, USA *Corresponding author: Michael W. Greene [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2021.08.31.21262900; this version posted September 2, 2021. 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. It is made available under a CC-BY-NC-ND 4.0 International license . Abstract Background Colorectal cancer (CRC) is the third-leading cause of cancer-related deaths in the United States and worldwide. -
Computational Studies of Charge in G Protein Coupled Receptors
Computational Studies of Charge in G Protein Coupled Receptors A thesis submitted to the University of Manchester for the degree of MPhil Bioinformatics in the Faculty of Life Sciences 2013 Spyros Charonis Contents Abstract …………………………………………………………………………….. 4 Declaration …………………………………………………………………………. 5 Copyright …………………………………………………………………………... 6 Acknowledgements ………………………………………………………………… 7 Abbreviations ………………………………………………………………………. 8 1 Introduction ………………………………………………………. ………. 9 1.1 Biology in the Silicon Era ………………………………………… 9 1.2 Structural Biology and Bioinformatics ………………………… 10 1.3 G Protein Coupled Receptors …………………………………... 11 1.3.1 GPCR Classification and Nomenclature ………………. 12 1.3.2 Structural modularity of GPCRs ……………………….. 17 1.3.3 GPCR Functional Mechanisms ………………………… 21 1.3.4 GPCRs as Drug Targets ………………………………… 24 1.4 Electrostatics …………………………………………………….. 25 1.4.1 pH and pKa ………………………………………………. 27 1.4.2 pH dependence of charge state for amino acids ………. 29 1.4.3 Electrostatics in Protein Interactions ………………….. 31 1.4.4 Modeling Electrostatics …………………………………. 33 1.4.4.1 Finite Difference Poisson Boltzmann …………... 34 1.4.4.2 Debye-Hückel Theory …………………………… 35 1.5 Bioinformatics Tools and Methodologies ………………………. 37 1.5.1 Sequence Analysis Methods ……………………………... 38 1.5.1.1 BLAST and PSI-BLAST ………………………... 40 1 1.5.2 Structure Prediction ……………………………………. 41 1.5.2.1 Homology Modeling ……………………………. 42 1.5.3 GPCR Information Repositories ………………………. 45 1.6 Aims and Objectives ………………………………………………... 47 2 Methods …………………………………………………………………. 48 2.1 Sequence Analysis Methodologies ……………………………... 48 2.1.1 Detecting Low-Complexity Regions …………………… 48 2.1.2 PSI-BLAST ……………………………………………... 50 2.2 Structural Analysis Methodologies …………………………… 51 2.3 GPCR Dataset Generation ……………………………………... 52 2.4 PDB File Processing ……………………………………............. 53 2.5 pKa Calculations ………………………………………………... 55 2.6 Molecular Visualization ………………………………………... 57 3 Results …………………………………………………………………… 59 3.1 Empirically Defined GPCR Topology ………………………… 59 3.2 GPCR Sequence Dataset ………………………………………. -
Immune Cells in Spleen and Mucosa + CD127 Neg Production of IL-17 and IL-22 by CD3 TLR5 Signaling Stimulates the Innate
Downloaded from http://www.jimmunol.org/ by guest on September 23, 2021 neg is online at: average * The Journal of Immunology , 23 of which you can access for free at: 2010; 185:1177-1185; Prepublished online 21 Immune Cells in Spleen and Mucosa from submission to initial decision + 4 weeks from acceptance to publication TLR5 Signaling Stimulates the Innate Production of IL-17 and IL-22 by CD3 CD127 Laurye Van Maele, Christophe Carnoy, Delphine Cayet, Pascal Songhet, Laure Dumoutier, Isabel Ferrero, Laure Janot, François Erard, Julie Bertout, Hélène Leger, Florent Sebbane, Arndt Benecke, Jean-Christophe Renauld, Wolf-Dietrich Hardt, Bernhard Ryffel and Jean-Claude Sirard June 2010; doi: 10.4049/jimmunol.1000115 http://www.jimmunol.org/content/185/2/1177 J Immunol cites 51 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://www.jimmunol.org/content/185/2/1177.full#ref-list-1 http://www.jimmunol.org/content/suppl/2010/06/21/jimmunol.100011 5.DC1 This article 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 © 2010 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. -
Thi Mongol Multumitur
THI MONGOLUS009739772B2MULTUMITUR (12 ) United States Patent ( 10 ) Patent No. : US 9 , 739 ,772 B2 Ryu et al. ( 45 ) Date of Patent: Aug. 22, 2017 ( 54 ) METHOD OF ANALYZING BINDING (51 ) Int. CI. ASPECT OF MEMBRANE PROTEIN IN A GOIN 33 /554 ( 2006 . 01 ) LIVING CELL GOIN 33 /557 (2006 .01 ) (71 ) Applicant: POSTECH ACADEMY- INDUSTRY (52 ) U . S . CI. FOUNDATION , Gyeongsangbuk - do CPC . .. GOIN 33/ 557 ( 2013 .01 ) ; GOIN 33/ 554 (2013 .01 ) (KR ) (58 ) Field of Classification Search ( 72 ) Inventors : Sung Ho Ryu , Gyeongsangbuk -do None (KR ) ; Dohyeon Kim , Seoul ( KR ) ; Nam See application file for complete search history. Ki Lee , Gyeongsangbuk -do (KR ) ; Dong Kyun Kim , Gyeongsangbuk - do (KR ) ; Soyeon Park , Seoul (KR ) ; Yonghoon ( 56 ) References Cited Kwon , Seoul (KR ) ; Kai Zhou , Gyeongsangbuk - do (KR ) PUBLICATIONS ( 73 ) Assignee : Postech Academy - Industry Stewart et al. Biochem J 1991 vol. 275 , p . 569 - 573. * Foundation , Gyeongsangbuk -Do (KR ) Daumas et al. Biophysical J . 2003 vol. 84 , p . 356 - 366 . * ( * ) Notice : Subject to any disclaimer , the term of this Jin et al . Biophysical J . 2007 vol. 93 , p . 1079 - 1088 . * patent is extended or adjusted under 35 Saxton Biophysical J . 1997 vol. 72, p . 1744 - 1753. * U . S . C . 154 (b ) by 0 days . * cited by examiner (21 ) Appl . No. : 14 / 891 , 555 Primary Examiner — Jacob Cheu (22 ) PCT Filed : May 16 , 2014 (74 ) Attorney , Agent, or Firm — Lathrop & Gage LLP ( 86 ) PCT No . : PCT /KR2014 / 004426 (57 ) ABSTRACT $ 371 ( C ) ( 1 ) , ( 2 ) Date : Nov. 16 , 2015 The present invention relates to a method for analyzing the pattern of live intercellular membrane protein binding . -
RT² Profiler PCR Array (384-Well Format) Mouse G Protein Coupled Receptors 384HT
RT² Profiler PCR Array (384-Well Format) Mouse G Protein Coupled Receptors 384HT Cat. no. 330231 PAMM-3009ZE For pathway expression analysis Format For use with the following real-time cyclers RT² Profiler PCR Array, Applied Biosystems® models 7900HT (384-well block), Format E ViiA™ 7 (384-well block); Bio-Rad CFX384™ RT² Profiler PCR Array, Roche® LightCycler® 480 (384-well block) Format G Description The Mouse G Protein Coupled Receptors 384HT RT² Profiler™ PCR Array profiles the expression of a comprehensive panel of 370 genes encoding the most important G Protein Coupled Receptors (GPCR). GPCR regulate a number of normal biological processes and play roles in the pathophysiology of many diseases upon dysregulation of their downstream signal transduction activities. As a result, they represent 30 percent of the targets for all current drug development. Developing drug screening assays requires a survey of which GPCR the chosen cell-based model system expresses, to determine not only the expression of the target GPCR, but also related GPCR to assess off-target side effects. Expression of other unrelated GPCR (even orphan receptors whose ligand are unknown) may also correlate with off-target side effects. The ligands that bind and activate the receptors on this array include neurotransmitters and neuropeptides, hormones, chemokines and cytokines, lipid signaling molecules, light-sensitive compounds, and odorants and pheromones. The normal biological processes regulated by GPCR include, but are not limited to, behavioral and mood regulation (serotonin, dopamine, GABA, glutamate, and other neurotransmitter receptors), autonomic (sympathetic and parasympathetic) nervous system transmission (blood pressure, heart rate, and digestive processes via hormone receptors), inflammation and immune system regulation (chemokine receptors, histamine receptors), vision (opsins like rhodopsin), and smell (olfactory receptors for odorants and vomeronasal receptors for pheromones). -
The Repertoire of Family A-Peptide Gpcrs in Archaic Hominins Xavier Mata, Gabriel Renaud, Catherine Mollereau
The repertoire of family A-peptide GPCRs in archaic hominins Xavier Mata, Gabriel Renaud, Catherine Mollereau To cite this version: Xavier Mata, Gabriel Renaud, Catherine Mollereau. The repertoire of family A-peptide GPCRs in archaic hominins. Peptides, Elsevier, 2019, 122, pp.170154. 10.1016/j.peptides.2019.170154. hal- 02322476 HAL Id: hal-02322476 https://hal.archives-ouvertes.fr/hal-02322476 Submitted on 18 Nov 2020 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. The repertoire of family A-peptide GPCRs in archaic hominins Xavier Mata1, Gabriel Renaud2 and Catherine Mollereau1* 1Laboratoire Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France. 2 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. *Correspondence: Corresponding Author [email protected] Abstract Given the importance of G-protein coupled receptors in the regulation of many physiological functions, deciphering the relationships between genotype and phenotype in past and present hominin GPCRs is of main interest to understand the evolutionary process that contributed to the present-day variability in human traits and health. Here, we carefully examined the publicly available genomic and protein sequence databases of the archaic hominins (Neanderthal and Denisova) to draw up the catalog of coding variations in GPCRs for peptide ligands, in comparison with living humans. -
Transcriptional Profiling of Somatostatin Interneurons
www.nature.com/scientificreports OPEN Transcriptional Profling of Somatostatin Interneurons in the Spinal Dorsal Horn Received: 13 December 2017 Alexander Chamessian1,3,4, Michael Young2, Yawar Qadri1, Temugin Berta5, Ru-Rong Ji1,2 & Accepted: 13 April 2018 Thomas Van de Ven1 Published: xx xx xxxx The spinal dorsal horn (SDH) is comprised of distinct neuronal populations that process diferent somatosensory modalities. Somatostatin (SST)-expressing interneurons in the SDH have been implicated specifcally in mediating mechanical pain. Identifying the transcriptomic profle of SST neurons could elucidate the unique genetic features of this population and enable selective analgesic targeting. To that end, we combined the Isolation of Nuclei Tagged in Specifc Cell Types (INTACT) method and Fluorescence Activated Nuclei Sorting (FANS) to capture tagged SST nuclei in the SDH of adult male mice. Using RNA-sequencing (RNA-seq), we uncovered more than 13,000 genes. Diferential gene expression analysis revealed more than 900 genes with at least 2-fold enrichment. In addition to many known dorsal horn genes, we identifed and validated several novel transcripts from pharmacologically tractable functional classes: Carbonic Anhydrase 12 (Car12), Phosphodiesterase 11 A (Pde11a), and Protease-Activated Receptor 3 (F2rl2). In situ hybridization of these novel genes showed diferential expression patterns in the SDH, demonstrating the presence of transcriptionally distinct subpopulations within the SST population. Overall, our fndings provide new insights into the gene repertoire of SST dorsal horn neurons and reveal several novel targets for pharmacological modulation of this pain-mediating population and treatment of pathological pain. Mechanical pain is one of the chief symptoms in many pathological pain conditions1. -
The Emerging Mutational Landscape of G Proteins and G-Protein-Coupled
ANALYSIS The emerging mutational landscape of G proteins and G‑protein‑coupled receptors in cancer Morgan O’Hayre1, José Vázquez-Prado2, Irina Kufareva3, Eric W. Stawiski4,5, Tracy M. Handel3, Somasekar Seshagiri4 and J. Silvio Gutkind1 Abstract | Aberrant expression and activity of G proteins and G-protein-coupled receptors (GPCRs) are frequently associated with tumorigenesis. Deep sequencing studies show that 4.2% of tumours carry activating mutations in GNAS (encoding Gαs), and that oncogenic activating mutations in genes encoding Gαq family members (GNAQ or GNA11) are present in ~66% and ~6% of melanomas arising in the eye and skin, respectively. Furthermore, nearly 20% of human tumours harbour mutations in GPCRs. Many human cancer-associated viruses also express constitutively active viral GPCRs. These studies indicate that G proteins, GPCRs and their linked signalling circuitry represent novel therapeutic targets for cancer prevention and treatment. The G-protein-coupled receptor (GPCR) family of proteins G protein and GPCR signalling comprises approximately 4% of the encoded human genes: The widely accepted model for GPCR activation involves 1Oral and Pharyngeal Cancer Branch, Dental and with over 800 members, it is the largest family of cell- the binding of an agonist ligand at the extracellular side Craniofacial Research, surface receptors involved in signal transduction. These of the receptor, which induces a conformational change in National Institutes of Health, proteins are characterized by a seven-transmembrane the receptor and alters the position of its transmembrane Bethesda, Maryland 20892, domain structure with an extracellular amino terminus helices and intracellular loops. In this active conforma- USA. and an intracellular carboxyl terminus. -
Supporting Online Material For
www.sciencemag.org/cgi/content/full/1163673/DC1 Supporting Online Material for Innate Immunity in Caenorhabditis elegans Is Regulated by Neurons Expressing NPR-1/GPCR Katie L. Styer, Varsha Singh, Evan Macosko, Sarah E. Steele, Cornelia I. Bargmann, Alejandro Aballay* *To whom correspondence should be addressed. E-mail: [email protected] Published 18 September 2008 on Science Express DOI: 10.1126/science.1163673 This PDF file includes: Materials and Methods Figs. S1 to S6 Tables S1 to S4 References Supporting Online Material Materials and Methods Bacterial Strains The following bacterial strains were used: Escherichia coli OP50 (1), Salmonella enterica serovar typhimurium SL1344 (2), Enterococcus faecalis OG1RF (3), and Pseudomonas aeruginosa PA14 (4). E. coli, P. aeruginosa, and S. enterica cultures were grown in Luria–Bertani (LB) broth at 37°C. E. faecalis liquid cultures were grown in brain–heart infusion broth at 37°C. Nematode Strains The following C. elegans strains were cultured under standard conditions and fed E. coli OP50 (1). Wild-type animals were C. elegans Bristol strain N2. Other strains used in this work include: DA609 npr-1 (ad609) X, RB1321 C56G3.1 (ok1439) X, RB1349 F57H12.4 (ok1504) IV, VC224 tag-24 (ok371) X, CX4148 npr-1(ky13) X, DA508 npr- 1(n1353) X, DA650 npr-1(g320) X, IM222 npr-1(ur89) X, RC301 npr-1(g320)X, CX6448 gcy-35 (ok769) I, CX7157 gcy-35 (ok769) I; npr-1 (ad609) X, PR691, tax- 2(p691) I, AX826, tax-2(p691) I; npr-1(ad609) X, PR678, tax-4(p678) III, CX4819, tax- 4(p678) III; npr-1(ad609) X, CX7102 lin-15 (n765) qaIs2241 [gcy-36::egl-1, gcy- 35::gfp, lin-15(+)] X, CX9742 npr-1(ad609);kyEx2145 [pnpr-1::npr-1], AX351, npr- 1(ad609) lin-15(n765ts) X; dbEx3 [lin-15(+) gcy-32::npr-1::gfp].