A Focus on Microglia and P2X4R
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Functions of the Mineralocorticoid Receptor in the Hippocampus By
Functions of the Mineralocorticoid Receptor in the Hippocampus by Aaron M. Rozeboom A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cellular and Molecular Biology) in The University of Michigan 2008 Doctoral Committee: Professor Audrey F. Seasholtz, Chair Professor Elizabeth A. Young Professor Ronald Jay Koenig Associate Professor Gary D. Hammer Assistant Professor Jorge A. Iniguez-Lluhi Acknowledgements There are more people than I can possibly name here that I need to thank who have helped me throughout the process of writing this thesis. The first and foremost person on this list is my mentor, Audrey Seasholtz. Between working in her laboratory as a research assistant and continuing my training as a graduate student, I spent 9 years in Audrey’s laboratory and it would be no exaggeration to say that almost everything I have learned regarding scientific research has come from her. Audrey’s boundless enthusiasm, great patience, and eager desire to teach students has made my time in her laboratory a richly rewarding experience. I cannot speak of Audrey’s laboratory without also including all the past and present members, many of whom were/are not just lab-mates but also good friends. I also need to thank all the members of my committee, an amazing group of people whose scientific prowess combined with their open-mindedness allowed me to explore a wide variety of interests while maintaining intense scientific rigor. Outside of Audrey’s laboratory, there have been many people in Ann Arbor without whom I would most assuredly have gone crazy. -
Single-Cell Rnaseq Reveals Seven Classes of Colonic Sensory Neuron
Gut Online First, published on February 26, 2018 as 10.1136/gutjnl-2017-315631 Neurogastroenterology ORIGINAL ARTICLE Gut: first published as 10.1136/gutjnl-2017-315631 on 26 February 2018. Downloaded from Single-cell RNAseq reveals seven classes of colonic sensory neuron James R F Hockley,1,2 Toni S Taylor,1 Gerard Callejo,1 Anna L Wilbrey,2 Alex Gutteridge,2 Karsten Bach,1 Wendy J Winchester,2 David C Bulmer,1 Gordon McMurray,2 Ewan St John Smith1 ► Additional material is ABSTRact pathways to the central nervous system (CNS).1 In published online only. To view Objective Integration of nutritional, microbial and the colorectum, sensory innervation is organised please visit the journal online (http:// dx. doi. org/ 10. 1136/ inflammatory events along the gut-brain axis can alter into two main pathways: thoracolumbar (TL) spinal gutjnl- 2017- 315631). bowel physiology and organism behaviour. Colonic afferents projecting via the lumbar splanchnic sensory neurons activate reflex pathways and give nerve (LSN) and lumbosacral (LS) spinal afferents 1Department of Pharmacology, University of Cambridge, rise to conscious sensation, but the diversity and projecting via the pelvic nerve (PN) that are respon- Cambridge, UK division of function within these neurons is poorly sible for transducing conscious sensations of full- 2Neuroscience and Pain understood. The identification of signalling pathways ness, discomfort, urgency and pain, in addition to Research Unit, Pfizer, contributing to visceral sensation is constrained by a reflex actions.2 Cambridge, UK paucity of molecular markers. Here we address this by Visceral sensory afferents act to maintain many comprehensive transcriptomic profiling and unsupervised aspects of GI physiology, such as continence and Correspondence to James R F Hockley, Department clustering of individual mouse colonic sensory neurons. -
Funktionelle in Vitro Und in Vivo Charakterisierung Des Putativen Tumorsuppressorgens SFRP1 Im Humanen Mammakarzinom
Funktionelle in vitro und in vivo Charakterisierung des putativen Tumorsuppressorgens SFRP1 im humanen Mammakarzinom Von der Fakult¨at fur¨ Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades einer Doktorin der Naturwissenschaften genehmigte Dissertation vorgelegt von Diplom-Biologin Laura Huth (geb. Franken) aus Julich¨ Berichter: Universit¨atsprofessor Dr. rer. nat. Edgar Dahl Universit¨atsprofessor Dr. rer. nat. Ralph Panstruga Tag der mundlichen¨ Prufung:¨ 6. August 2014 Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verfugbar.¨ Zusammenfassung Krebserkrankungen stellen weltweit eine der h¨aufigsten Todesursachen dar. Aus diesem Grund ist die Aufkl¨arung der zugrunde liegenden Mechanismen und Ur- sachen ein essentielles Ziel der molekularen Onkologie. Die Tumorforschung der letzten Jahre hat gezeigt, dass die Entstehung solider Karzinome ein Mehrstufen- Prozess ist, bei dem neben Onkogenen auch Tumorsuppresorgene eine entschei- dende Rolle spielen. Viele der heute bekannten Gene des WNT-Signalweges wur- den bereits als Onkogene oder Tumorsuppressorgene charakterisiert. Eine Dere- gulation des WNT-Signalweges wird daher mit der Entstehung und Progression vieler humaner Tumorentit¨aten wie beispielsweise auch dem Mammakarzinom, der weltweit h¨aufigsten Krebserkrankung der Frau, assoziiert. SFRP1, ein nega- tiver Regulator der WNT-Signalkaskade, wird in Brusttumoren haupts¨achlich durch den epigenetischen Mechanismus der Promotorhypermethylierung -
Molecular Dissection of G-Protein Coupled Receptor Signaling and Oligomerization
MOLECULAR DISSECTION OF G-PROTEIN COUPLED RECEPTOR SIGNALING AND OLIGOMERIZATION BY MICHAEL RIZZO A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVERSITY GRADUATE SCHOOL OF ARTS AND SCIENCES in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Biology December, 2019 Winston-Salem, North Carolina Approved By: Erik C. Johnson, Ph.D. Advisor Wayne E. Pratt, Ph.D. Chair Pat C. Lord, Ph.D. Gloria K. Muday, Ph.D. Ke Zhang, Ph.D. ACKNOWLEDGEMENTS I would first like to thank my advisor, Dr. Erik Johnson, for his support, expertise, and leadership during my time in his lab. Without him, the work herein would not be possible. I would also like to thank the members of my committee, Dr. Gloria Muday, Dr. Ke Zhang, Dr. Wayne Pratt, and Dr. Pat Lord, for their guidance and advice that helped improve the quality of the research presented here. I would also like to thank members of the Johnson lab, both past and present, for being valuable colleagues and friends. I would especially like to thank Dr. Jason Braco, Dr. Jon Fisher, Dr. Jake Saunders, and Becky Perry, all of whom spent a great deal of time offering me advice, proofreading grants and manuscripts, and overall supporting me through the ups and downs of the research process. Finally, I would like to thank my family, both for instilling in me a passion for knowledge and education, and for their continued support. In particular, I would like to thank my wife Emerald – I am forever indebted to you for your support throughout this process, and I will never forget the sacrifices you made to help me get to where I am today. -
Identification of Human N-Myristoylated Proteins from Human Complementary DNA Resources by Cell-Free and Cellular Metabolic Labeling Analyses
RESEARCH ARTICLE Identification of Human N-Myristoylated Proteins from Human Complementary DNA Resources by Cell-Free and Cellular Metabolic Labeling Analyses Emi Takamitsu1, Motoaki Otsuka1, Tatsuki Haebara1, Manami Yano1, Kanako Matsuzaki1, Hirotsugu Kobuchi3, Koko Moriya1, Toshihiko Utsumi1,2* 1 Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Yamaguchi, 753– 8515, Japan, 2 Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753–8515, Japan, 3 Department of Cell Chemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700–8558, Japan * [email protected] OPEN ACCESS Abstract Citation: Takamitsu E, Otsuka M, Haebara T, Yano To identify physiologically important human N-myristoylated proteins, 90 cDNA clones pre- M, Matsuzaki K, Kobuchi H, et al. (2015) Identification dicted to encode human N-myristoylated proteins were selected from a human cDNA of Human N-Myristoylated Proteins from Human resource (4,369 Kazusa ORFeome project human cDNA clones) by two bioinformatic Complementary DNA Resources by Cell-Free and N Cellular Metabolic Labeling Analyses. PLoS ONE 10 -myristoylation prediction systems, NMT-The MYR Predictor and Myristoylator. After data- (8): e0136360. doi:10.1371/journal.pone.0136360 base searches to exclude known human N-myristoylated proteins, 37 cDNA clones were N Editor: Jamil Saad, University of Alabama at selected as potential human -myristoylated proteins. The susceptibility of these cDNA Birmingham, UNITED STATES clones to protein N-myristoylation was first evaluated using fusion proteins in which the N- Received: May 12, 2015 terminal ten amino acid residues were fused to an epitope-tagged model protein. Then, pro- tein N-myristoylation of the gene products of full-length cDNAs was evaluated by metabolic Accepted: July 31, 2015 labeling experiments both in an insect cell-free protein synthesis system and in transfected Published: August 26, 2015 human cells. -
Activation of Hypermethylated P2RY1 Mitigates Gastric Cancer by Promoting Apoptosis and Inhibiting Proliferation
Activation of hypermethylated P2RY1 mitigates gastric cancer by promoting apoptosis and inhibiting proliferation Yinggang Hua Xiamen University Medical College Long Li Xiamen University Medical College Liangliang Cai Zhongshan Hospital Xiamen University Guoyan Liu ( [email protected] ) Zhongshan Hospital Xiamen University Research Article Keywords: Diffuse type gastric cancer, DNA methylation 450K array, P2RY1 receptor, ERK signal pathway, Tumor suppressor gene Posted Date: July 26th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-351723/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/16 Abstract P2RY1 receptor is known to cause cancer by activating the ERK signal pathway, its DNA methylation status or even the corresponding regulatory mechanism remains unknown. In this study, DNA methylation chip was used to prole the genome-wide DNA methylation level in gastric cancer tissues. Proliferation and apoptosis of the SGC7901 gastric cancer cell line were determined after treatment with a selective P2RY1 receptor agonist, MRS2365. The promoter region of P2RY1 was found to be highly methylated with 4 hypermethylated sites (|Δβ value| >0.2) in diffuse gastric cancer and then were validated by bioinformatic analysis in TCGA database. Analysis of MRS2365-treated cells by annexin-V/PI staining and Caspase-3 activity assays indicated the induction of apoptosis in SGC7901 cells. P2RY1 receptor activation in human SGC7901 gastric cancer cells via the MRS2365 agonist induced apoptosis and reduced cell growth. High DNA methylation in the promoter region of P2RY1 may have contributed to the reduced expression of P2RY1’s mRNA, which is likely responsible for the “aggressive” nature of the diffuse type gastric cancer. -
Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 -
Identification of C3 As a Therapeutic Target for Diabetic Nephropathy By
www.nature.com/scientificreports OPEN Identifcation of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis ShuMei Tang, XiuFen Wang, TianCi Deng, HuiPeng Ge & XiangCheng Xiao* The pathogenesis of diabetic nephropathy is not completely understood, and the efects of existing treatments are not satisfactory. Various public platforms already contain extensive data for deeper bioinformatics analysis. From the GSE30529 dataset based on diabetic nephropathy tubular samples, we identifed 345 genes through diferential expression analysis and weighted gene coexpression correlation network analysis. GO annotations mainly included neutrophil activation, regulation of immune efector process, positive regulation of cytokine production and neutrophil-mediated immunity. KEGG pathways mostly included phagosome, complement and coagulation cascades, cell adhesion molecules and the AGE-RAGE signalling pathway in diabetic complications. Additional datasets were analysed to understand the mechanisms of diferential gene expression from an epigenetic perspective. Diferentially expressed miRNAs were obtained to construct a miRNA-mRNA network from the miRNA profles in the GSE57674 dataset. The miR-1237-3p/SH2B3, miR-1238-5p/ ZNF652 and miR-766-3p/TGFBI axes may be involved in diabetic nephropathy. The methylation levels of the 345 genes were also tested based on the gene methylation profles of the GSE121820 dataset. The top 20 hub genes in the PPI network were discerned using the CytoHubba tool. Correlation analysis with GFR showed that SYK, CXCL1, LYN, VWF, ANXA1, C3, HLA-E, RHOA, SERPING1, EGF and KNG1 may be involved in diabetic nephropathy. Eight small molecule compounds were identifed as potential therapeutic drugs using Connectivity Map. It is estimated that a total of 451 million people sufered from diabetes by 2017, and the number is speculated to be 693 million by 2045 1. -
WO 2015/130968 A2 3 September 2015 (03.09.2015) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/130968 A2 3 September 2015 (03.09.2015) P O P C T (51) International Patent Classification: Inc., 75 Francis Street, Boston, MA 021 15 (US). YOSEF, C12Q 1/68 (2006.01) Nir; 1520 Laurel Ave., Richmond, CA 94805 (US). (21) International Application Number: (74) Agents: KOWALSKI, Thomas J. et al; Vedder Price PCT/US20 15/0 17826 P.C., 1633 Broadway, New York, NY 1001 9 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 26 February 2015 (26.02.2015) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, 61/945,641 27 February 2014 (27.02.2014) US MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (71) Applicants: THE BROAD INSTITUTE INC. [US/US]; PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 415 Main Street, Cambridge, MA 02142 (US). THE SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, BRIGHAM AND WOMEN'S HOSPITAL, INC. -
Supplemental Information
Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig. -
13809 P2X7 Receptor (E1E8T) Rabbit Mab
Revision 1 C 0 2 - t P2X7 Receptor (E1E8T) Rabbit mAb a e r o t S Orders: 877-616-CELL (2355) [email protected] 9 Support: 877-678-TECH (8324) 0 8 Web: [email protected] 3 www.cellsignal.com 1 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source/Isotype: UniProt ID: Entrez-Gene Id: WB, IP H Endogenous 78 Rabbit IgG Q99572 5027 Product Usage Information 2. Valera, S. et al. (1994) Nature 371, 516-9. 3. North, R.A. and Surprenant, A. (2000) Annu Rev Pharmacol Toxicol 40, 563-80. Application Dilution 4. Skaper, S.D. et al. (2010) FASEB J 24, 337-45. 5. Bernardino, L. et al. (2008) J Neurochem 106, 271-80. Western Blotting 1:1000 6. Volonté, C. et al. (2003) Curr Drug Targets CNS Neurol Disord 2, 403-12. Immunoprecipitation 1:50 7. Chessell, I.P. et al. (2005) Pain 114, 386-96. 8. Dell'Antonio, G. et al. (2002) Neurosci Lett 327, 87-90. 9. Barden, N. et al. (2006) Am J Med Genet B Neuropsychiatr Genet 141B, 374-82. Storage 10. Lucae, S. et al. (2006) Hum Mol Genet 15, 2438-45. Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA, 50% glycerol and less than 0.02% sodium azide. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity P2X7 Receptor (E1E8T) Rabbit mAb recognizes endogenous levels of total P2X7 receptor protein. Species Reactivity: Human Source / Purification Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues surrounding Leu462 of human P2X7 receptor protein. -
Supplementary Table 1. Pain and PTSS Associated Genes (N = 604
Supplementary Table 1. Pain and PTSS associated genes (n = 604) compiled from three established pain gene databases (PainNetworks,[61] Algynomics,[52] and PainGenes[42]) and one PTSS gene database (PTSDgene[88]). These genes were used in in silico analyses aimed at identifying miRNA that are predicted to preferentially target this list genes vs. a random set of genes (of the same length). ABCC4 ACE2 ACHE ACPP ACSL1 ADAM11 ADAMTS5 ADCY5 ADCYAP1 ADCYAP1R1 ADM ADORA2A ADORA2B ADRA1A ADRA1B ADRA1D ADRA2A ADRA2C ADRB1 ADRB2 ADRB3 ADRBK1 ADRBK2 AGTR2 ALOX12 ANO1 ANO3 APOE APP AQP1 AQP4 ARL5B ARRB1 ARRB2 ASIC1 ASIC2 ATF1 ATF3 ATF6B ATP1A1 ATP1B3 ATP2B1 ATP6V1A ATP6V1B2 ATP6V1G2 AVPR1A AVPR2 BACE1 BAMBI BDKRB2 BDNF BHLHE22 BTG2 CA8 CACNA1A CACNA1B CACNA1C CACNA1E CACNA1G CACNA1H CACNA2D1 CACNA2D2 CACNA2D3 CACNB3 CACNG2 CALB1 CALCRL CALM2 CAMK2A CAMK2B CAMK4 CAT CCK CCKAR CCKBR CCL2 CCL3 CCL4 CCR1 CCR7 CD274 CD38 CD4 CD40 CDH11 CDK5 CDK5R1 CDKN1A CHRM1 CHRM2 CHRM3 CHRM5 CHRNA5 CHRNA7 CHRNB2 CHRNB4 CHUK CLCN6 CLOCK CNGA3 CNR1 COL11A2 COL9A1 COMT COQ10A CPN1 CPS1 CREB1 CRH CRHBP CRHR1 CRHR2 CRIP2 CRYAA CSF2 CSF2RB CSK CSMD1 CSNK1A1 CSNK1E CTSB CTSS CX3CL1 CXCL5 CXCR3 CXCR4 CYBB CYP19A1 CYP2D6 CYP3A4 DAB1 DAO DBH DBI DICER1 DISC1 DLG2 DLG4 DPCR1 DPP4 DRD1 DRD2 DRD3 DRD4 DRGX DTNBP1 DUSP6 ECE2 EDN1 EDNRA EDNRB EFNB1 EFNB2 EGF EGFR EGR1 EGR3 ENPP2 EPB41L2 EPHB1 EPHB2 EPHB3 EPHB4 EPHB6 EPHX2 ERBB2 ERBB4 EREG ESR1 ESR2 ETV1 EZR F2R F2RL1 F2RL2 FAAH FAM19A4 FGF2 FKBP5 FLOT1 FMR1 FOS FOSB FOSL2 FOXN1 FRMPD4 FSTL1 FYN GABARAPL1 GABBR1 GABBR2 GABRA2 GABRA4