DOCSLIB.ORG

A System Level Approach to Identify Novel Cell Size Regulators [Phd

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A System Level Approach to Identify Novel Cell Size Regulators [Phd This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ A system level approach to identify novel cell size regulators Dul, Zoltan Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 03. Oct. 2021 A system level approach to identify novel cell size regulators ZOLTAN DUL A THESIS PRESENTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY 2019 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul Declaration I declare that this thesis has been composed solely by myself and that it has not been submitted, in whole or in part, in any previous application for a degree. Except where stated otherwise by reference or acknowledgement, the work presented is entirely my own. Zoltán Dul January 2019 2 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul Acknowledgements Thank you to my primary supervisor Dr Attila Csikász-Nagy for giving me the opportunity to work in his computational biology group in London and for guiding me so well throughout my PhD studies. His sound ideas and plans immeasurably helped my way to complete my PhD. I’m also exceptionally grateful to my second supervisor Professor Shaun Thomas for helping and introducing myself to wet lab experiments with T-Cells. His academic experience and inspirational ideas have been invaluable to me. I also would like to thank you, my Italian supervisor, Dr Azeddine Si-Ammour for guiding my path in Arabidopsis research and giving me research ideas. I’m very grateful to him introducing me to a new research area in science. I would like to acknowledge the help of the Leukaemia Cell Cycle Lab members in the Rayne Institute, King’s College London especially to Dr Stephen Orr who introduced me the various techniques of T-Cell experimentation and guided my path until I mastered the technique. Also, I’m thankful to Dr Nermina Lamadema and Dr Sun Sook Chung without whom this work would not have been possible to complete. Moreover, I’m indebted to Dr Loretta Brown and others at King’s College Hospital for helping me in some areas of research. I would like you to thank the current and former members and Csikasz-Nagy group: Dr Federico Vaggi, Rosa Hernansaiz and Kirsten Jenkins for their help in the Bioinformatic field. Moreover, I’m very grateful to Dr Asquini Elisa, Dr Mirko Moser and Dr Valentina Cappelletti and all other people from Fondazione Edmund Mach, San Michele all’ Adige, Italy for guiding me in the endless field of Arabidopsis research. Finally, I would like to thank the Research and Innovation Centre in Fondazione Edmund Mach, San Michele all’ Adige, Italy for funding my PhD studies. Last but not least to my family and friends, thank you for all the support and encouragement. 3 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul Abstract It is known that evolutionarily conserved pathways regulate several essential biological processes, such as the cell cycle, DNA replication and protein synthesis. I hypothesise that there exists a conserved regulatory mechanism which controls cell size as well. To test this proposition, I carried out two types of experiment: Bioinformatics. Development of a bioinformatics tool to predict cell size regulators, based on information of evolutionarily-conserved proteins which have been described as cell size regulators in genome-wide studies. I collected existing large-scale data from the literature from five evolutionarily distant organisms (A. thaliana, D. melanogaster, H. sapiens, S. cerevisiae and S. pombe), then looked for conserved orthologous proteins with conserved cell size regulatory functions. I used the eggNOG orthology database as the primary source for orthology information, in addition to one manually curated list by PomBase curators. I added biological pathway information from KEGG and functional data from Gene Ontology. This approach allowed me to identify a core conserved cell size regulatory network and based on data on three of these species I created a list of predicted novel cell size regulators for the remaining two organisms. I focussed on those orthologous groups of proteins, which have only one ortholog in all five organisms and further reduced the list by concentrating on those which lack pathway annotations. 20 conserved orthologous groups matched these criteria. Some of these were tested in wet- lab experiments. Additionally, I have extended this tool with the capability to find the conserved core of any biological function, listed in the Gene Ontology SLIM database and extended the list of the investigated model species to seven (A. thaliana, C. elegans, D. melanogaster, D. rerio, H. sapiens, S. cerevisiae and S. pombe). This bioinformatics tool is also able to predict novel functional annotations to Gene Ontology, based on orthologous group involvement in eggNOG. Wet-lab experiments. Analysis of some of the predicted cell size regulators by carrying out experiments on Arabidopsis thaliana and human T-Cells. 4 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul T-Cells. I isolated human peripheral blood T-Cells that are in a quiescent state, which increase in size and enter the cell cycle when stimulated via CD3/CD28. The quiescent T-Cells were transfected with siRNA to reduce the induction of each of the predicted proteins, which normally occurs as the cells respond to CD3/CD28. I analysed the size distribution by Flow Cytometry, measuring FSC-A values. My data show that reducing the induction of TCTP, a protein that plays a role in microtubule stabilisation, apoptosis and calcium binding, affects T-Cell size. I also show that reducing the expression of the MCM7 protein, a member of the mini-chromosome maintenance protein complex, reduced the size of T-Cells in G1 and increased their size in the S-phase of the cell cycle. Arabidopsis thaliana. I confirmed previously published data that knockout mutants of pfd6, a member of the prefoldin complex, produce small plants. I show that knock-out pfd3 mutants have a significantly smaller cell size compared with the control. The knock-out pfd3 mutants also have significantly different seed and silique sizes. Furthermore, I found that the knockout of mos14, encoding a nuclear import receptor, results in significantly smaller leaves. In summary, I have created a flexible bioinformatics tool that can predict novel cell size regulators, some of which are verified by experiments on human cells and Arabidopsis. 5 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul Table of Contents 2 3 4 6 13 16 17 20 21 22 22 22 24 25 26 28 28 30 31 31 33 35 36 37 38 39 6 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul 41 42 43 44 45 46 46 47 47 48 48 49 51 51 52 53 53 54 55 55 55 55 55 56 57 57 58 58 59 60 60 60 61 61 61 62 62 64 7 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul 64 64 64 65 65 66 66 67 67 69 73 74 74 75 75 76 77 78 78 79 81 81 83 86 88 88 91 91 91 93 94 94 95 96 96 97 98 98 99 99 100 101 103 105 8 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul 105 106 108 112 112 113 114 114 114 115 115 117 118 119 119 119 120 120 120 121 121 121 123 123 124 124 125 125 126 126 126 126 127 128 129 130 130 132 132 135 136 137 138 139 139 139 140 141 9 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul 142 143 144 146 147 147 148 148 149 149 150 153 156 158 158 159 159 162 164 164 167 167 170 170 172 172 173 178 182 186 186 187 188 188 189 190 190 192 10 A system level approach to identify novel cell size regulators A Thesis presented for the degree of Doctor of Philosophy by Zoltán Dul 193 194 194 194 196 196 197 200 200 200 200 201 201 201 202 202 202 203 204 204 204 208 209 209 210 211 212 213 213 214 215 216 217 217 220 220 223 #1 225
Load more

Recommended publications
  • Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice
    Loyola University Chicago Loyola eCommons Biology: Faculty Publications and Other Works Faculty Publications 2013 Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice Mihaela Palicev Gunter P. Wagner James P. Noonan Benedikt Hallgrimsson James M. Cheverud Loyola University Chicago, [email protected] Follow this and additional works at: https://ecommons.luc.edu/biology_facpubs Part of the Biology Commons Recommended Citation Palicev, M, GP Wagner, JP Noonan, B Hallgrimsson, and JM Cheverud. "Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice." Genome Biology and Evolution 5(10), 2013. This Article is brought to you for free and open access by the Faculty Publications at Loyola eCommons. It has been accepted for inclusion in Biology: Faculty Publications and Other Works by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. © Palicev et al., 2013. GBE Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice Mihaela Pavlicev1,2,*, Gu¨ nter P. Wagner3, James P. Noonan4, Benedikt Hallgrı´msson5,and James M. Cheverud6 1Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria 2Department of Pediatrics, Cincinnati Children‘s Hospital Medical Center, Cincinnati, Ohio 3Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University 4Department of Genetics, Yale University School of Medicine 5Department of Cell Biology and Anatomy, The McCaig Institute for Bone and Joint Health and the Alberta Children’s Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Canada 6Department of Anatomy and Neurobiology, Washington University *Corresponding author: E-mail: [email protected].
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,603,824 B2 Ramseier Et Al
    USOO8603824B2 (12) United States Patent (10) Patent No.: US 8,603,824 B2 Ramseier et al. (45) Date of Patent: Dec. 10, 2013 (54) PROCESS FOR IMPROVED PROTEIN 5,399,684 A 3, 1995 Davie et al. EXPRESSION BY STRAIN ENGINEERING 5,418, 155 A 5/1995 Cormier et al. 5,441,934 A 8/1995 Krapcho et al. (75) Inventors: Thomas M. Ramseier, Poway, CA 5,508,192 A * 4/1996 Georgiou et al. .......... 435/252.3 (US); Hongfan Jin, San Diego, CA 5,527,883 A 6/1996 Thompson et al. (US); Charles H. Squires, Poway, CA 5,558,862 A 9, 1996 Corbinet al. 5,559,015 A 9/1996 Capage et al. (US) 5,571,694 A 11/1996 Makoff et al. (73) Assignee: Pfenex, Inc., San Diego, CA (US) 5,595,898 A 1/1997 Robinson et al. 5,610,044 A 3, 1997 Lam et al. (*) Notice: Subject to any disclaimer, the term of this 5,621,074 A 4/1997 Bjorn et al. patent is extended or adjusted under 35 5,622,846 A 4/1997 Kiener et al. 5,641,671 A 6/1997 Bos et al. U.S.C. 154(b) by 471 days. 5,641,870 A 6/1997 Rinderknecht et al. 5,643,774 A 7/1997 Ligon et al. (21) Appl. No.: 11/189,375 5,662,898 A 9/1997 Ligon et al. (22) Filed: Jul. 26, 2005 5,677,127 A 10/1997 Hogan et al. 5,683,888 A 1 1/1997 Campbell (65) Prior Publication Data 5,686,282 A 11/1997 Lam et al.
    [Show full text]
  • Original Communication Genomic and Expression Array Profiling of Chromosome 20Q Amplicon in Human Colon Cancer Cells
    128 Original Communication Genomic and expression array profiling of chromosome 20q amplicon in human colon cancer cells Jennifer l Carter, Li Jin,1 Subrata Sen University of Texas - M. D. Anderson Cancer Center, 1PD, University of Cincinnati sion and metastasis.[1,2] Characterization of genomic BACKGROUND: Gain of the q arm of chromosome 20 in human colorectal cancer has been associated with poorer rearrangements is, therefore, a major area of investiga- survival time and has been reported to increase in frequency tion being pursued by the cancer research community. from adenomas to metastasis. The increasing frequency of chromosome 20q amplification during colorectal cancer Amplification of genomic DNA is one such form of rear- progression and the presence of this amplification in carci- rangement that leads to an increase in the copy num- nomas of other tissue origin has lead us to hypothesize ber of specific genes frequently detected in a variety of that 20q11-13 harbors one or more genes which, when over expressed promote tumor invasion and metastasis. human cancer cell types. Our laboratory has been in- AIMS: Generate genomic and expression profiles of the terested in characterizing amplified genomic regions in 20q amplicon in human cancer cell lines in order to identify genes with increased copy number and expression. cancer cells based on the hypothesis that these seg- MATERIALS AND METHODS: Utilizing genomic sequenc- ments harbor critical genes associated with initiation and/ ing clones and amplification mapping data from our lab or progression of cancer. Gain of chromosome 20q in and other previous studies, BAC/ PAC tiling paths span- ning the 20q amplicon and genomic microarrays were gen- human colorectal cancer has been associated with erated.
    [Show full text]
  • 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
    [Show full text]
  • Placenta-Derived Exosomes Continuously Increase in Maternal
    Sarker et al. Journal of Translational Medicine 2014, 12:204 http://www.translational-medicine.com/content/12/1/204 RESEARCH Open Access Placenta-derived exosomes continuously increase in maternal circulation over the first trimester of pregnancy Suchismita Sarker1, Katherin Scholz-Romero1, Alejandra Perez2, Sebastian E Illanes1,2,3, Murray D Mitchell1, Gregory E Rice1,2 and Carlos Salomon1,2* Abstract Background: Human placenta releases specific nanovesicles (i.e. exosomes) into the maternal circulation during pregnancy, however, the presence of placenta-derived exosomes in maternal blood during early pregnancy remains to be established. The aim of this study was to characterise gestational age related changes in the concentration of placenta-derived exosomes during the first trimester of pregnancy (i.e. from 6 to 12 weeks) in plasma from women with normal pregnancies. Methods: A time-series experimental design was used to establish pregnancy-associated changes in maternal plasma exosome concentrations during the first trimester. A series of plasma were collected from normal healthy women (10 patients) at 6, 7, 8, 9, 10, 11 and 12 weeks of gestation (n = 70). We measured the stability of these vesicles by quantifying and observing their protein and miRNA contents after the freeze/thawing processes. Exosomes were isolated by differential and buoyant density centrifugation using a sucrose continuous gradient and characterised by their size distribution and morphology using the nanoparticles tracking analysis (NTA; Nanosight™) and electron microscopy (EM), respectively. The total number of exosomes and placenta-derived exosomes were determined by quantifying the immunoreactive exosomal marker, CD63 and a placenta-specific marker (Placental Alkaline Phosphatase PLAP).
    [Show full text]
  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
    [Show full text]
  • Confirmation of Pathogenic Mechanisms by SARS-Cov-2–Host
    Messina et al. Cell Death and Disease (2021) 12:788 https://doi.org/10.1038/s41419-021-03881-8 Cell Death & Disease ARTICLE Open Access Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2–host interactome Francesco Messina 1, Emanuela Giombini1, Chiara Montaldo1, Ashish Arunkumar Sharma2, Antonio Zoccoli3, Rafick-Pierre Sekaly2, Franco Locatelli4, Alimuddin Zumla5, Markus Maeurer6,7, Maria R. Capobianchi1, Francesco Nicola Lauria1 and Giuseppe Ippolito 1 Abstract In the last months, many studies have clearly described several mechanisms of SARS-CoV-2 infection at cell and tissue level, but the mechanisms of interaction between host and SARS-CoV-2, determining the grade of COVID-19 severity, are still unknown. We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. A host-virus interactome was inferred, applying an explorative algorithm (Random Walk with Restart, RWR) triggered by 28 proteins of SARS-CoV-2. The analysis of PPI allowed to estimate the distribution of SARS-CoV-2 proteins in the host cell. Interactome built around one single viral protein allowed to define a different response, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. Finally, the network-based approach highlighted a possible direct action of ORF3a and NS7b to enhancing Bradykinin Storm. This network-based representation of SARS-CoV-2 infection could be a framework for pathogenic evaluation of specific 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; clinical outcomes.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2006/0110747 A1 Ramseier Et Al
    US 200601 10747A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2006/0110747 A1 Ramseier et al. (43) Pub. Date: May 25, 2006 (54) PROCESS FOR IMPROVED PROTEIN (60) Provisional application No. 60/591489, filed on Jul. EXPRESSION BY STRAIN ENGINEERING 26, 2004. (75) Inventors: Thomas M. Ramseier, Poway, CA Publication Classification (US); Hongfan Jin, San Diego, CA (51) Int. Cl. (US); Charles H. Squires, Poway, CA CI2O I/68 (2006.01) (US) GOIN 33/53 (2006.01) CI2N 15/74 (2006.01) Correspondence Address: (52) U.S. Cl. ................................ 435/6: 435/7.1; 435/471 KING & SPALDING LLP 118O PEACHTREE STREET (57) ABSTRACT ATLANTA, GA 30309 (US) This invention is a process for improving the production levels of recombinant proteins or peptides or improving the (73) Assignee: Dow Global Technologies Inc., Midland, level of active recombinant proteins or peptides expressed in MI (US) host cells. The invention is a process of comparing two genetic profiles of a cell that expresses a recombinant (21) Appl. No.: 11/189,375 protein and modifying the cell to change the expression of a gene product that is upregulated in response to the recom (22) Filed: Jul. 26, 2005 binant protein expression. The process can improve protein production or can improve protein quality, for example, by Related U.S. Application Data increasing solubility of a recombinant protein. Patent Application Publication May 25, 2006 Sheet 1 of 15 US 2006/0110747 A1 Figure 1 09 010909070£020\,0 10°0 Patent Application Publication May 25, 2006 Sheet 2 of 15 US 2006/0110747 A1 Figure 2 Ester sers Custer || || || || || HH-I-H 1 H4 s a cisiers TT closers | | | | | | Ya S T RXFO 1961.
    [Show full text]
  • Identification of Differentially Expressed Genes in Human Bladder Cancer Through Genome-Wide Gene Expression Profiling
    521-531 24/7/06 18:28 Page 521 ONCOLOGY REPORTS 16: 521-531, 2006 521 Identification of differentially expressed genes in human bladder cancer through genome-wide gene expression profiling KAZUMORI KAWAKAMI1,3, HIDEKI ENOKIDA1, TOKUSHI TACHIWADA1, TAKENARI GOTANDA1, KENGO TSUNEYOSHI1, HIROYUKI KUBO1, KENRYU NISHIYAMA1, MASAKI TAKIGUCHI2, MASAYUKI NAKAGAWA1 and NAOHIKO SEKI3 1Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8520; Departments of 2Biochemistry and Genetics, and 3Functional Genomics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan Received February 15, 2006; Accepted April 27, 2006 Abstract. Large-scale gene expression profiling is an effective CKS2 gene not only as a potential biomarker for diagnosing, strategy for understanding the progression of bladder cancer but also for staging human BC. This is the first report (BC). The aim of this study was to identify genes that are demonstrating that CKS2 expression is strongly correlated expressed differently in the course of BC progression and to with the progression of human BC. establish new biomarkers for BC. Specimens from 21 patients with pathologically confirmed superficial (n=10) or Introduction invasive (n=11) BC and 4 normal bladder samples were studied; samples from 14 of the 21 BC samples were subjected Bladder cancer (BC) is among the 5 most common to microarray analysis. The validity of the microarray results malignancies worldwide, and the 2nd most common tumor of was verified by real-time RT-PCR. Of the 136 up-regulated the genitourinary tract and the 2nd most common cause of genes we detected, 21 were present in all 14 BCs examined death in patients with cancer of the urinary tract (1-7).
    [Show full text]
  • Genetics of Gene Expression: 2010 Lab
    Genetics of gene expression: 2010 lab VJ Carey July 28, 2010 Contents 1 eQTL concepts and discovery tools 2 1.1 Checking for informative variants for a specified gene . .3 1.2 Components of the workflow; refinements . .4 1.2.1 Data representation: smlSet .....................6 1.2.2 Analysis: snp.rhs.tests; permutation testing . .8 1.2.3 Context: GenomicRanges and rtracklayer .............9 2 Comprehensive eQTL surveys: performance issues 11 2.1 A study of genes coresident on chromosome 20 . 11 2.2 Expanding to genes on multiple chromosomes . 13 2.3 Exercises . 15 3 Investigating allele-specific expression with RNA-seq data 17 3.1 Thedata.................................... 17 3.2 Filtering to \coding SNP"; checking for de novo variants . 18 3.3 Assessing allelic imbalance in transcripts harboring SNPs . 20 3.4 Checking consistency of findings with GENEVAR expression arrays . 23 3.5 Exercises . 24 4 Appendix: samtools pileup format, from samtools distribution site 25 5 Session information 26 1 Figure 1: A schematic illustrating various nonexclusive mechanisms by which DNA variants can affect transcript abundance (Williams et al., 2007). 1 eQTL concepts and discovery tools The basic concern in the lab is the relationship between structural variation in DNA and variation in mRNA abundance. DNA variants of interest are primarily SNP as identified through • direct genotyping in the Sanger sequencing paradigm (yielding HapMap phase II genotypes, for example) • array-based genotyping (yielding HapMap phase III) • NGS-based variant calling (as provided for 1000 genomes (1KG)) • hybrids of array-based and imputed genotypes (imputation to the 1KG panel) mRNA variation is typically characterized using gene expression microarrays, but RNA- seq can also be considered.
    [Show full text]
  • Comprehensive Genome Sequence Analysis of a Breast Cancer Amplicon
    Letter Comprehensive Genome Sequence Analysis of a Breast Cancer Amplicon Colin Collins,1,6 Stanislav Volik,1 David Kowbel,1 David Ginzinger,1 Bauke Ylstra,1 Thomas Cloutier,2 Trevor Hawkins,3 Paul Predki,3 Christopher Martin,4 Meredith Wernick,1 Wen-Lin Kuo,1 Arthur Alberts,5 and Joe W. Gray1 1University of California San Francisco Cancer Center, San Francisco, California 94143-0808, USA; 2Lawrence Berkeley National Laboratory, Berkeley, California 94143, USA; 3Department of Energy Joint Genome Institute, Walnut Creek, California 94958, USA; 4Novartis Agricultural Discovery Institute, San Diego, California 92121, USA; 5Van Andel Institute, Grand Rapids, Michigan 49503, USA Gene amplification occurs in most solid tumors and is associated with poor prognosis. Amplification of 20q13.2 is common to several tumor types including breast cancer. The 1 Mb of sequence spanning the 20q13.2 breast cancer amplicon is one of the most exhaustively studied segments of the human genome. These studies have included amplicon mapping by comparative genomic hybridization (CGH), fluorescent in-situ hybridization (FISH), array-CGH, quantitative microsatellite analysis (QUMA), and functional genomic studies. Together these studies revealed a complex amplicon structure suggesting the presence of at least two driver genes in some tumors. One of these, ZNF217, is capable of immortalizing human mammary epithelial cells (HMEC) when overexpressed. In addition, we now report the sequencing of this region in human and mouse, and on quantitative expression studies in tumors. Amplicon localization now is straightforward and the availability of human and mouse genomic sequence facilitates their functional analysis. However, comprehensive annotation of megabase-scale regions requires integration of vast amounts of information.
    [Show full text]
  • Human Prefoldin Modulates Co-Transcriptional Pre-Mrna Splicing
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.14.150466; this version posted July 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. BIOLOGICAL SCIENCES: Biochemistry Human prefoldin modulates co-transcriptional pre-mRNA splicing Payán-Bravo L 1,2, Peñate X 1,2 *, Cases I 3, Pareja-Sánchez Y 1, Fontalva S 1,2, Odriozola Y 1,2, Lara E 1, Jimeno-González S 2,5, Suñé C 4, Reyes JC 5, Chávez S 1,2. 1 Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain. 2 Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain. 3 Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Seville, Spain. 4 Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" IPBLN-CSIC, PTS, Granada, Spain. 5 Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain. Correspondence: Sebastián Chávez, IBiS, campus HUVR, Avda. Manuel Siurot s/n, Sevilla, 41013, Spain. Phone: +34-955923127: e-mail: [email protected]. * Co- corresponding; [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/2020.06.14.150466; this version posted July 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the cotranslational folding of actin and tubulin monomers.
    [Show full text]