DOCSLIB.ORG

AMPK–Akt Double-Negative Feedback Loop in Breast Cancer Cells Regulates Their Adaptation to Matrix Deprivation Manipa Saha1, Saurav Kumar1, Shoiab Bukhari1, Sai A

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
AMPK–Akt Double-Negative Feedback Loop in Breast Cancer Cells Regulates Their Adaptation to Matrix Deprivation Manipa Saha1, Saurav Kumar1, Shoiab Bukhari1, Sai A Published OnlineFirst January 16, 2018; DOI: 10.1158/0008-5472.CAN-17-2090 Cancer Tumor Biology and Immunology Research AMPK–Akt Double-Negative Feedback Loop in Breast Cancer Cells Regulates Their Adaptation to Matrix Deprivation Manipa Saha1, Saurav Kumar1, Shoiab Bukhari1, Sai A. Balaji1, Prashant Kumar2, Sravanth K. Hindupur1, and Annapoorni Rangarajan1 Abstract Cell detachment from the extracellular matrix triggers anoi- of the pAkthigh/pAMPKlow state. Clinical specimens of primary kis. Disseminated tumor cells must adapt to survive matrix and metastatic breast cancer displayed an Akt-associated gene deprivation, while still retaining the ability to attach at sec- expression signature, whereas circulating breast tumor cells ondary sites and reinitiate cell division. In this study, we displayed an elevated AMPK-dependent gene expression signa- elucidatemechanismsthatenablereversiblematrixattachment ture. Our work establishes a double-negative feedback loop by breast cancer cells. Matrix deprival triggered AMPK activity between Akt and AMPK to control the switch between matrix- and concomitantly inhibited AKT activity by upregulating the attached and matrix-detached states needed to coordinate cell Akt phosphatase PHLPP2. The resultant pAMPKhigh/pAktlow growth and survival during metastasis. state was critical for cell survival in suspension, as PHLPP2 Significance: These findings reveal a molecular switch that silencing also increased anoikis while impairing autophagy regulates cancer cell survival during metastatic dissemination, and metastasis. In contrast, matrix reattachment led to Akt- with the potential to identify targets to prevent metastasis in mediated AMPK inactivation via PP2C-a-mediated restoration breast cancer. Cancer Res; 78(6); 1497–510. Ó2018 AACR. Introduction vival, and metabolism, and plays a major role in tumor progres- sion (4). Akt is recruited to the plasma membrane by binding to Metastasis accounts for the vast majority of cancer-associated PIP3 and is subsequently phosphorylated by PDK1 and mTOR deaths. The metastatic process involves detachment of cells from complex 2 (mTORC2) at T308 and S473, respectively, leading to the primary site of tumor initiation, entry into the blood stream or its full activation. Conversely, Akt signaling is attenuated by the lymphatics, exit from the circulation and reattachment at dephosphorylation of these sites by protein phosphatase 2A distant sites to spawn metastatic growth (1). Integrins mediate (PP2A) and pleckstrin homology domain leucine-rich repeat cell adhesion to the extracellular matrix that provides growth and protein phosphatases (PHLPP 1 and 2; ref. 5). Upon activation survival signals (2), whereas matrix deprivation leads to pro- by growth factor signaling, Akt promotes anabolic processes grammed cell death termed "anoikis" (3). Therefore, detached including lipid biosynthesis and protein translation, thus driving tumor cells must develop resistance to anoikis, while retaining the cell growth and proliferation. ability to reattach and grow at a distal site to spawn a successful In contrast, the AMP-activated protein kinase (AMPK) is acti- metastasis. Yet, little is known about cellular signaling pathways vated under metabolically stressed conditions and brings about that coordinate cell growth and stress-survival signals during the cellular homeostasis by switching on energy-generating catabolic attachment–detachment cascade of metastatic colonization. processes like fatty acid oxidation and glycolysis, while inhibiting The serine/threonine protein kinase Akt (also known as PKB) energy-consuming anabolic pathways including carbohydrate, regulates several cellular processes, including proliferation, sur- lipid, and protein biosynthesis (6–8). AMPK is a heterotrimeric protein consisting of a, b, and g subunits (encoded by a1, a2; b1, b2; and g1, g2, g3). It is allosterically activated by AMP and 1Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India. 2Institute of Bioinformatics, International positively regulated by phosphorylation of T172 residue by Technology Park, Whitefield, Bangalore, India. upstream kinases LKB1 and CaMKKb, while negatively regulated by dephosphorylation (9, 10). Although considered a tumor Note: Supplementary data for this article are available at Cancer Research Online (http://cancerres.aacrjournals.org/). suppressor owing to its growth retarding effects, recent studies have identified context specific protumorigenic roles for AMPK by M. Saha and S. Kumar contributed equally to this article. promoting cell survival under glucose deprivation and hypoxia Current address for Sravanth K. Hindupur: Biozentrum, University of Basel, stress (11, 12). Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland. Under matrix-deprivation stress, Akt activation is sufficient for Corresponding Author: Annapoorni Rangarajan, Indian Institute of Science, Lab anoikis resistance in immortalized MDCK cells (13). ErbB2-over- GA 10 MRDG IISc Bangalore, Bangalore 560012, Karnataka, India. Phone: 91-80- expressing breast cancer cells show increased dependence on Akt 22933263; E-mail: [email protected] for anchorage-independent growth (14). In contrast, pharmaco- doi: 10.1158/0008-5472.CAN-17-2090 logic inhibition of the PI3K/Akt pathway failed to render T-47D Ó2018 American Association for Cancer Research. breast cancer cells sensitive to anoikis (15). Thus, the role of Akt in www.aacrjournals.org 1497 Downloaded from cancerres.aacrjournals.org on September 28, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst January 16, 2018; DOI: 10.1158/0008-5472.CAN-17-2090 Saha et al. anoikis resistance remains to be fully understood. On the other respectively, as kind gifts. shRNAs against PHLPP2 (RHS4531- hand, recent work from our laboratory and that of others has EG23035) and the corresponding control nontargeting shRNA in shown matrix deprivation-triggered activation of AMPK and its pGIPZ vector (NT); and inducible shRNA against AMPKa2 critical role in anoikis resistance in breast cancer cells (16–18). (V2THS_57674) and the corresponding control empty pTRIPZ Thus, independent studies have implicated Akt and AMPK in vector (EV) were procured from Dharmacon. Lipofectamine anoikis resistance, although they have opposing effects on cellular (Invitrogen) was used to transfect plasmid DNA into cells. growth and metabolism. MDA-MB-231 cells stably expressing GFP-HA-Akt-T308D Synergistic and antagonistic relationship between Akt and S473D were generated by transfection followed by FACS-based AMPK has been documented under different cellular contexts; sorting for GFP-expressing cells; cells stably expressing HA myr- however, little is known about their interplay in maintaining the Akt were generated by cotransfecting a puromycin resistance adherent versus detached states of cells. Intriguingly, we show plasmid at a 10:1 ratio followed by selection with puromycin here that detachment-triggered AMPK concomitantly represses (0.5 mg/mL) treatment. MDA-MB-231 cells stably expressing Akt activity. We identify a novel AMPK-mediated PHLPP2 upre- specific shRNAs were generated by selection with puromycin gulation that inactivates Akt to promote AMPK-induced autop- followed by sorting cells for high GFP (in case of plasmids in hagy and that inhibits anoikis in suspension. Finally, we show that pGIPZ vector) or high RFP (in case of plasmids in pTRIPZ vector) matrix reattachment triggers Akt activity, which in turn represses expression. AMPK through PP2C-a. Our data, thus, identify a novel, recip- siRNA oligos against Akt (targeting both isoforms Akt1 and rocal, inhibitory relationship between AMPK and Akt that reg- Akt2 [6211 and 6510]) were purchased from Cell Signaling ulates adaptation to matrix detachment. Technology and transfected using oligofectamine (Invitrogen). Materials and Methods Pharmacologic compounds Pharmacologic compounds used in cell culture include the Primary cells and culture conditions AMPK inhibitor 6-[4-(2-piperidin-1-ylethoxy-phenyl)]-3-pyridin- Primary breast tissues (cancer and adjacent normal) obtained 4-yl-pyrrazolo [1, 5-a]-pyrimidine (compound C; Cat. No. 171260; from the Kidwai Memorial Institute of Oncology (KMIO), Ban- 10 mmol/L; referred to as CC in figures), PI3K/Akt inhibitor galore, as per IRB and in compliance with ethical guidelines of LY294002 (Cat. No. 440202; 20 mmol/L; referred to as LY in KMIO and the Indian Institute of Science (IISc), were processed figures), Akt inhibitor Akti VIII (Cat. No. 124018; 10 mmol/L), and into single cells and cultured as described previously (16, 19) in MG132 (Cat. No. 474790; 10 mmol/L) from Calbiochem (Merck), serum-free media containing 10 ng/mL hEGF, 1 mg/mL hydro- AMPK activator A-769662 (100 mmol/L; referred to as A76 in cortisone, 10 mg/mL insulin, 4 ng/mL heparin and B27. Single figures) from the University of Dundee, Scotland, cycloheximide cells were seeded in regular TC plates for adherent culture or in (Cat. No. C7698; 0.1 mg/mL; referred to as CHX) and lysosomal ultralow attachment plates (Corning Inc.) for mammosphere inhibitor chloroquine (Cat. No. C6628; 50 mmol/L; referred to as culture (16). CQ in figures) from Sigma-Aldrich. Dimethyl sulfoxide (DMSO) was used as vehicle control for all compounds except cyclohexi- Cell lines and cell culture conditions mide, which was dissolved in water. In experiments carried out in Breast cancer cell lines MDA-MB-231, MCF7, BT474 (from suspension, adherent cells were pretreated
Load more

Recommended publications
  • Haploinsufficiency of Cardiac Myosin Binding Protein-C in the Development of Hypertrophic Cardiomyopathy
    Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 2014 Haploinsufficiency of Cardiac Myosin Binding Protein-C in the Development of Hypertrophic Cardiomyopathy David Barefield Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Physiology Commons Recommended Citation Barefield, David, "Haploinsufficiency of Cardiac Myosin Binding Protein-C in the Development of Hypertrophic Cardiomyopathy" (2014). Dissertations. 1249. https://ecommons.luc.edu/luc_diss/1249 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations 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. Copyright © 2014 David Barefield LOYOLA UNIVERSITY CHICAGO HAPLOINSUFFICIENCY OF CARDIAC MYOSIN BINDING PROTEIN-C IN THE DEVELOPMENT OF HYPERTROPHIC CARDIOMYOPATHY A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY PROGRAM IN CELL AND MOLECULAR PHYSIOLOGY BY DAVID YEOMANS BAREFIELD CHICAGO, IL AUGUST 2014 Copyright by David Yeomans Barefield, 2014 All Rights Reserved. ii ACKNOWLEDGEMENTS The completion of this work would not have been possible without the support of excellent mentors, colleagues, friends, and family. I give tremendous thanks to my mentor, Dr. Sakthivel Sadayappan, who has facilitated my growth as a scientist and as a human being over the past five years. I would like to thank my dissertation committee: Drs. Pieter de Tombe, Kenneth Byron, Leanne Cribbs, Kyle Henderson, and Christine Seidman for their erudite guidance of my project and my development as a scientist.
    [Show full text]
  • Analysis and Interpretation of Next-Generation Sequencing Data for the Identification of Genetic Variants Involved in Cardiovascular Malformation
    Analysis and interpretation of next-generation sequencing data for the identification of genetic variants involved in cardiovascular malformation Darren T. Houniet For the degree of Doctor of Philosophy Newcastle University Faculty of Medical Sciences Institute of Genetic Medicine February 2013 Abstract Congenital cardiovascular malformation (CVM) affects 7/1000 live births. Approximately 20% of cases are caused by chromosomal and syndromic conditions. Rare Mendelian families segregating particular forms of CVM have also been described. Among the remaining 80% of non-syndromic cases, there is a familial predisposition implicating as yet unidentified genetic factors. Since the reproductive consequences to an individual of CVM are usually severe, evolutionary considerations suggest predisposing variants are likely to be rare. The overall aim of my PhD was to use next generation sequencing (NGS) methods to identify such rare, potentially disease causing variants in CVM. First, I developed a novel approach to calculate the sensitivity and specificity of NGS data in detecting variants using publicly available population frequency data. My aim was to provide a method that would yield sound estimates of the quality of a sequencing experiment without the need for additional genotyping in the sequenced samples. I developed such a method and demonstrated that it provided comparable results to methods using microarray data as a reference. Furthermore, I evaluated different variant calling pipelines and showed that they have a large effect on sensitivity and specificity. Following this, the NovoAlign-Samtools and BWA-Dindel pipelines were used to identify single base substitution and indel variants in three pedigrees, where predisposition to a different disease appears to segregate following an autosomal dominant mode of inheritance.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2016/0289762 A1 KOH Et Al
    US 201602897.62A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0289762 A1 KOH et al. (43) Pub. Date: Oct. 6, 2016 (54) METHODS FOR PROFILIING AND Publication Classification QUANTITATING CELL-FREE RNA (51) Int. Cl. (71) Applicant: The Board of Trustees of the Leland CI2O I/68 (2006.01) Stanford Junior University, Palo Alto, (52) U.S. Cl. CA (US) CPC ....... CI2O 1/6883 (2013.01); C12O 2600/112 (2013.01); C12O 2600/118 (2013.01); C12O (72) Inventors: Lian Chye Winston KOH, Stanford, 2600/158 (2013.01) CA (US); Stephen R. QUAKE, Stanford, CA (US); Hei-Mun Christina FAN, Fremont, CA (US); Wenying (57) ABSTRACT PAN, Stanford, CA (US) The invention generally relates to methods for assessing a (21) Appl. No.: 15/034,746 neurological disorder by characterizing circulating nucleic acids in a blood sample. According to certain embodiments, (22) PCT Filed: Nov. 6, 2014 methods for S. a Nial disorder include (86). PCT No.: PCT/US2O14/064355 obtaining RNA present in a blood sample of a patient Suspected of having a neurological disorder, determining a S 371 (c)(1), level of RNA present in the sample that is specific to brain (2) Date: May 5, 2016 tissue, comparing the sample level of RNA to a reference O O level of RNA specific to brain tissue, determining whether a Related U.S. Application Data difference exists between the sample level and the reference (60) Provisional application No. 61/900,927, filed on Nov. level, and indicating a neurological disorder if a difference 6, 2013.
    [Show full text]
  • View of All NF-Κb Post-Translational Modifications See Review by Perkins [179]
    UNIVERSITY OF CINCINNATI Date: 8-May-2010 I, Michael Wilhide , hereby submit this original work as part of the requirements for the degree of: Master of Science in Molecular, Cellular & Biochemical Pharmacology It is entitled: Student Signature: Michael Wilhide This work and its defense approved by: Committee Chair: Walter Jones, PhD Walter Jones, PhD Mohammed Matlib, PhD Mohammed Matlib, PhD Basilia Zingarelli, MD, PhD Basilia Zingarelli, MD, PhD Jo El Schultz, PhD Jo El Schultz, PhD Muhammad Ashraf, PhD Muhammad Ashraf, PhD 5/8/2010 646 Hsp70.1 contributes to the NF-κΒ paradox after myocardial ischemic insults A thesis submitted to the Graduate School of the University of Cincinnati in partial fulfillment of the requirement for the degree of Master of Science (M.S.) in the Department of Pharmacology and Biophysics of the College of Medicine by Michael E. Wilhide B.S. College of Mount St. Joseph 2002 Committee Chair: W. Keith Jones, Ph.D. Abstract One of the leading causes of death globally is cardiovascular disease, with most of these deaths related to myocardial ischemia. Myocardial ischemia and reperfusion causes several biochemical and metabolic changes that result in the activation of transcription factors that are involved in cell survival and cell death. The transcription factor Nuclear Factor-Kappa B (NF-κB) is associated with cardioprotection (e.g. after permanent coronary occlusion, PO) and cell injury (e.g. after ischemia/reperfusion, I/R). However, there is a lack of knowledge regarding how NF- κB mediates cell survival vs. cell death after ischemic insults, preventing the identification of novel therapeutic targets for enhanced cardioprotection and decreased injurious effects.
    [Show full text]
  • Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis
    Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis Ugo Ala1., Rosario Michael Piro1., Elena Grassi1, Christian Damasco1, Lorenzo Silengo1, Martin Oti2, Paolo Provero1*, Ferdinando Di Cunto1* 1 Molecular Biotechnology Center, Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy, 2 Department of Human Genetics and Centre for Molecular and Biomolecular Informatics, University Medical Centre Nijmegen, Nijmegen, The Netherlands Abstract Background: Even in the post-genomic era, the identification of candidate genes within loci associated with human genetic diseases is a very demanding task, because the critical region may typically contain hundreds of positional candidates. Since genes implicated in similar phenotypes tend to share very similar expression profiles, high throughput gene expression data may represent a very important resource to identify the best candidates for sequencing. However, so far, gene coexpression has not been used very successfully to prioritize positional candidates. Methodology/Principal Findings: We show that it is possible to reliably identify disease-relevant relationships among genes from massive microarray datasets by concentrating only on genes sharing similar expression profiles in both human and mouse. Moreover, we show systematically that the integration of human-mouse conserved coexpression with a phenotype similarity map allows the efficient identification of disease genes in large genomic regions. Finally, using this approach on 850 OMIM loci characterized by an unknown molecular basis, we propose high-probability candidates for 81 genetic diseases. Conclusion: Our results demonstrate that conserved coexpression, even at the human-mouse phylogenetic distance, represents a very strong criterion to predict disease-relevant relationships among human genes. Citation: Ala U, Piro RM, Grassi E, Damasco C, Silengo L, et al.
    [Show full text]
  • Genome-Wide Association Meta-Analysis for Early Age-Related
    bioRxiv preprint doi: https://doi.org/10.1101/2019.12.20.883801; this version posted December 20, 2019. 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. 1 Genome-wide association meta-analysis for early age-related 2 macular degeneration highlights novel loci and insights for 3 advanced disease 4 5 Authors 6 Thomas W Winkler1*, Felix Grassmann2,3*, Caroline Brandl1,2,4, Christina Kiel2, Felix Günther1,5, 7 Tobias Strunz2, Lorraine Weidner1, Martina E Zimmermann1, Christina A. Korb6, Alicia 8 Poplawski7, Alexander K Schuster6, Martina Müller-Nurasyid8,9,10, Annette Peters11,12, 9 Franziska G Rauscher13,14, Tobias Elze13,15, Katrin Horn13,14, Markus Scholz13,14, Marisa 10 Cañadas-Garre16, Amy Jayne McKnight16, Nicola Quinn16, Ruth E Hogg16, Helmut Küchenhoff5, 11 Iris M Heid1§, Klaus J Stark1§ and Bernhard HF Weber2§ 12 Affiliations 13 1: Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany; 2: Institute of Human Genetics, 14 University of Regensburg, Regensburg, Germany; 3: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 15 Stockholm, Sweden; 4: Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany; 5: Statistical 16 Consulting Unit StaBLab, Department of Statistics, Ludwig-Maximilians-Universität Munich, Munich, Germany; 6: Department of 17 Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; 7:
    [Show full text]
  • A Genome-Wide Association Study Meta-Analysis
    Insights into the Genetic Architecture of Early Stage Age- Related Macular Degeneration: A Genome-Wide Association Study Meta-Analysis Elizabeth G. Holliday1*., Albert V. Smith2,3., Belinda K. Cornes4., Gabrie¨lle H. S. Buitendijk5,6., Richard A. Jensen7,8., Xueling Sim9,10., Thor Aspelund2,3, Tin Aung4, Paul N. Baird11, Eric Boerwinkle12, Ching Yu Cheng4,13,14,15, Cornelia M. van Duijn6, Gudny Eiriksdottir2, Vilmundur Gudnason2,3, Tamara Harris16, Alex W. Hewitt11, Michael Inouye17, Fridbert Jonasson3,18, Barbara E. K. Klein19, Lenore Launer16, Xiaohui Li20, Gerald Liew21, Thomas Lumley7,22, Patrick McElduff1, Barbara McKnight7,23, Paul Mitchell21, Bruce M. Psaty7,8,24,25,26, Elena Rochtchina21, Jerome I. Rotter20, Rodney J. Scott27, Wanting Tay4, Kent Taylor20, Yik Ying Teo28, Andre´ G. Uitterlinden6,29,30, Ananth Viswanathan31, Sophia Xie11, Wellcome Trust Case Control Consortium 2{, Johannes R. Vingerling5,6", Caroline C. W. Klaver5,6", E. Shyong Tai28,32,33", David Siscovick7,8,24", Ronald Klein19", Mary Frances Cotch34", Tien Y. Wong4,11,35", John Attia1,36", Jie Jin Wang11,21" 1 Centre for Clinical Epidemiology and Biostatistics, and School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia, 2 Icelandic Heart Association, Kopavogur, Iceland, 3 Faculty of Medicine, University of Iceland, Reykjavik, Iceland, 4 Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore, 5 Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands, 6 Department
    [Show full text]
  • UC San Diego Electronic Theses and Dissertations
    UC San Diego UC San Diego Electronic Theses and Dissertations Title Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent Permalink https://escholarship.org/uc/item/7m04f0b0 Author Buchholz, Kyle Stephen Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Kyle Stephen Buchholz Committee in Charge: Professor Jeffrey Omens, Chair Professor Andrew McCulloch, Co-Chair Professor Ju Chen Professor Karen Christman Professor Robert Ross Professor Alexander Zambon 2016 Copyright Kyle Stephen Buchholz, 2016 All rights reserved Signature Page The Dissertation of Kyle Stephen Buchholz is approved and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2016 iii Dedication To my beautiful wife, Rhia. iv Table of Contents Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Table of Contents ................................................................................................................ v List of Figures ...................................................................................................................
    [Show full text]
  • Predict AID Targeting in Non-Ig Genes Multiple Transcription Factor
    Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 is online at: average * The Journal of Immunology published online 20 March 2013 from submission to initial decision 4 weeks from acceptance to publication Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke, Man Liu, Gur Yaari, Ashraf M. Khalil, Mary M. Tomayko, Mark J. Shlomchik, David G. Schatz and Steven H. Kleinstein J Immunol http://www.jimmunol.org/content/early/2013/03/20/jimmun ol.1202547 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/suppl/2013/03/20/jimmunol.120254 7.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 26, 2021. Published March 20, 2013, doi:10.4049/jimmunol.1202547 The Journal of Immunology Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke,* Man Liu,†,1 Gur Yaari,‡ Ashraf M. Khalil,x Mary M. Tomayko,{ Mark J. Shlomchik,†,x David G.
    [Show full text]
  • Characterization of Gene Expression Patterns in the Wild Pacific Salmon
    Characterization of Gene Expression Patterns in the Wild Pacific Salmon by Evan Morien B.Sc., State University of New York at Buffalo, 2007 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in The Faculty of Graduate Studies (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) December 2012 c Evan Morien 2012 Abstract Declines in Pacific salmon stocks in recent decades have spurred much re- search into their physiology and survivorship, but comparatively little into their genomics. Sockeye salmon in particular are experiencing high levels of mortality during their migration upriver, and the numbers of returning sockeye have fluxuated wildly with respect to predictions in recent years. The goal of my project is to gain insight into the basic genomics of Pacific salmon stocks, including the sockeye, through bioinformatic approaches to gene expression profiling. Using microarray technology, I have conducted a large-scale analysis of over 1,000 samples from multiple tissues, stocks, and species of salmon. I identified tissue-specific and housekeeping genes and compared them to orthologs in mouse and human, respectively. I have also classified a number of microarray samples with a support vector machine (SVM) using qPCR data showing the presence of several common pathogens affecting Pacific salmon populations. Using identified housekeeping genes as normalizing factors, I modeled in silico a qPCR assay designed to identify salmon as infected or uninfected with a particular pathogen. With these data I hope to increase basic knowledge of the genomics of the Pacific salmon. ii Preface Contributions The data used in this thesis were generated at the Department of Fish- eries and Oceans Pacific Biological Station in Nanaimo, British Columbia by Kristina M.
    [Show full text]
  • An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice
    bioRxiv preprint doi: https://doi.org/10.1101/378711; this version posted August 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title: 2 An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice 3 Short Title: 4 Genomic response to selection for longer limbs 5 One-sentence summary: 6 Genome sequencing of mice selected for longer limbs reveals that rapid selection response is 7 due to both discrete loci and polygenic adaptation 8 Authors: 9 João P. L. Castro 1,*, Michelle N. Yancoskie 1,*, Marta Marchini 2, Stefanie Belohlavy 3, Marek 10 Kučka 1, William H. Beluch 1, Ronald Naumann 4, Isabella Skuplik 2, John Cobb 2, Nick H. 11 Barton 3, Campbell Rolian2,†, Yingguang Frank Chan 1,† 12 Affiliations: 13 1. Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany 14 2. University of Calgary, Calgary AB, Canada 15 3. IST Austria, Klosterneuburg, Austria 16 4. Max Planck Institute for Cell Biology and Genetics, Dresden, Germany 17 Corresponding author: 18 Campbell Rolian 19 Yingguang Frank Chan 20 * indicates equal contribution 21 † indicates equal contribution 22 Abstract: 23 Evolutionary studies are often limited by missing data that are critical to understanding the 24 history of selection. Selection experiments, which reproduce rapid evolution under controlled 25 conditions, are excellent tools to study how genomes evolve under strong selection. Here we 1 bioRxiv preprint doi: https://doi.org/10.1101/378711; this version posted August 19, 2018.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,383,086 B2 Brenner (45) Date of Patent: *Feb
    USOO8383O86B2 (12) United States Patent (10) Patent No.: US 8,383,086 B2 Brenner (45) Date of Patent: *Feb. 26, 2013 (54) NICOTINAMIDE RIBOSIDE KINASE 5'-monophosphate (FdUMP): a strategy to introduce nucleotides into COMPOSITIONS AND METHODS FOR cells.”J Med Chem 1994 37(23):3902-3909. Fleishchmann et al., “Whole-Genome Random Sequencing and USING THE SAME Assembly of Haemophilus Influenzae Rd.” Science 1995 269:496 512. (75) Inventor: Charles M. Brenner, Lyme, NH (US) Gingrich et al., “Codehydrogenase I and Other Pyridinium Com pounds as V-Factor for Hemophilus Influenzae and H. (73) Assignee: Trustees of Dartmouth College, Parainfluenzae, J. Bacteriol. 199447:535-550. Hanover, NH (US) Godek et al., “In Vitro Evaluation of Nicotinamide Riboside Analogs Against Haemophilus Influenzae.” Antimicrobal Agents and Chemo (*) Notice: Subject to any disclaimer, the term of this therapy 199034(8): 1473-1479. Han et al., “Cellular Uptake Mechanism of Amino Acid Ester patent is extended or adjusted under 35 Prodrugs in Caco-2/hPEPT1 Cells Overexpressing a Human Peptide U.S.C. 154(b) by 0 days. Transporter.” Pharmaceutical Research 1998 15(9): 1382-1386. Holdsworth et al., “A fraction derived from brewer's yeast inhibits This patent is Subject to a terminal dis cholesterol synthesis by rat liver preparations in vitro.” Br. J. Nutr. claimer. 1991 65:285-299. Leder et al., “Synthesis of Nicotinamide Mononucleotide by Human (21) Appl. No.: 13/445.289 Erythrocytes in Vitro”. J. Biol. Chem. 1951 189:889-899. Li et al., “A Novel Muscle-specific Beta 1 Integrin Binding Protein (22) Filed: Apr. 12, 2012 (MIBP) that Modulates Myogenic Differentiation.” J.
    [Show full text]