Protein Phosphatase 2A As a Therapeutic Target in Inflammation and Neurodegeneration Clark, Andrew R.; Ohlmeyer, Michael

Total Page:16

File Type:pdf, Size:1020Kb

Protein Phosphatase 2A As a Therapeutic Target in Inflammation and Neurodegeneration Clark, Andrew R.; Ohlmeyer, Michael University of Birmingham Protein phosphatase 2A as a therapeutic target in inflammation and neurodegeneration Clark, Andrew R.; Ohlmeyer, Michael DOI: 10.1016/j.pharmthera.2019.05.016 License: Creative Commons: Attribution (CC BY) Document Version Publisher's PDF, also known as Version of record Citation for published version (Harvard): Clark, AR & Ohlmeyer, M 2019, 'Protein phosphatase 2A as a therapeutic target in inflammation and neurodegeneration', Pharmacology & Therapeutics, vol. 201, pp. 181-201. https://doi.org/10.1016/j.pharmthera.2019.05.016 Link to publication on Research at Birmingham portal General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. •Users may freely distribute the URL that is used to identify this publication. •Users may download and/or print one copy of the publication from the University of Birmingham research portal for the purpose of private study or non-commercial research. •User may use extracts from the document in line with the concept of ‘fair dealing’ under the Copyright, Designs and Patents Act 1988 (?) •Users may not further distribute the material nor use it for the purposes of commercial gain. Where a licence is displayed above, please note the terms and conditions of the licence govern your use of this document. When citing, please reference the published version. Take down policy While the University of Birmingham exercises care and attention in making items available there are rare occasions when an item has been uploaded in error or has been deemed to be commercially or otherwise sensitive. If you believe that this is the case for this document, please contact [email protected] providing details and we will remove access to the work immediately and investigate. Download date: 25. Sep. 2021 Pharmacology & Therapeutics 201 (2019) 181–201 Contents lists available at ScienceDirect Pharmacology & Therapeutics journal homepage: www.elsevier.com/locate/pharmthera Protein phosphatase 2A as a therapeutic target in inflammation and neurodegeneration Andrew R. Clark a,⁎, Michael Ohlmeyer b a Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom b Atux Iskay LLC, Plainsboro, NJ, USA article info abstract Available online 1 June 2019 Protein phosphatase 2A (PP2A) is a highly complex heterotrimeric enzyme that catalyzes the selective removal of phosphate groups from protein serine and threonine residues. Emerging evidence suggests that it functions as a Keywords: tumor suppressor by constraining phosphorylation-dependent signalling pathways that regulate cellular trans- Protein phosphatase 2A formation and metastasis. Therefore, PP2A-activating drugs (PADs) are being actively sought and investigated fl In ammation as potential novel anti-cancer treatments. Here we explore the concept that PP2A also constrains inflammatory Cancer responses through its inhibitory effects on various signalling pathways, suggesting that PADs may be effective in Neurodegeneration the treatment of inflammation-mediated pathologies. Alzheimer’sdisease Multiple sclerosis © 2019 Published by Elsevier Inc. Contents 1. Introduction............................................... 181 2. TheregulationofPP2Afunction...................................... 182 3. PP2Aandcancer............................................. 184 4. Involvement of PP2A in the control of inflammation............................. 186 5. Neuro-inflammationandneuro-degeneration............................... 190 6. Remainingquestions........................................... 192 7. Conclusion............................................... 193 Conflictofintereststatement......................................... 193 Acknowledgements.............................................. 193 References.................................................. 193 1. Introduction translational odification alters the charge, local shape and global confor- mation of substrate proteins, influencing their interactions with other Protein phosphorylation, the reversible, covalent addition of phos- molecules, and modulating their subcellular localization, stability or phate groups to serine, threonine or tyrosine residues, is a rapid and function. The human genome encodes more than 500 kinases that cata- efficient mechanism for modulating protein function. This post- lyze protein phosphorylation, and fewer than 200 protein phosphatases Abbreviations: AD, Alzheimer’s disease; AP-1, activator protein 1; BBB, blood-brain barrier; CCR4/NOT, carbon catabolite repressor 4/never on TATA-less; CIP2A, cancerous inhibitor of PP2A; CNS, central nervous system; DC, dendritic cell; EAE, experimental autoimmune encephalopathy; HEAT, Huntingtin - Elongation factor - A subunit of PP2A - Target of rapamycin domain; IκBα, α inhibitor of NF-κB; IKK, IκBα kinase; IL, interleukin; IRF, interferon-regulatory factor; JNK, cJun N-terminal kinase; LCMT-1, leucine carboxymethyl transferase 1; LUBAC, linear ubiquitin chain assembly complex; MAPK, mitogen-activated protein kinase; MK2, MAPK-activated kinase 2; MKK, MAPK kinase; MS, multiple sclerosis; MyD88, myeloid differentiation factor 88; NF-κB, nuclear factor κ enhancer of activated B cells; NFT, neurofibrillary tangles; PAD, PP2A-activating drug; PAMP, pathogen-associated molecular pattern; PME- 1, protein phosphatase methylesterase 1; PP2A, protein phosphatase 2A; PRR, pattern recognition receptor; ROS, reactive oxygen species; S1P, sphingosine-1-phosphate; S1PR, S1P recep- tor; SphK, sphingosine kinase; STRN, striatin; TAB, TAK1 binding protein; TAK1, transforming growth factor β-activated kinase; TGFβ, transforming growth factor β; TIRAP, Toll/interleukin 1 receptor domain-containing adaptor protein; TLR, Toll-like receptor; TNF, tumor necrosis factor; TRAF, TNF receptor interacting factor; TRAM, Toll/interleukin 1 receptor domain- containing adaptor molecule; TRIF, Toll/interleukin 1 receptor domain-containing adaptor inducing interferon β; TTP, tristetraprolin; UVB, ultraviolet B. ⁎ Corresponding author. E-mail address: [email protected] (A.R. Clark). https://doi.org/10.1016/j.pharmthera.2019.05.016 0163-7258/© 2019 Published by Elsevier Inc. 182 A.R. Clark, M. Ohlmeyer / Pharmacology & Therapeutics 201 (2019) 181–201 that catalyze the reverse reaction. However, these numbers may be mis- leading. In some cases substrate specificity can be conferred by regula- tory subunits distinct from the proteins that possess catalytic activity. Duplication and evolutionary diversification of regulatory subunits can therefore greatly expand the functional roles of kinases or phosphatases without a parallel increase in the number of kinase- and phosphatase- encoding genes. Such diversification appears to have been particularly important in the evolution of protein phosphatase(s) 2A (PP2A), the Fig. 1. Composition of the PP2A holoenzyme. Systematic names are indicated for subject of this review. scaffolding (A), regulatory (B) and catalytic (C) protein subunits. Alternative names are Since protein phosphorylation has profound effects on every aspect indicated in Table 1. of cell biology, precise balance between the activities of kinases and phosphatases is required for the proper regulation of cell function. Strik- this review we will adhere to the systematic names for B subunits. Alter- ingly, such balance is not seen in scientific literature, where published native names are listed in Table 1. articles with “kinase” outnumber those with “phosphatase” in their PP2A profoundly influences all aspects of cell biology, therefore its titles by a factor of almost ten to one. There are several possible explana- function is tightly regulated at several levels. As reviewed extensively tions for such bias. By definition phosphorylation is an energy- elsewhere (Janssens, Longin, & Goris, 2008; Sents, Ivanova, Lambrecht, dependent process requiring the consumption of ATP. For reasons of Haesen, & Janssens, 2013), assembly of holoenzymes is strictly con- energy economy, evolution may have favored use of protein phosphor- trolled to prevent the formation of catalytically active complexes lack- ylation as a means of response to perturbation, and dephosphorylation ing correct substrate specificity. Unpartnered catalytic subunits are as a means of restoring or maintaining equilibrium. This generalization subject to ubiquitination and proteasomal degradation. The protein α4 seems broadly true, although many readers will readily think of excep- (otherwise known as Immunoglobulin Binding Protein 1 or IGBP1) tions. In this perspective, phosphatase activity may be seen as rather both stabilizes and inactivates free C subunits, thereby regulating their non-specific, unregulated, and consequently not very interesting as a availability for assembly into holoenzymes (Kong, Ditsworth, Lindsten, subject of study. Recent advances suggest that these are all misconcep- & Thompson, 2009). The ATP-dependent chaperone phosphotyrosyl tions. Inhibition of kinases to prevent harmful cell activation is more phosphatase activator (encoded by PPP2R4) is required for correct fold- conceptually and practically straightforward than stimulation of phos- ing of the catalytic subunit and incorporation of manganese ions at the phatases to promote restoration of homeostasis.
Recommended publications
  • Neurodegenerative Triplet Repeat Expansion Disorders
    The Pharma Innovation Journal 2018; 7(11): 34-40 ISSN (E): 2277- 7695 ISSN (P): 2349-8242 NAAS Rating: 5.03 Neurodegenerative triplet repeat expansion disorders: TPI 2018; 7(11): 34-40 © 2018 TPI A review www.thepharmajournal.com Received: 15-09-2018 Accepted: 20-10-2018 Mitesh Patel, RK Patel, Tushar Chauhan, Jigar Suthar and Sanjay Dave Mitesh Patel Genetics Group of Gujarat Abstract Diagnostic Centre, Mehsana, Epigenetic alterations are the major causes of triplet repeat expansion. The repetitive DNA expands of its Gujarat, India normal length results in sever neurodegenerative conditions. The common types of triplet repeat expansion (TNE) disorders are: Huntington disease, Friedreich ataxia, myotonic dystrophy, SBMA and RK Patel SCA1 out of which Huntington disease, SBMA and SCA1 are categorized as a poly glutamine disorder Sandor Animal Biogenics Pvt. due to the repeat of CAG. In contrast, the friedreich ataxia is occurred due to expansion of the GAA Ltd., Hyderabad, Telangana, whereas myotonic dystrophy is due to the expansion of CTG. The triplet disease follows the mechanism India of anticipation in which the onset of the disease increases with age. Conclusively, no clear mechanism can explain the origin of the disease. The pre mutation can be expanded in full mutation in successive Tushar Chauhan Genetics Group of Gujarat generations and the number of repeats increased with each generation. TNE can observe in both somatic Diagnostic Centre, Mehsana, as well as germ line tissues. Gujarat, India Keywords: triplet repeat expansion disorder, trinucleotide repeats, Huntington disease, SBMA, SCA1, Jigar Suthar friedreich ataxia Genetics Group of Gujarat Diagnostic Centre, Mehsana, Introduction Gujarat, India Since the early 1990s, a new class of molecular disease has been characterized based upon the Sanjay Dave presence of unstable and abnormal expansions of DNA-triplets (Trinucleotides).
    [Show full text]
  • Phospholipase C-Related Catalytically Inactive Protein: a Novel Signaling Molecule for Modulating Fat Metabolism and Energy Expenditure
    Journal of Oral Biosciences 61 (2019) 65e72 Contents lists available at ScienceDirect Journal of Oral Biosciences journal homepage: www.elsevier.com/locate/job Review Phospholipase C-related catalytically inactive protein: A novel signaling molecule for modulating fat metabolism and energy expenditure * Takashi Kanematsu a, b, , Kana Oue a, c, Toshiya Okumura a, Kae Harada a, 1, Yosuke Yamawaki a, 2, Satoshi Asano a, Akiko Mizokami d, Masahiro Irifune c, Masato Hirata e a Department of Cellular and Molecular Pharmacology, Division of Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan b Department of Cell Biology and Pharmacology, Faculty of Dental Science, Kyushu University, Fukuoka, 812-8582, Japan c Department of Dental Anesthesiology, Division of Applied Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734- 8553, Japan d OBT Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, 812-8582, Japan e Fukuoka Dental College, Fukuoka, 814-0193, Japan article info abstract Article history: Background: Overweight and obesity are defined as excessive or abnormal fat accumulation in adipose Received 16 March 2019 tissues, and increase the risk of morbidity in many diseases, including hypertension, dyslipidemia, type 2 Received in revised form diabetes, coronary heart disease, and stroke, through pathophysiological mechanisms. There is strong 17 April 2019 evidence that weight loss reduces the risk of metabolic syndrome by limiting blood pressure and Accepted 19 April 2019 improving the levels of serum triglycerides, total cholesterol, low-density lipoprotein-cholesterol, and Available online 15 May 2019 high-density lipoprotein-cholesterol. To date, several attempts have been made to develop effective anti- obesity medication or weight-loss drugs; however, satisfactory drugs for clinical use have not yet been Keywords: Adipose tissue developed.
    [Show full text]
  • 1 Supporting Information for a Microrna Network Regulates
    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
    [Show full text]
  • The Protein Phosphatase PP2A Plays Multiple Roles in Plant Development by Regulation of Vesicle Traffic—Facts and Questions
    International Journal of Molecular Sciences Review The Protein Phosphatase PP2A Plays Multiple Roles in Plant Development by Regulation of Vesicle Traffic—Facts and Questions Csaba Máthé *, Márta M-Hamvas, Csongor Freytag and Tamás Garda Department of Botany, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; [email protected] (M.M.-H.); [email protected] (C.F.); [email protected] (T.G.) * Correspondence: [email protected] Abstract: The protein phosphatase PP2A is essential for the control of integrated eukaryotic cell functioning. Several cellular and developmental events, e.g., plant growth regulator (PGR) mediated signaling pathways are regulated by reversible phosphorylation of vesicle traffic proteins. Reviewing present knowledge on the relevant role of PP2A is timely. We discuss three aspects: (1) PP2A regulates microtubule-mediated vesicle delivery during cell plate assembly. PP2A dephosphorylates members of the microtubule associated protein family MAP65, promoting their binding to microtubules. Regulation of phosphatase activity leads to changes in microtubule organization, which affects vesicle traffic towards cell plate and vesicle fusion to build the new cell wall between dividing cells. (2) PP2A-mediated inhibition of target of rapamycin complex (TORC) dependent signaling pathways contributes to autophagy and this has possible connections to the brassinosteroid signaling pathway. (3) Transcytosis of vesicles transporting PIN auxin efflux carriers. PP2A regulates vesicle localization and recycling of PINs related to GNOM (a GTP–GDP exchange factor) mediated pathways. The proper intracellular traffic of PINs is essential for auxin distribution in the plant body, thus in whole Citation: Máthé, C.; M-Hamvas, M.; plant development.
    [Show full text]
  • Studies on Cellular Nutrient Responses and Protein Degradation
    STUDIES ON CELLULAR NUTRIENT RESPONSES AND PROTEIN DEGRADATION APPROVED BY SUPERVISORY COMMITTEE Melanie Cobb, Ph.D. (Mentor) Joel Goodman, Ph.D. (Chair) Paul Sternweis, Ph.D. Joseph Albanesi, Ph.D. DEDICATION: I dedicate this dissertation to my parents and grandparents, for inspiring me to pursue science, and for their unconditional love and support. STUDIES ON CELLULAR NUTRIENT RESPONSES AND PROTEIN DEGRADATION by ANWESHA GHOSH DISSERTATION / THESIS Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY / MASTER OF SCIENCE / MASTER OF ARTS The University of Texas Southwestern Medical Center at Dallas Dallas, Texas August, 2015 Copyright by Anwesha Ghosh, 2015 All Rights Reserved iv STUDIES ON CELLULAR NUTRIENT RESPONSES AND PROTEIN DEGRADATION Publication No. Anwesha Ghosh The University of Texas Southwestern Medical Center at Dallas, Graduation Year Supervising Professor: Melanie H. Cobb (Ph.D.) I have worked on two projects. The first project investigates mechanisms involved in cellular responses to amino acids. Amino-acid abundance promotes protein synthesis and cell growth via activation of the protein kinase mTOR, while amino-acid deprivation promotes protein degradation by autophagy. The heterodimeric G protein coupled receptor (GPCR) T1R1-T1R3 can act as an extracellular sensor for amino acids, promoting mTOR activity while repressing autophagy in cells. Quantitative PCR analysis revealed that T1R3 depletion increases mRNA expression of amino acid transporters as a compensatory mechanism induced by perceived starvation. The arrestin proteins can bind GPCRs to mediate their internalization or to facilitate downstream signaling.
    [Show full text]
  • The MAP4K4-STRIPAK Complex Promotes Growth and Tissue Invasion In
    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.07.442906; this version posted May 8, 2021. 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 The MAP4K4-STRIPAK complex promotes growth and tissue invasion in 2 medulloblastoma 3 Jessica Migliavacca1, Buket Züllig1, Charles Capdeville1, Michael Grotzer2 and Martin Baumgartner1,* 4 1 Division of Oncology, Children’s Research Center, University Children’s Hospital Zürich, Zürich, 5 Switzerland 6 2 Division of Oncology, University Children’s Hospital Zürich, Zürich, Switzerland 7 8 *e-mail: [email protected] 9 10 Abstract 11 Proliferation and motility are mutually exclusive biological processes associated with cancer that depend 12 on precise control of upstream signaling pathways with overlapping functionalities. We find that STRN3 13 and STRN4 scaffold subunits of the STRIPAK complex interact with MAP4K4 for pathway regulation in 14 medulloblastoma. Disruption of the MAP4K4-STRIPAK complex impairs growth factor-induced 15 migration and tissue invasion and stalls YAP/TAZ target gene expression and oncogenic growth. The 16 migration promoting functions of the MAP4K4-STRIPAK complex involve the activation of novel PKCs 17 and the phosphorylation of the membrane targeting S157 residue of VASP through MAP4K4. The anti- 18 proliferative effect of complex disruption is associated with reduced YAP/TAZ target gene expression 19 and results in repressed tumor growth in the brain tissue. This dichotomous functionality of the STRIPAK 20 complex in migration and proliferation control acts through MAP4K4 regulation in tumor cells and 21 provides relevant mechanistic insights into novel tumorigenic functions of the STRIPAK complex in 22 medulloblastoma.
    [Show full text]
  • Analyses of PDE-Regulated Phosphoproteomes Reveal Unique and Specific Camp-Signaling Modules in T Cells
    Analyses of PDE-regulated phosphoproteomes reveal unique and specific cAMP-signaling modules in T cells Michael-Claude G. Beltejara, Ho-Tak Laua, Martin G. Golkowskia, Shao-En Onga, and Joseph A. Beavoa,1 aDepartment of Pharmacology, University of Washington, Seattle, WA 98195 Contributed by Joseph A. Beavo, May 28, 2017 (sent for review March 10, 2017; reviewed by Paul M. Epstein, Donald H. Maurice, and Kjetil Tasken) Specific functions for different cyclic nucleotide phosphodiester- to bias T-helper polarization toward Th2, Treg, or Th17 pheno- ases (PDEs) have not yet been identified in most cell types. types (13, 14). In a few cases increased cAMP may even potentiate Conventional approaches to study PDE function typically rely on the T-cell activation signal (15), particularly at early stages of measurements of global cAMP, general increases in cAMP- activation. Recent MS-based proteomic studies have been useful dependent protein kinase (PKA), or the activity of exchange in characterizing changes in the phosphoproteome of T cells under protein activated by cAMP (EPAC). Although newer approaches various stimuli such as T-cell receptor stimulation (16), prosta- using subcellularly targeted FRET reporter sensors have helped glandin signaling (17), and oxidative stress (18), so much of the define more compartmentalized regulation of cAMP, PKA, and total Jurkat phosphoproteome is known. Until now, however, no EPAC, they have limited ability to link this regulation to down- information on the regulation of phosphopeptides by PDEs has stream effector molecules and biological functions. To address this been available in these cells. problem, we have begun to use an unbiased mass spectrometry- Inhibitors of cAMP PDEs are useful tools to study PKA/EPAC- based approach coupled with treatment using PDE isozyme- mediated signaling, and selective inhibitors for each of the 11 PDE – selective inhibitors to characterize the phosphoproteomes of the families have been developed (19 21).
    [Show full text]
  • Molecular Effects of Isoflavone Supplementation Human Intervention Studies and Quantitative Models for Risk Assessment
    Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis committee Promotors Prof. Dr Pieter van ‘t Veer Professor of Nutritional Epidemiology Wageningen University Prof. Dr Evert G. Schouten Emeritus Professor of Epidemiology and Prevention Wageningen University Co-promotors Dr Anouk Geelen Assistant professor, Division of Human Nutrition Wageningen University Dr Lydia A. Afman Assistant professor, Division of Human Nutrition Wageningen University Other members Prof. Dr Jaap Keijer, Wageningen University Dr Hubert P.J.M. Noteborn, Netherlands Food en Consumer Product Safety Authority Prof. Dr Yvonne T. van der Schouw, UMC Utrecht Dr Wendy L. Hall, King’s College London This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences). Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 20 June 2014 at 13.30 p.m. in the Aula. Vera van der Velpen Molecular effects of isoflavone supplementation: Human intervention studies and quantitative models for risk assessment 154 pages PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in Dutch and English ISBN: 978-94-6173-952-0 ABSTRact Background: Risk assessment can potentially be improved by closely linked experiments in the disciplines of epidemiology and toxicology.
    [Show full text]
  • Associated 16P11.2 Deletion in Drosophila Melanogaster
    ARTICLE DOI: 10.1038/s41467-018-04882-6 OPEN Pervasive genetic interactions modulate neurodevelopmental defects of the autism- associated 16p11.2 deletion in Drosophila melanogaster Janani Iyer1, Mayanglambam Dhruba Singh1, Matthew Jensen1,2, Payal Patel 1, Lucilla Pizzo1, Emily Huber1, Haley Koerselman3, Alexis T. Weiner 1, Paola Lepanto4, Komal Vadodaria1, Alexis Kubina1, Qingyu Wang 1,2, Abigail Talbert1, Sneha Yennawar1, Jose Badano 4, J. Robert Manak3,5, Melissa M. Rolls1, Arjun Krishnan6,7 & 1234567890():,; Santhosh Girirajan 1,2,8 As opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of indi- vidual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interac- tions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes. 1 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. 2 Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
    [Show full text]
  • Downloaded the “Top Edge” Version
    bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 2019. 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 4.0 International license. 1 Drosophila models of pathogenic copy-number variant genes show global and 2 non-neuronal defects during development 3 Short title: Non-neuronal defects of fly homologs of CNV genes 4 Tanzeen Yusuff1,4, Matthew Jensen1,4, Sneha Yennawar1,4, Lucilla Pizzo1, Siddharth 5 Karthikeyan1, Dagny J. Gould1, Avik Sarker1, Yurika Matsui1,2, Janani Iyer1, Zhi-Chun Lai1,2, 6 and Santhosh Girirajan1,3* 7 8 1. Department of Biochemistry and Molecular Biology, Pennsylvania State University, 9 University Park, PA 16802 10 2. Department of Biology, Pennsylvania State University, University Park, PA 16802 11 3. Department of Anthropology, Pennsylvania State University, University Park, PA 16802 12 4 contributed equally to work 13 14 *Correspondence: 15 Santhosh Girirajan, MBBS, PhD 16 205A Life Sciences Building 17 Pennsylvania State University 18 University Park, PA 16802 19 E-mail: [email protected] 20 Phone: 814-865-0674 21 1 bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 2019. 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 4.0 International license. 22 ABSTRACT 23 While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non- 24 neuronal phenotypes, functional studies evaluating these regions have focused on the molecular 25 basis of neuronal defects.
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [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]